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Lemley BA, Okunowo O, Ampah SB, Wu L, Shinohara RT, Goldberg DJ, Rychik J, Glatz AC, Amaral S, O'Byrne ML. Effect of patient factors, center, and era on Fontan timing: An observational study using the Pediatric Health Information Systems Database. Am Heart J 2024; 271:156-163. [PMID: 38412896 DOI: 10.1016/j.ahj.2024.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 02/21/2024] [Indexed: 02/29/2024]
Abstract
BACKGROUND There are no consensus guidelines defining optimal timing for the Fontan operation, the last planned surgery in staged palliation for single-ventricle heart disease. OBJECTIVES Identify patient-level characteristics, center-level variation, and secular trends driving Fontan timing. METHODS A retrospective observational study of subjects who underwent Fontan from 2007 to 2021 at centers in the Pediatric Health Information Systems database was performed using linear mixed-effects modeling in which age at Fontan was regressed on patient characteristics and date of operation with center as random effect. RESULTS We included 10,305 subjects (40.4% female, 44% non-white) at 47 centers. Median age at Fontan was 3.4 years (IQR 2.6-4.4). Hypoplastic left heart syndrome (-4.4 months, 95%CI -5.5 to -3.3) and concomitant conditions (-2.6 months, 95%CI -4.1 to -1.1) were associated with younger age at Fontan. Subjects with technology-dependence (+4.6 months, 95%CI 3.1-6.1) were older at Fontan. Black (+4.1 months, 95%CI 2.5-5.7) and Asian (+8.3 months, 95%CI 5.4-11.2) race were associated with older age at Fontan. There was significant variation in Fontan timing between centers. Center accounted for 10% of variation (ICC 0.10, 95%CI 0.07-0.14). Center surgical volume was not associated with Fontan timing (P = .21). Operation year was associated with age at Fontan, with a 3.1 month increase in age for every 5 years (+0.61 months, 95%CI 0.48-0.75). CONCLUSIONS After adjusting for patient-level characteristics there remains significant inter-center variation in Fontan timing. Age at Fontan has increased. Future studies addressing optimal Fontan timing are warranted.
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Affiliation(s)
- Bethan A Lemley
- Division of Cardiology, Lurie Children's Hospital and Department of Pediatrics, Feinberg School of Medicine Northwestern University, Chicago IL.
| | - Oluwatimilehin Okunowo
- Department of Computational and Quantitative Medicine, Division of Biostatistics, Beckman Research Institute of City of Hope, Duarte, CA
| | - Steve B Ampah
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Lezhou Wu
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Russell T Shinohara
- Department of Biostatistics Epidemiology and Informatics, Perelman School of Medicine at The University of Pennsylvania, Philadelphia PA
| | - David J Goldberg
- Division of Cardiology, The Children's Hospital of Philadelphia Department of Pediatrics Perelman School of Medicine at The University of Pennsylvania, Philadelphia PA
| | - Jack Rychik
- Division of Cardiology, The Children's Hospital of Philadelphia Department of Pediatrics Perelman School of Medicine at The University of Pennsylvania, Philadelphia PA
| | - Andrew C Glatz
- Division of Cardiology, St. Louis Children's Hospital and Department of Pediatrics Washington University School of Medicine, St. Louis MO
| | - Sandra Amaral
- Division of Nephrology, The Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine at The University of Pennsylvania, Philadelphia PA
| | - Michael L O'Byrne
- Division of Cardiology, The Children's Hospital of Philadelphia Department of Pediatrics Perelman School of Medicine at The University of Pennsylvania, Philadelphia PA; Clinical Futures, The Children's Hospital of Philadelphia and Leonard Davis Institute and Cardiovascular Outcomes, Quality, and Evaluative Research Center, Perelman School of Medicine at The University of Pennsylvania, Philadelphia PA
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2
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Luo AC, Sydnor VJ, Pines A, Larsen B, Alexander-Bloch AF, Cieslak M, Covitz S, Chen AA, Esper NB, Feczko E, Franco AR, Gur RE, Gur RC, Houghton A, Hu F, Keller AS, Kiar G, Mehta K, Salum GA, Tapera T, Xu T, Zhao C, Salo T, Fair DA, Shinohara RT, Milham MP, Satterthwaite TD. Functional connectivity development along the sensorimotor-association axis enhances the cortical hierarchy. Nat Commun 2024; 15:3511. [PMID: 38664387 PMCID: PMC11045762 DOI: 10.1038/s41467-024-47748-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Human cortical maturation has been posited to be organized along the sensorimotor-association axis, a hierarchical axis of brain organization that spans from unimodal sensorimotor cortices to transmodal association cortices. Here, we investigate the hypothesis that the development of functional connectivity during childhood through adolescence conforms to the cortical hierarchy defined by the sensorimotor-association axis. We tested this pre-registered hypothesis in four large-scale, independent datasets (total n = 3355; ages 5-23 years): the Philadelphia Neurodevelopmental Cohort (n = 1207), Nathan Kline Institute-Rockland Sample (n = 397), Human Connectome Project: Development (n = 625), and Healthy Brain Network (n = 1126). Across datasets, the development of functional connectivity systematically varied along the sensorimotor-association axis. Connectivity in sensorimotor regions increased, whereas connectivity in association cortices declined, refining and reinforcing the cortical hierarchy. These consistent and generalizable results establish that the sensorimotor-association axis of cortical organization encodes the dominant pattern of functional connectivity development.
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Affiliation(s)
- Audrey C Luo
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Valerie J Sydnor
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Adam Pines
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Bart Larsen
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Aaron F Alexander-Bloch
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Matthew Cieslak
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sydney Covitz
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Andrew A Chen
- Division of Biostatistics and Bioinformatics, Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, 29425, USA
| | | | - Eric Feczko
- Center for the Developing Brain, Child Mind Institute, New York, NY, 10022, USA
| | - Alexandre R Franco
- Center for the Developing Brain, Child Mind Institute, New York, NY, 10022, USA
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, 10962, USA
- Department of Psychiatry, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Raquel E Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Ruben C Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Audrey Houghton
- Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Fengling Hu
- Penn Statistics in Imaging and Visualization Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arielle S Keller
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gregory Kiar
- Center for the Developing Brain, Child Mind Institute, New York, NY, 10022, USA
| | - Kahini Mehta
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Giovanni A Salum
- Center for the Developing Brain, Child Mind Institute, New York, NY, 10022, USA
- Section on Negative Affect and Social Processes, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Tinashe Tapera
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, 02115, USA
| | - Ting Xu
- Center for the Developing Brain, Child Mind Institute, New York, NY, 10022, USA
| | - Chenying Zhao
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Taylor Salo
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Damien A Fair
- Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, 55455, USA
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
- Institute of Child Development, College of Education and Human Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Michael P Milham
- Center for the Developing Brain, Child Mind Institute, New York, NY, 10022, USA
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, 10962, USA
| | - Theodore D Satterthwaite
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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3
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Keller AS, Moore TM, Luo A, Visoki E, Gataviņš MM, Shetty A, Cui Z, Fan Y, Feczko E, Houghton A, Li H, Mackey AP, Miranda-Dominguez O, Pines A, Shinohara RT, Sun KY, Fair DA, Satterthwaite TD, Barzilay R. A general exposome factor explains individual differences in functional brain network topography and cognition in youth. Dev Cogn Neurosci 2024; 66:101370. [PMID: 38583301 PMCID: PMC11004064 DOI: 10.1016/j.dcn.2024.101370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 04/09/2024] Open
Abstract
Childhood environments are critical in shaping cognitive neurodevelopment. With the increasing availability of large-scale neuroimaging datasets with deep phenotyping of childhood environments, we can now build upon prior studies that have considered relationships between one or a handful of environmental and neuroimaging features at a time. Here, we characterize the combined effects of hundreds of inter-connected and co-occurring features of a child's environment ("exposome") and investigate associations with each child's unique, multidimensional pattern of functional brain network organization ("functional topography") and cognition. We apply data-driven computational models to measure the exposome and define personalized functional brain networks in pre-registered analyses. Across matched discovery (n=5139, 48.5% female) and replication (n=5137, 47.1% female) samples from the Adolescent Brain Cognitive Development study, the exposome was associated with current (ages 9-10) and future (ages 11-12) cognition. Changes in the exposome were also associated with changes in cognition after accounting for baseline scores. Cross-validated ridge regressions revealed that the exposome is reflected in functional topography and can predict performance across cognitive domains. Importantly, a single measure capturing a child's exposome could more accurately and parsimoniously predict cognition than a wealth of personalized neuroimaging data, highlighting the importance of children's complex, multidimensional environments in cognitive neurodevelopment.
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Affiliation(s)
- Arielle S Keller
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, USA; Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Tyler M Moore
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA; Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Audrey Luo
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, USA; Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Elina Visoki
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA; Department of Child and Adolescent Psychiatry and Behavioral Science, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mārtiņš M Gataviņš
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, USA; Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA; Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alisha Shetty
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, USA; Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Zaixu Cui
- Chinese Institute for Brain Research, Beijing, China
| | - Yong Fan
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Eric Feczko
- Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, USA
| | - Audrey Houghton
- Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, USA
| | - Hongming Li
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Allyson P Mackey
- Department of Psychology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Adam Pines
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Kevin Y Sun
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, USA; Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Damien A Fair
- Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, USA; Institute of Child Development, College of Education and Human Development, Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN 55414, USA
| | - Theodore D Satterthwaite
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, USA; Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA; Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Ran Barzilay
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA; Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Child and Adolescent Psychiatry and Behavioral Science, Children's Hospital of Philadelphia, Philadelphia, PA, USA
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4
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White BR, Adepoju TE, Fisher HB, Shinohara RT, Vandekar S. Spatial nonstationarity of image noise in widefield optical imaging and its effects on cluster-based inference for resting-state functional connectivity. J Neurosci Methods 2024; 404:110076. [PMID: 38331258 PMCID: PMC10940215 DOI: 10.1016/j.jneumeth.2024.110076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 02/04/2024] [Indexed: 02/10/2024]
Abstract
BACKGROUND Resting-state functional connectivity (RSFC) analysis with widefield optical imaging (WOI) is a potentially powerful tool to develop imaging biomarkers in mouse models of disease before translating them to human neuroimaging with functional magnetic resonance imaging (fMRI). The delineation of such biomarkers depends on rigorous statistical analysis. However, statistical understanding of WOI data is limited. In particular, cluster-based analysis of neuroimaging data depends on assumptions of spatial stationarity (i.e., that the distribution of cluster sizes under the null is equal at all brain locations). Whether actual data deviate from this assumption has not previously been examined in WOI. NEW METHOD In this manuscript, we characterize the effects of spatial nonstationarity in WOI RSFC data and adapt a "two-pass" technique from fMRI to correct cluster sizes and mitigate spatial bias, both parametrically and nonparametrically. These methods are tested on multi-institutional data. RESULTS AND COMPARISON WITH EXISTING METHODS We find that spatial nonstationarity has a substantial effect on inference in WOI RSFC data with false positives much more likely at some brain regions than others. This pattern of bias varies between imaging systems, contrasts, and mouse ages, all of which could affect experimental reproducibility if not accounted for. CONCLUSIONS Both parametric and nonparametric corrections for nonstationarity result in significant improvements in spatial bias. The proposed methods are simple to implement and will improve the robustness of inference in optical neuroimaging data.
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Affiliation(s)
- Brian R White
- Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Division of Cardiology, Department of Pediatrics, USA.
| | - Temilola E Adepoju
- Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Division of Cardiology, Department of Pediatrics, USA
| | - Hayden B Fisher
- Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Division of Cardiology, Department of Pediatrics, USA
| | - Russell T Shinohara
- University of Pennsylvania, Perelman School of Medicine, Department of Biostatistics, Epidemiology, and Informatics, USA; University of Pennsylvania, Center for Biomedical Image Computing and Analysis, Department of Radiology, USA; University of Pennsylvania, Penn Statistics in Imaging and Visualization Endeavor, Department of Biostatistics, Epidemiology, and Informatics, USA
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5
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Radhakrishnan H, Zhao C, Sydnor VJ, Baller EB, Cook PA, Fair DA, Giesbrecht B, Larsen B, Murtha K, Roalf DR, Rush‐Goebel S, Shinohara RT, Shou H, Tisdall MD, Vettel JM, Grafton ST, Cieslak M, Satterthwaite TD. A practical evaluation of measures derived from compressed sensing diffusion spectrum imaging. Hum Brain Mapp 2024; 45:e26580. [PMID: 38520359 PMCID: PMC10960521 DOI: 10.1002/hbm.26580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 03/25/2024] Open
Abstract
Diffusion Spectrum Imaging (DSI) using dense Cartesian sampling of q-space has been shown to provide important advantages for modeling complex white matter architecture. However, its adoption has been limited by the lengthy acquisition time required. Sparser sampling of q-space combined with compressed sensing (CS) reconstruction techniques has been proposed as a way to reduce the scan time of DSI acquisitions. However prior studies have mainly evaluated CS-DSI in post-mortem or non-human data. At present, the capacity for CS-DSI to provide accurate and reliable measures of white matter anatomy and microstructure in the living human brain remains unclear. We evaluated the accuracy and inter-scan reliability of 6 different CS-DSI schemes that provided up to 80% reductions in scan time compared to a full DSI scheme. We capitalized on a dataset of 26 participants who were scanned over eight independent sessions using a full DSI scheme. From this full DSI scheme, we subsampled images to create a range of CS-DSI images. This allowed us to compare the accuracy and inter-scan reliability of derived measures of white matter structure (bundle segmentation, voxel-wise scalar maps) produced by the CS-DSI and the full DSI schemes. We found that CS-DSI estimates of both bundle segmentations and voxel-wise scalars were nearly as accurate and reliable as those generated by the full DSI scheme. Moreover, we found that the accuracy and reliability of CS-DSI was higher in white matter bundles that were more reliably segmented by the full DSI scheme. As a final step, we replicated the accuracy of CS-DSI in a prospectively acquired dataset (n = 20, scanned once). Together, these results illustrate the utility of CS-DSI for reliably delineating in vivo white matter architecture in a fraction of the scan time, underscoring its promise for both clinical and research applications.
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Affiliation(s)
- Hamsanandini Radhakrishnan
- Lifespan Informatics and Neuroimaging CenterUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Psychiatry, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Chenying Zhao
- Lifespan Informatics and Neuroimaging CenterUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Psychiatry, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Lifespan Brain Institute, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Bioengineering, School of Engineering and Applied ScienceUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Valerie J. Sydnor
- Lifespan Informatics and Neuroimaging CenterUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Psychiatry, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Erica B. Baller
- Lifespan Informatics and Neuroimaging CenterUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Psychiatry, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Philip A. Cook
- Department of Radiology, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Damien A. Fair
- Masonic Institute for the Developing BrainUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - Barry Giesbrecht
- Department of Psychological and Brain SciencesUniversity of CaliforniaSanta BarbaraCaliforniaUSA
| | - Bart Larsen
- Lifespan Informatics and Neuroimaging CenterUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Psychiatry, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Kristin Murtha
- Lifespan Informatics and Neuroimaging CenterUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Psychiatry, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - David R. Roalf
- Department of Psychiatry, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Lifespan Brain Institute, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Sage Rush‐Goebel
- Lifespan Informatics and Neuroimaging CenterUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Psychiatry, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Russell T. Shinohara
- Department of Biostatistics, Epidemiology and InformaticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Center for Biomedical Image Computing & AnalyticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Haochang Shou
- Department of Biostatistics, Epidemiology and InformaticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Center for Biomedical Image Computing & AnalyticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - M. Dylan Tisdall
- Department of Radiology, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Jean M. Vettel
- Department of Psychological and Brain SciencesUniversity of CaliforniaSanta BarbaraCaliforniaUSA
- U.S. Army Research LaboratoryAberdeen Proving GroundAberdeenMarylandUSA
| | - Scott T. Grafton
- Department of Psychological and Brain SciencesUniversity of CaliforniaSanta BarbaraCaliforniaUSA
| | - Matthew Cieslak
- Lifespan Informatics and Neuroimaging CenterUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Psychiatry, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Theodore D. Satterthwaite
- Lifespan Informatics and Neuroimaging CenterUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Psychiatry, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
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6
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Baldwin A, Copeland J, Azage M, Dratch L, Johnson K, Paul RA, Amado DA, Baer M, Deik A, Elman LB, Guo M, Hamedani AG, Irwin DJ, Lasker A, Orthmann-Murphy J, Quinn CC, Tropea TF, Scherer SS, Shinohara RT, Hamilton RH, Ellis CA. Disparities in Genetic Testing for Neurologic Disorders. Neurology 2024; 102:e209161. [PMID: 38447117 DOI: 10.1212/wnl.0000000000209161] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/01/2023] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND AND OBJECTIVES Genetic testing is now the standard of care for many neurologic conditions. Health care disparities are unfortunately widespread in the US health care system, but disparities in the utilization of genetic testing for neurologic conditions have not been studied. We tested the hypothesis that access to and results of genetic testing vary according to race, ethnicity, sex, socioeconomic status, and insurance status for adults with neurologic conditions. METHODS We analyzed retrospective data from patients who underwent genetic evaluation and testing through our institution's neurogenetics program. We tested for differences between demographic groups in 3 steps of a genetic evaluation pathway: (1) attending a neurogenetic evaluation, (2) completing genetic testing, and (3) receiving a diagnostic result. We compared patients on this genetic evaluation pathway with the population of all neurology outpatients at our institution, using univariate and multivariable logistic regression analyses. RESULTS Between 2015 and 2022, a total of 128,440 patients were seen in our outpatient neurology clinics and 2,540 patients underwent genetic evaluation. Black patients were less than half as likely as White patients to be evaluated (odds ratio [OR] 0.49, p < 0.001), and this disparity was similar after controlling for other demographic factors in multivariable analysis. Patients from the least wealthy quartile of zip codes were also less likely to be evaluated (OR 0.67, p < 0.001). Among patients who underwent evaluation, there were no disparities in the likelihood of completing genetic testing, nor in the likelihood of a diagnostic result after adjusting for age. Analyses restricted to specific indications for genetic testing supported these findings. DISCUSSION We observed unequal utilization of our clinical neurogenetics program for patients from marginalized and minoritized demographic groups, especially Black patients. Among patients who do undergo evaluation, all groups benefit similarly from genetic testing when it is indicated. Understanding and removing barriers to accessing genetic testing will be essential to health care equity and optimal care for all patients with neurologic disorders.
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Affiliation(s)
- Aaron Baldwin
- From the Department of Neurology (A.B., J.C., M.A., L.D., K.J., R.A.P., D.A.A., M.B., A.D., L.B.E., M.G., A.G.H., D.J.I., A.L., J.O.-M., C.C.Q., T.F.T., S.S.S., R.H.H., C.A.E.), Penn Statistics in Imaging and Visualization Center (PennSIVE) (R.T.S.), Department of Biostatistics, Epidemiology, and Informatics, and Center for Biomedical Image Computing and Analytics (R.T.S.), Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Juliette Copeland
- From the Department of Neurology (A.B., J.C., M.A., L.D., K.J., R.A.P., D.A.A., M.B., A.D., L.B.E., M.G., A.G.H., D.J.I., A.L., J.O.-M., C.C.Q., T.F.T., S.S.S., R.H.H., C.A.E.), Penn Statistics in Imaging and Visualization Center (PennSIVE) (R.T.S.), Department of Biostatistics, Epidemiology, and Informatics, and Center for Biomedical Image Computing and Analytics (R.T.S.), Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Meron Azage
- From the Department of Neurology (A.B., J.C., M.A., L.D., K.J., R.A.P., D.A.A., M.B., A.D., L.B.E., M.G., A.G.H., D.J.I., A.L., J.O.-M., C.C.Q., T.F.T., S.S.S., R.H.H., C.A.E.), Penn Statistics in Imaging and Visualization Center (PennSIVE) (R.T.S.), Department of Biostatistics, Epidemiology, and Informatics, and Center for Biomedical Image Computing and Analytics (R.T.S.), Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Laynie Dratch
- From the Department of Neurology (A.B., J.C., M.A., L.D., K.J., R.A.P., D.A.A., M.B., A.D., L.B.E., M.G., A.G.H., D.J.I., A.L., J.O.-M., C.C.Q., T.F.T., S.S.S., R.H.H., C.A.E.), Penn Statistics in Imaging and Visualization Center (PennSIVE) (R.T.S.), Department of Biostatistics, Epidemiology, and Informatics, and Center for Biomedical Image Computing and Analytics (R.T.S.), Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Kelsey Johnson
- From the Department of Neurology (A.B., J.C., M.A., L.D., K.J., R.A.P., D.A.A., M.B., A.D., L.B.E., M.G., A.G.H., D.J.I., A.L., J.O.-M., C.C.Q., T.F.T., S.S.S., R.H.H., C.A.E.), Penn Statistics in Imaging and Visualization Center (PennSIVE) (R.T.S.), Department of Biostatistics, Epidemiology, and Informatics, and Center for Biomedical Image Computing and Analytics (R.T.S.), Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Rachel A Paul
- From the Department of Neurology (A.B., J.C., M.A., L.D., K.J., R.A.P., D.A.A., M.B., A.D., L.B.E., M.G., A.G.H., D.J.I., A.L., J.O.-M., C.C.Q., T.F.T., S.S.S., R.H.H., C.A.E.), Penn Statistics in Imaging and Visualization Center (PennSIVE) (R.T.S.), Department of Biostatistics, Epidemiology, and Informatics, and Center for Biomedical Image Computing and Analytics (R.T.S.), Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Defne A Amado
- From the Department of Neurology (A.B., J.C., M.A., L.D., K.J., R.A.P., D.A.A., M.B., A.D., L.B.E., M.G., A.G.H., D.J.I., A.L., J.O.-M., C.C.Q., T.F.T., S.S.S., R.H.H., C.A.E.), Penn Statistics in Imaging and Visualization Center (PennSIVE) (R.T.S.), Department of Biostatistics, Epidemiology, and Informatics, and Center for Biomedical Image Computing and Analytics (R.T.S.), Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Michael Baer
- From the Department of Neurology (A.B., J.C., M.A., L.D., K.J., R.A.P., D.A.A., M.B., A.D., L.B.E., M.G., A.G.H., D.J.I., A.L., J.O.-M., C.C.Q., T.F.T., S.S.S., R.H.H., C.A.E.), Penn Statistics in Imaging and Visualization Center (PennSIVE) (R.T.S.), Department of Biostatistics, Epidemiology, and Informatics, and Center for Biomedical Image Computing and Analytics (R.T.S.), Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Andres Deik
- From the Department of Neurology (A.B., J.C., M.A., L.D., K.J., R.A.P., D.A.A., M.B., A.D., L.B.E., M.G., A.G.H., D.J.I., A.L., J.O.-M., C.C.Q., T.F.T., S.S.S., R.H.H., C.A.E.), Penn Statistics in Imaging and Visualization Center (PennSIVE) (R.T.S.), Department of Biostatistics, Epidemiology, and Informatics, and Center for Biomedical Image Computing and Analytics (R.T.S.), Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Lauren B Elman
- From the Department of Neurology (A.B., J.C., M.A., L.D., K.J., R.A.P., D.A.A., M.B., A.D., L.B.E., M.G., A.G.H., D.J.I., A.L., J.O.-M., C.C.Q., T.F.T., S.S.S., R.H.H., C.A.E.), Penn Statistics in Imaging and Visualization Center (PennSIVE) (R.T.S.), Department of Biostatistics, Epidemiology, and Informatics, and Center for Biomedical Image Computing and Analytics (R.T.S.), Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Michael Guo
- From the Department of Neurology (A.B., J.C., M.A., L.D., K.J., R.A.P., D.A.A., M.B., A.D., L.B.E., M.G., A.G.H., D.J.I., A.L., J.O.-M., C.C.Q., T.F.T., S.S.S., R.H.H., C.A.E.), Penn Statistics in Imaging and Visualization Center (PennSIVE) (R.T.S.), Department of Biostatistics, Epidemiology, and Informatics, and Center for Biomedical Image Computing and Analytics (R.T.S.), Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Ali G Hamedani
- From the Department of Neurology (A.B., J.C., M.A., L.D., K.J., R.A.P., D.A.A., M.B., A.D., L.B.E., M.G., A.G.H., D.J.I., A.L., J.O.-M., C.C.Q., T.F.T., S.S.S., R.H.H., C.A.E.), Penn Statistics in Imaging and Visualization Center (PennSIVE) (R.T.S.), Department of Biostatistics, Epidemiology, and Informatics, and Center for Biomedical Image Computing and Analytics (R.T.S.), Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - David J Irwin
- From the Department of Neurology (A.B., J.C., M.A., L.D., K.J., R.A.P., D.A.A., M.B., A.D., L.B.E., M.G., A.G.H., D.J.I., A.L., J.O.-M., C.C.Q., T.F.T., S.S.S., R.H.H., C.A.E.), Penn Statistics in Imaging and Visualization Center (PennSIVE) (R.T.S.), Department of Biostatistics, Epidemiology, and Informatics, and Center for Biomedical Image Computing and Analytics (R.T.S.), Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Aaron Lasker
- From the Department of Neurology (A.B., J.C., M.A., L.D., K.J., R.A.P., D.A.A., M.B., A.D., L.B.E., M.G., A.G.H., D.J.I., A.L., J.O.-M., C.C.Q., T.F.T., S.S.S., R.H.H., C.A.E.), Penn Statistics in Imaging and Visualization Center (PennSIVE) (R.T.S.), Department of Biostatistics, Epidemiology, and Informatics, and Center for Biomedical Image Computing and Analytics (R.T.S.), Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Jennifer Orthmann-Murphy
- From the Department of Neurology (A.B., J.C., M.A., L.D., K.J., R.A.P., D.A.A., M.B., A.D., L.B.E., M.G., A.G.H., D.J.I., A.L., J.O.-M., C.C.Q., T.F.T., S.S.S., R.H.H., C.A.E.), Penn Statistics in Imaging and Visualization Center (PennSIVE) (R.T.S.), Department of Biostatistics, Epidemiology, and Informatics, and Center for Biomedical Image Computing and Analytics (R.T.S.), Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Colin C Quinn
- From the Department of Neurology (A.B., J.C., M.A., L.D., K.J., R.A.P., D.A.A., M.B., A.D., L.B.E., M.G., A.G.H., D.J.I., A.L., J.O.-M., C.C.Q., T.F.T., S.S.S., R.H.H., C.A.E.), Penn Statistics in Imaging and Visualization Center (PennSIVE) (R.T.S.), Department of Biostatistics, Epidemiology, and Informatics, and Center for Biomedical Image Computing and Analytics (R.T.S.), Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Thomas F Tropea
- From the Department of Neurology (A.B., J.C., M.A., L.D., K.J., R.A.P., D.A.A., M.B., A.D., L.B.E., M.G., A.G.H., D.J.I., A.L., J.O.-M., C.C.Q., T.F.T., S.S.S., R.H.H., C.A.E.), Penn Statistics in Imaging and Visualization Center (PennSIVE) (R.T.S.), Department of Biostatistics, Epidemiology, and Informatics, and Center for Biomedical Image Computing and Analytics (R.T.S.), Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Steven S Scherer
- From the Department of Neurology (A.B., J.C., M.A., L.D., K.J., R.A.P., D.A.A., M.B., A.D., L.B.E., M.G., A.G.H., D.J.I., A.L., J.O.-M., C.C.Q., T.F.T., S.S.S., R.H.H., C.A.E.), Penn Statistics in Imaging and Visualization Center (PennSIVE) (R.T.S.), Department of Biostatistics, Epidemiology, and Informatics, and Center for Biomedical Image Computing and Analytics (R.T.S.), Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Russell T Shinohara
- From the Department of Neurology (A.B., J.C., M.A., L.D., K.J., R.A.P., D.A.A., M.B., A.D., L.B.E., M.G., A.G.H., D.J.I., A.L., J.O.-M., C.C.Q., T.F.T., S.S.S., R.H.H., C.A.E.), Penn Statistics in Imaging and Visualization Center (PennSIVE) (R.T.S.), Department of Biostatistics, Epidemiology, and Informatics, and Center for Biomedical Image Computing and Analytics (R.T.S.), Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Roy H Hamilton
- From the Department of Neurology (A.B., J.C., M.A., L.D., K.J., R.A.P., D.A.A., M.B., A.D., L.B.E., M.G., A.G.H., D.J.I., A.L., J.O.-M., C.C.Q., T.F.T., S.S.S., R.H.H., C.A.E.), Penn Statistics in Imaging and Visualization Center (PennSIVE) (R.T.S.), Department of Biostatistics, Epidemiology, and Informatics, and Center for Biomedical Image Computing and Analytics (R.T.S.), Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Colin A Ellis
- From the Department of Neurology (A.B., J.C., M.A., L.D., K.J., R.A.P., D.A.A., M.B., A.D., L.B.E., M.G., A.G.H., D.J.I., A.L., J.O.-M., C.C.Q., T.F.T., S.S.S., R.H.H., C.A.E.), Penn Statistics in Imaging and Visualization Center (PennSIVE) (R.T.S.), Department of Biostatistics, Epidemiology, and Informatics, and Center for Biomedical Image Computing and Analytics (R.T.S.), Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
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7
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Xie K, Ojemann WKS, Gallagher RS, Shinohara RT, Lucas A, Hill CE, Hamilton RH, Johnson KB, Roth D, Litt B, Ellis CA. Disparities in seizure outcomes revealed by large language models. J Am Med Inform Assoc 2024:ocae047. [PMID: 38481027 DOI: 10.1093/jamia/ocae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/26/2024] Open
Abstract
OBJECTIVE Large-language models (LLMs) can potentially revolutionize health care delivery and research, but risk propagating existing biases or introducing new ones. In epilepsy, social determinants of health are associated with disparities in care access, but their impact on seizure outcomes among those with access remains unclear. Here we (1) evaluated our validated, epilepsy-specific LLM for intrinsic bias, and (2) used LLM-extracted seizure outcomes to determine if different demographic groups have different seizure outcomes. MATERIALS AND METHODS We tested our LLM for differences and equivalences in prediction accuracy and confidence across demographic groups defined by race, ethnicity, sex, income, and health insurance, using manually annotated notes. Next, we used LLM-classified seizure freedom at each office visit to test for demographic outcome disparities, using univariable and multivariable analyses. RESULTS We analyzed 84 675 clinic visits from 25 612 unique patients seen at our epilepsy center. We found little evidence of bias in the prediction accuracy or confidence of outcome classifications across demographic groups. Multivariable analysis indicated worse seizure outcomes for female patients (OR 1.33, P ≤ .001), those with public insurance (OR 1.53, P ≤ .001), and those from lower-income zip codes (OR ≥1.22, P ≤ .007). Black patients had worse outcomes than White patients in univariable but not multivariable analysis (OR 1.03, P = .66). CONCLUSION We found little evidence that our LLM was intrinsically biased against any demographic group. Seizure freedom extracted by LLM revealed disparities in seizure outcomes across several demographic groups. These findings quantify the critical need to reduce disparities in the care of people with epilepsy.
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Affiliation(s)
- Kevin Xie
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, United States
- Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - William K S Ojemann
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, United States
- Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Ryan S Gallagher
- Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, United States
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Russell T Shinohara
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Alfredo Lucas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, United States
- Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, United States
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Chloé E Hill
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Roy H Hamilton
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Kevin B Johnson
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, United States
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA 19104, United States
- Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA 19104, United States
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Dan Roth
- Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Brian Litt
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, United States
- Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, United States
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Colin A Ellis
- Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, United States
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, United States
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8
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Shafiei G, Keller AS, Bertolero M, Shanmugan S, Bassett DS, Chen AA, Covitz S, Houghton A, Luo A, Mehta K, Salo T, Shinohara RT, Fair D, Hallquist MN, Satterthwaite TD. Generalizable Links Between Borderline Personality Traits and Functional Connectivity. Biol Psychiatry 2024:S0006-3223(24)01140-5. [PMID: 38460580 DOI: 10.1016/j.biopsych.2024.02.1016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 02/02/2024] [Accepted: 02/29/2024] [Indexed: 03/11/2024]
Abstract
BACKGROUND Symptoms of borderline personality disorder (BPD) often manifest during adolescence, but the underlying relationship between these debilitating symptoms and the development of functional brain networks is not well understood. Here, we aimed to investigate how multivariate patterns of functional connectivity are associated with borderline personality traits in large samples of young adults and adolescents. METHODS We used functional magnetic resonance imaging data from young adults and adolescents from the HCP-YA (Human Connectome Project Young Adult) (n = 870, ages 22-37 years, 457 female) and the HCP-D (Human Connectome Project Development) (n = 223, ages 16-21 years, 121 female). A previously validated BPD proxy score was derived from the NEO Five-Factor Inventory. A ridge regression model with cross-validation and nested hyperparameter tuning was trained and tested in HCP-YA to predict BPD scores in unseen data from regional functional connectivity. The trained model was further tested on data from HCP-D without further tuning. Finally, we tested how the connectivity patterns associated with BPD aligned with age-related changes in connectivity. RESULTS Multivariate functional connectivity patterns significantly predicted out-of-sample BPD scores in unseen data in young adults (HCP-YA ppermuted = .001) and older adolescents (HCP-D ppermuted = .001). Regional predictive capacity was heterogeneous; the most predictive regions were found in functional systems relevant for emotion regulation and executive function, including the ventral attention network. Finally, regional functional connectivity patterns that predicted BPD scores aligned with those associated with development in youth. CONCLUSIONS Individual differences in functional connectivity in developmentally sensitive regions are associated with borderline personality traits.
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Affiliation(s)
- Golia Shafiei
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Lifespan Brain Institute of Perelman School of Medicine and Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Arielle S Keller
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Lifespan Brain Institute of Perelman School of Medicine and Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Maxwell Bertolero
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Lifespan Brain Institute of Perelman School of Medicine and Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sheila Shanmugan
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Lifespan Brain Institute of Perelman School of Medicine and Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Dani S Bassett
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Physics & Astronomy, College of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Electrical & Systems Engineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania; Santa Fe Institute, Santa Fe, New Mexico
| | - Andrew A Chen
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sydney Covitz
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Lifespan Brain Institute of Perelman School of Medicine and Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Audrey Houghton
- Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, Minnesota
| | - Audrey Luo
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Lifespan Brain Institute of Perelman School of Medicine and Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kahini Mehta
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Lifespan Brain Institute of Perelman School of Medicine and Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Taylor Salo
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Lifespan Brain Institute of Perelman School of Medicine and Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Damien Fair
- Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, Minnesota; Institute of Child Development, College of Education and Human Development, Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, Minnesota
| | - Michael N Hallquist
- Department of Psychology and Neuroscience, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Theodore D Satterthwaite
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Lifespan Brain Institute of Perelman School of Medicine and Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania.
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9
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Taghvaei M, Mechanic-Hamilton DJ, Sadaghiani S, Shakibajahromi B, Dolui S, Das S, Brown C, Tackett W, Khandelwal P, Cook P, Shinohara RT, Yushkevich P, Bassett DS, Wolk DA, Detre JA. Impact of white matter hyperintensities on structural connectivity and cognition in cognitively intact ADNI participants. Neurobiol Aging 2024; 135:79-90. [PMID: 38262221 PMCID: PMC10872454 DOI: 10.1016/j.neurobiolaging.2023.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 10/19/2023] [Accepted: 10/22/2023] [Indexed: 01/25/2024]
Abstract
We used indirect brain mapping with virtual lesion tractography to test the hypothesis that the extent of white matter tract disconnection due to white matter hyperintensities (WMH) is associated with corresponding tract-specific cognitive performance decrements. To estimate tract disconnection, WMH masks were extracted from FLAIR MRI data of 481 cognitively intact participants in the Alzheimer's Disease Neuroimaging Initiative (ADNI) and used as regions of avoidance for fiber tracking in diffusion MRI data from 50 healthy young participants from the Human Connectome Project. Estimated tract disconnection in the right inferior fronto-occipital fasciculus, right frontal aslant tract, and right superior longitudinal fasciculus mediated the effects of WMH volume on executive function. Estimated tract disconnection in the left uncinate fasciculus mediated the effects of WMH volume on memory and in the right frontal aslant tract on language. In a subset of ADNI control participants with amyloid data, positive status increased the probability of periventricular WMH and moderated the relationship between WMH burden and tract disconnection in executive function performance.
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Affiliation(s)
- Mohammad Taghvaei
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | - Sudipto Dolui
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Sandhitsu Das
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher Brown
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - William Tackett
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Pulkit Khandelwal
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Philip Cook
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Paul Yushkevich
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Danielle S Bassett
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - David A Wolk
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - John A Detre
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA.
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10
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Guo J, Fathi Kazerooni A, Toorens E, Akbari H, Yu F, Sako C, Mamourian E, Shinohara RT, Koumenis C, Bagley SJ, Morrissette JJD, Binder ZA, Brem S, Mohan S, Lustig RA, O'Rourke DM, Ganguly T, Bakas S, Nasrallah MP, Davatzikos C. Integrating imaging and genomic data for the discovery of distinct glioblastoma subtypes: a joint learning approach. Sci Rep 2024; 14:4922. [PMID: 38418494 PMCID: PMC10902376 DOI: 10.1038/s41598-024-55072-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 02/19/2024] [Indexed: 03/01/2024] Open
Abstract
Glioblastoma is a highly heterogeneous disease, with variations observed at both phenotypical and molecular levels. Personalized therapies would be facilitated by non-invasive in vivo approaches for characterizing this heterogeneity. In this study, we developed unsupervised joint machine learning between radiomic and genomic data, thereby identifying distinct glioblastoma subtypes. A retrospective cohort of 571 IDH-wildtype glioblastoma patients were included in the study, and pre-operative multi-parametric MRI scans and targeted next-generation sequencing (NGS) data were collected. L21-norm minimization was used to select a subset of 12 radiomic features from the MRI scans, and 13 key driver genes from the five main signal pathways most affected in glioblastoma were selected from the genomic data. Subtypes were identified using a joint learning approach called Anchor-based Partial Multi-modal Clustering on both radiomic and genomic modalities. Kaplan-Meier analysis identified three distinct glioblastoma subtypes: high-risk, medium-risk, and low-risk, based on overall survival outcome (p < 0.05, log-rank test; Hazard Ratio = 1.64, 95% CI 1.17-2.31, Cox proportional hazard model on high-risk and low-risk subtypes). The three subtypes displayed different phenotypical and molecular characteristics in terms of imaging histogram, co-occurrence of genes, and correlation between the two modalities. Our findings demonstrate the synergistic value of integrated radiomic signatures and molecular characteristics for glioblastoma subtyping. Joint learning on both modalities can aid in better understanding the molecular basis of phenotypical signatures of glioblastoma, and provide insights into the biological underpinnings of tumor formation and progression.
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Affiliation(s)
- Jun Guo
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, 3700 Hamilton Walk, 7Th Floor, Philadelphia, PA, 19104, USA
- Center for AI and Data Science for Integrated Diagnostics, University of Pennsylvania, Philadelphia, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anahita Fathi Kazerooni
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, 3700 Hamilton Walk, 7Th Floor, Philadelphia, PA, 19104, USA
- Center for AI and Data Science for Integrated Diagnostics, University of Pennsylvania, Philadelphia, USA
- Center for Data-Driven Discovery in Biomedicine (D3b), Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erik Toorens
- Penn Genomic Analysis Core, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hamed Akbari
- Department of Bioengineering, School of Engineering, Santa Clara University, Santa Clara, CA, USA
| | - Fanyang Yu
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, 3700 Hamilton Walk, 7Th Floor, Philadelphia, PA, 19104, USA
- Center for AI and Data Science for Integrated Diagnostics, University of Pennsylvania, Philadelphia, USA
| | - Chiharu Sako
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, 3700 Hamilton Walk, 7Th Floor, Philadelphia, PA, 19104, USA
- Center for AI and Data Science for Integrated Diagnostics, University of Pennsylvania, Philadelphia, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth Mamourian
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, 3700 Hamilton Walk, 7Th Floor, Philadelphia, PA, 19104, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Russell T Shinohara
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, 3700 Hamilton Walk, 7Th Floor, Philadelphia, PA, 19104, USA
- Penn Statistics in Imaging and Visualization (PennSIVE) Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Constantinos Koumenis
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stephen J Bagley
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Glioblastoma Translational Center of Excellence, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer J D Morrissette
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zev A Binder
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Glioblastoma Translational Center of Excellence, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Steven Brem
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Glioblastoma Translational Center of Excellence, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Suyash Mohan
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, 3700 Hamilton Walk, 7Th Floor, Philadelphia, PA, 19104, USA
- Center for AI and Data Science for Integrated Diagnostics, University of Pennsylvania, Philadelphia, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert A Lustig
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Donald M O'Rourke
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Glioblastoma Translational Center of Excellence, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Tapan Ganguly
- Penn Genomic Analysis Core, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Spyridon Bakas
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, 3700 Hamilton Walk, 7Th Floor, Philadelphia, PA, 19104, USA
- Center for AI and Data Science for Integrated Diagnostics, University of Pennsylvania, Philadelphia, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Computational Pathology, Department of Pathology & Laboratory Medicine, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - MacLean P Nasrallah
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, 3700 Hamilton Walk, 7Th Floor, Philadelphia, PA, 19104, USA
- Center for AI and Data Science for Integrated Diagnostics, University of Pennsylvania, Philadelphia, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christos Davatzikos
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, 3700 Hamilton Walk, 7Th Floor, Philadelphia, PA, 19104, USA.
- Center for AI and Data Science for Integrated Diagnostics, University of Pennsylvania, Philadelphia, USA.
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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11
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Tu D, Wrobel J, Satterthwaite TD, Goldsmith J, Gur RC, Gur RE, Gertheiss J, Bassett DS, Shinohara RT. Regression and Alignment for Functional Data and Network Topology. bioRxiv 2024:2023.07.13.548836. [PMID: 37503017 PMCID: PMC10370026 DOI: 10.1101/2023.07.13.548836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
In the brain, functional connections form a network whose topological organization can be described by graph-theoretic network diagnostics. These include characterizations of the community structure, such as modularity and participation coefficient, which have been shown to change over the course of childhood and adolescence. To investigate if such changes in the functional network are associated with changes in cognitive performance during development, network studies often rely on an arbitrary choice of pre-processing parameters, in particular the proportional threshold of network edges. Because the choice of parameter can impact the value of the network diagnostic, and therefore downstream conclusions, we propose to circumvent that choice by conceptualizing the network diagnostic as a function of the parameter. As opposed to a single value, a network diagnostic curve describes the connectome topology at multiple scales-from the sparsest group of the strongest edges to the entire edge set. To relate these curves to executive function and other covariates, we use scalar-on-function regression, which is more flexible than previous functional data-based models used in network neuroscience. We then consider how systematic differences between networks can manifest in misalignment of diagnostic curves, and consequently propose a supervised curve alignment method that incorporates auxiliary information from other variables. Our algorithm performs both functional regression and alignment via an iterative, penalized, and nonlinear likelihood optimization. The illustrated method has the potential to improve the interpretability and generalizability of neuroscience studies where the goal is to study heterogeneity among a mixture of function- and scalar-valued measures.
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Affiliation(s)
- Danni Tu
- The Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Julia Wrobel
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | - Theodore D. Satterthwaite
- Department of Psychiatry, Perelman School of Medicine, Philadelphia, PA USA
- Penn Lifespan Informatics and Neuroimaging Center, Philadelphia, PA, USA
| | - Jeff Goldsmith
- Department of Biostatistics, Columbia University, New York, NY, USA
| | - Ruben C. Gur
- Department of Psychiatry, Perelman School of Medicine, Philadelphia, PA USA
- The Penn Medicine-CHOP Lifespan Brain Institute, Philadelphia, PA, USA
| | - Raquel E. Gur
- Department of Psychiatry, Perelman School of Medicine, Philadelphia, PA USA
- The Penn Medicine-CHOP Lifespan Brain Institute, Philadelphia, PA, USA
| | - Jan Gertheiss
- Department of Mathematics and Statistics, School of Economics and Social Sciences, Helmut Schmidt University, Hamburg, Germany
| | - Dani S. Bassett
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, USA
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Russell T. Shinohara
- The Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, USA
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12
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Skampardoni I, Nasrallah IM, Abdulkadir A, Wen J, Melhem R, Mamourian E, Erus G, Doshi J, Singh A, Yang Z, Cui Y, Hwang G, Ren Z, Pomponio R, Srinivasan D, Govindarajan ST, Parmpi P, Wittfeld K, Grabe HJ, Bülow R, Frenzel S, Tosun D, Bilgel M, An Y, Marcus DS, LaMontagne P, Heckbert SR, Austin TR, Launer LJ, Sotiras A, Espeland MA, Masters CL, Maruff P, Fripp J, Johnson SC, Morris JC, Albert MS, Bryan RN, Yaffe K, Völzke H, Ferrucci L, Benzinger TL, Ezzati A, Shinohara RT, Fan Y, Resnick SM, Habes M, Wolk D, Shou H, Nikita K, Davatzikos C. Genetic and Clinical Correlates of AI-Based Brain Aging Patterns in Cognitively Unimpaired Individuals. JAMA Psychiatry 2024:2814597. [PMID: 38353984 PMCID: PMC10867779 DOI: 10.1001/jamapsychiatry.2023.5599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 11/29/2023] [Indexed: 02/17/2024]
Abstract
Importance Brain aging elicits complex neuroanatomical changes influenced by multiple age-related pathologies. Understanding the heterogeneity of structural brain changes in aging may provide insights into preclinical stages of neurodegenerative diseases. Objective To derive subgroups with common patterns of variation in participants without diagnosed cognitive impairment (WODCI) in a data-driven manner and relate them to genetics, biomedical measures, and cognitive decline trajectories. Design, Setting, and Participants Data acquisition for this cohort study was performed from 1999 to 2020. Data consolidation and harmonization were conducted from July 2017 to July 2021. Age-specific subgroups of structural brain measures were modeled in 4 decade-long intervals spanning ages 45 to 85 years using a deep learning, semisupervised clustering method leveraging generative adversarial networks. Data were analyzed from July 2021 to February 2023 and were drawn from the Imaging-Based Coordinate System for Aging and Neurodegenerative Diseases (iSTAGING) international consortium. Individuals WODCI at baseline spanning ages 45 to 85 years were included, with greater than 50 000 data time points. Exposures Individuals WODCI at baseline scan. Main Outcomes and Measures Three subgroups, consistent across decades, were identified within the WODCI population. Associations with genetics, cardiovascular risk factors (CVRFs), amyloid β (Aβ), and future cognitive decline were assessed. Results In a sample of 27 402 individuals (mean [SD] age, 63.0 [8.3] years; 15 146 female [55%]) WODCI, 3 subgroups were identified in contrast with the reference group: a typical aging subgroup, A1, with a specific pattern of modest atrophy and white matter hyperintensity (WMH) load, and 2 accelerated aging subgroups, A2 and A3, with characteristics that were more distinct at age 65 years and older. A2 was associated with hypertension, WMH, and vascular disease-related genetic variants and was enriched for Aβ positivity (ages ≥65 years) and apolipoprotein E (APOE) ε4 carriers. A3 showed severe, widespread atrophy, moderate presence of CVRFs, and greater cognitive decline. Genetic variants associated with A1 were protective for WMH (rs7209235: mean [SD] B = -0.07 [0.01]; P value = 2.31 × 10-9) and Alzheimer disease (rs72932727: mean [SD] B = 0.1 [0.02]; P value = 6.49 × 10-9), whereas the converse was observed for A2 (rs7209235: mean [SD] B = 0.1 [0.01]; P value = 1.73 × 10-15 and rs72932727: mean [SD] B = -0.09 [0.02]; P value = 4.05 × 10-7, respectively); variants in A3 were associated with regional atrophy (rs167684: mean [SD] B = 0.08 [0.01]; P value = 7.22 × 10-12) and white matter integrity measures (rs1636250: mean [SD] B = 0.06 [0.01]; P value = 4.90 × 10-7). Conclusions and Relevance The 3 subgroups showed distinct associations with CVRFs, genetics, and subsequent cognitive decline. These subgroups likely reflect multiple underlying neuropathologic processes and affect susceptibility to Alzheimer disease, paving pathways toward patient stratification at early asymptomatic stages and promoting precision medicine in clinical trials and health care.
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Affiliation(s)
- Ioanna Skampardoni
- Centre for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia
- School of Electrical and Computer Engineering, National Technical University of Athens, Greece
| | - Ilya M. Nasrallah
- Centre for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia
- Department of Radiology, University of Pennsylvania, Philadelphia
| | - Ahmed Abdulkadir
- Centre for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia
- Laboratory for Research in Neuroimaging, Department of Clinical Neurosciences, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Junhao Wen
- Centre for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia
- Laboratory of AI and Biomedical Science, Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles
| | - Randa Melhem
- Centre for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia
| | - Elizabeth Mamourian
- Centre for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia
| | - Guray Erus
- Centre for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia
| | - Jimit Doshi
- Centre for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia
| | - Ashish Singh
- Centre for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia
| | - Zhijian Yang
- Centre for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia
| | - Yuhan Cui
- Centre for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia
| | - Gyujoon Hwang
- Centre for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia
| | - Zheng Ren
- Laboratory of AI and Biomedical Science, Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles
| | - Raymond Pomponio
- Centre for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia
| | - Dhivya Srinivasan
- Centre for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia
| | | | - Paraskevi Parmpi
- Centre for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia
| | - Katharina Wittfeld
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Germany
- German Centre for Neurodegenerative Diseases, Site Greifswald, Greifswald, Germany
| | - Hans J. Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Germany
- German Centre for Neurodegenerative Diseases, Site Greifswald, Greifswald, Germany
| | - Robin Bülow
- Institute of Diagnostic Radiology and Neuroradiology, University Medicine Greifswald, Greifswald, Germany
| | - Stefan Frenzel
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Germany
| | - Duygu Tosun
- Department of Radiology and Biomedical Imaging, University of California, San Francisco
| | - Murat Bilgel
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Yang An
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Daniel S. Marcus
- Department of Radiology, Washington University School of Medicine, St Louis, Missouri
| | - Pamela LaMontagne
- Department of Radiology, Washington University School of Medicine, St Louis, Missouri
| | - Susan R. Heckbert
- Cardiovascular Health Research Unit, University of Washington, Seattle
- Department of Epidemiology, University of Washington, Seattle
| | - Thomas R. Austin
- Cardiovascular Health Research Unit, University of Washington, Seattle
- Department of Epidemiology, University of Washington, Seattle
| | - Lenore J. Launer
- Neuroepidemiology Section, Intramural Research Program, National Institute on Aging, Bethesda, Maryland
| | - Aristeidis Sotiras
- Department of Radiology and Institute of Informatics, Washington University in St Louis, St Louis, Missouri
| | - Mark A. Espeland
- Sticht Centre for Healthy Aging and Alzheimer’s Prevention, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Colin L. Masters
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Paul Maruff
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Jurgen Fripp
- CSIRO Health and Biosecurity, Australian e-Health Research Centre CSIRO, Brisbane, Queensland, Australia
| | - Sterling C. Johnson
- Wisconsin Alzheimer’s Institute, University of Wisconsin School of Medicine and Public Health, Madison
| | - John C. Morris
- Knight Alzheimer Disease Research Centre, Washington University in St Louis, St Louis, Missouri
| | - Marilyn S. Albert
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - R. Nick Bryan
- Department of Radiology, University of Pennsylvania, Philadelphia
| | - Kristine Yaffe
- Departments of Neurology, Psychiatry and Epidemiology and Biostatistics, University of California San Francisco, San Francisco
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Tammie L.S. Benzinger
- Mallinckrodt Institute of Radiology, Washington University School of Medicine in St Louis, St Louis, Missouri
| | - Ali Ezzati
- Department of Neurology, University of California, Irvine
| | - Russell T. Shinohara
- Centre for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, & Informatics, University of Pennsylvania, Philadelphia
| | - Yong Fan
- Centre for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia
| | - Susan M. Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Mohamad Habes
- Centre for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia
- Neuroimage Analytics Laboratory and the Biggs Institute Neuroimaging Core, Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health Science Center San Antonio, San Antonio
| | - David Wolk
- Department of Neurology, University of Pennsylvania, Philadelphia
| | - Haochang Shou
- Centre for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, & Informatics, University of Pennsylvania, Philadelphia
| | - Konstantina Nikita
- School of Electrical and Computer Engineering, National Technical University of Athens, Greece
| | - Christos Davatzikos
- Centre for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia
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13
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Wagstyl K, Adler S, Seidlitz J, Vandekar S, Mallard TT, Dear R, DeCasien AR, Satterthwaite TD, Liu S, Vértes PE, Shinohara RT, Alexander-Bloch A, Geschwind DH, Raznahan A. Transcriptional cartography integrates multiscale biology of the human cortex. eLife 2024; 12:RP86933. [PMID: 38324465 PMCID: PMC10945526 DOI: 10.7554/elife.86933] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024] Open
Abstract
The cerebral cortex underlies many of our unique strengths and vulnerabilities, but efforts to understand human cortical organization are challenged by reliance on incompatible measurement methods at different spatial scales. Macroscale features such as cortical folding and functional activation are accessed through spatially dense neuroimaging maps, whereas microscale cellular and molecular features are typically measured with sparse postmortem sampling. Here, we integrate these distinct windows on brain organization by building upon existing postmortem data to impute, validate, and analyze a library of spatially dense neuroimaging-like maps of human cortical gene expression. These maps allow spatially unbiased discovery of cortical zones with extreme transcriptional profiles or unusually rapid transcriptional change which index distinct microstructure and predict neuroimaging measures of cortical folding and functional activation. Modules of spatially coexpressed genes define a family of canonical expression maps that integrate diverse spatial scales and temporal epochs of human brain organization - ranging from protein-protein interactions to large-scale systems for cognitive processing. These module maps also parse neuropsychiatric risk genes into subsets which tag distinct cyto-laminar features and differentially predict the location of altered cortical anatomy and gene expression in patients. Taken together, the methods, resources, and findings described here advance our understanding of human cortical organization and offer flexible bridges to connect scientific fields operating at different spatial scales of human brain research.
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Affiliation(s)
- Konrad Wagstyl
- Wellcome Centre for Human Neuroimaging, University College LondonLondonUnited Kingdom
| | - Sophie Adler
- UCL Great Ormond Street Institute for Child HealthHolbornUnited Kingdom
| | - Jakob Seidlitz
- Department of Psychiatry, University of PennsylvaniaPhiladelphiaUnited States
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of PhiladelphiaPhiladelphiaUnited States
| | - Simon Vandekar
- Department of Biostatistics, Vanderbilt UniversityNashvilleUnited States
| | - Travis T Mallard
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Psychiatry, Harvard Medical SchoolBostonUnited States
| | - Richard Dear
- Department of Psychiatry, University of CambridgeCambridgeUnited Kingdom
| | - Alex R DeCasien
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental HealthBethesdaUnited States
| | - Theodore D Satterthwaite
- Department of Psychiatry, University of PennsylvaniaPhiladelphiaUnited States
- Lifespan Informatics and Neuroimaging Center, University of Pennsylvania School of MedicinePhiladelphiaUnited States
| | - Siyuan Liu
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental HealthBethesdaUnited States
| | - Petra E Vértes
- Department of Psychiatry, University of CambridgeCambridgeUnited Kingdom
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Aaron Alexander-Bloch
- Department of Psychiatry, University of PennsylvaniaPhiladelphiaUnited States
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of PhiladelphiaPhiladelphiaUnited States
| | - Daniel H Geschwind
- Center for Autism Research and Treatment, Semel Institute, Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Armin Raznahan
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental HealthBethesdaUnited States
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14
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Bagnato F, Sati P, Hemond CC, Elliott C, Gauthier SA, Harrison DM, Mainero C, Oh J, Pitt D, Shinohara RT, Smith SA, Trapp B, Azevedo CJ, Calabresi PA, Henry RG, Laule C, Ontaneda D, Rooney WD, Sicotte NL, Reich DS, Absinta M. Imaging chronic active lesions in multiple sclerosis: a consensus statement. Brain 2024:awae013. [PMID: 38226694 DOI: 10.1093/brain/awae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 11/21/2023] [Accepted: 12/08/2023] [Indexed: 01/17/2024] Open
Abstract
Chronic active lesions (CAL) are an important manifestation of chronic inflammation in multiple sclerosis (MS) and have implications for non-relapsing biological progression. In recent years, the discovery of innovative magnetic resonance imaging (MRI) and PET derived biomarkers has made it possible to detect CAL, and to some extent quantify them, in the brain of persons with MS, in vivo. Paramagnetic rim lesions on susceptibility-sensitive MRI sequences, MRI-defined slowly expanding lesions on T1-weighted (T1-w) and T2-w scans, and 18-kDa translocator protein-positive lesions on PET are promising candidate biomarkers of CAL. While partially overlapping, these biomarkers do not have equivalent sensitivity and specificity to histopathological CAL. Standardization in the use of available imaging measures for CAL identification, quantification, and monitoring is lacking. To fast-forward clinical translation of CAL, the North American Imaging in Multiple Sclerosis Cooperative developed a Consensus Statement, which provides guidance for the radiological definition and measurement of CAL. The proposed manuscript presents this Consensus Statement, summarizes the multistep process leading to it, and identifies the remaining major gaps in knowledge.
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Affiliation(s)
- Francesca Bagnato
- Neuroimaging Unit, Neuroimmunology Division, Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37212, USA
- Department of Neurology, Nashville VA Medical Center, Tennessee Valley Healthcare System, Nashville, TN 37212, USA
| | - Pascal Sati
- Neuroimaging Program, Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | | | | | - Susan A Gauthier
- Department of Neurology, Weill Cornell Medicine, NYC, NY 10021, USA
| | - Daniel M Harrison
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Department of Neurology, Baltimore VA Medical Center, VA Maryland Healthcare System; Baltimore, MD 21201, USA
| | - Caterina Mainero
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jiwon Oh
- Division of Neurology, St. Michael's Hospital, University of Toronto, Toronto, ON M5S, Canada
| | - David Pitt
- Department of Neurology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Endeavor, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Biomedical Image Computing and Analytics, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Seth A Smith
- Vanderbilt University Institute of Imaging Science, Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Bruce Trapp
- Department on Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Christina J Azevedo
- Department of Neurology, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90007, USA
| | - Peter A Calabresi
- Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Roland G Henry
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA 94158, USA
| | - Cornelia Laule
- Department of Radiology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Physics & Astronomy, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- International Collaboration on Repair Discoveries (ICORD), University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Daniel Ontaneda
- Mellen Center for Multiple Sclerosis, Cleveland Clinic, Cleveland, OH 44195, USA
| | - William D Rooney
- Advanced Imaging Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Nancy L Sicotte
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Daniel S Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Martina Absinta
- Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Translational Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, Vita-Salute San Raffaele University and Hospital, Milan, 20132, Italy
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15
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Daboul L, O’Donnell CM, Amin M, Rodrigues P, Derbyshire J, Azevedo C, Bar-Or A, Caverzasi E, Calabresi PA, Cree BA, Freeman L, Henry RG, Longbrake EE, Oh J, Papinutto N, Pelletier D, Prchkovska V, Raza P, Ramos M, Samudralwar RD, Schindler MK, Sotirchos ES, Sicotte NL, Solomon AJ, Shinohara RT, Reich DS, Sati P, Ontaneda D. A multicenter pilot study evaluating simplified central vein assessment for the diagnosis of multiple sclerosis. Mult Scler 2024; 30:25-34. [PMID: 38088067 PMCID: PMC11037932 DOI: 10.1177/13524585231214360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
BACKGROUND The central vein sign (CVS) is a proposed magnetic resonance imaging (MRI) biomarker for multiple sclerosis (MS); the optimal method for abbreviated CVS scoring is not yet established. OBJECTIVE The aim of this study was to evaluate the performance of a simplified approach to CVS assessment in a multicenter study of patients being evaluated for suspected MS. METHODS Adults referred for possible MS to 10 sites were recruited. A post-Gd 3D T2*-weighted MRI sequence (FLAIR*) was obtained in each subject. Trained raters at each site identified up to six CVS-positive lesions per FLAIR* scan. Diagnostic performance of CVS was evaluated for a diagnosis of MS which had been confirmed using the 2017 McDonald criteria at thresholds including three positive lesions (Select-3*) and six positive lesions (Select-6*). Inter-rater reliability assessments were performed. RESULTS Overall, 78 participants were analyzed; 37 (47%) were diagnosed with MS, and 41 (53%) were not. The mean age of participants was 45 (range: 19-64) years, and most were female (n = 55, 71%). The area under the receiver operating characteristic curve (AUROC) for the simplified counting method was 0.83 (95% CI: 0.73-0.93). Select-3* and Select-6* had sensitivity of 81% and 65% and specificity of 68% and 98%, respectively. Inter-rater agreement was 78% for Select-3* and 83% for Select-6*. CONCLUSION A simplified method for CVS assessment in patients referred for suspected MS demonstrated good diagnostic performance and inter-rater agreement.
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Affiliation(s)
- Lynn Daboul
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
- Cleveland Clinic Lerner College of Medicine, Cleveland, OH
| | - Carly M. O’Donnell
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Moein Amin
- Neurological Institute, Cleveland Clinic, Cleveland, OH
| | | | - John Derbyshire
- Functional MRI Facility, NIMH, National Institutes of Health, Bethesda, MD
| | - Christina Azevedo
- Department of Neurology, University of Southern California, Los Angeles, CA
| | - Amit Bar-Or
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Eduardo Caverzasi
- Department of Neurology, University of California at San Francisco, San Francisco, CA
| | | | - Bruce A.C. Cree
- Department of Neurology, University of California at San Francisco, San Francisco, CA
| | - Leorah Freeman
- Department of Neurology, Dell Medical School, The University of Texas, Austin, TX
| | - Roland G. Henry
- Department of Neurology, University of California at San Francisco, San Francisco, CA
| | | | - Jiwon Oh
- Division of Neurology, St. Michael’s Hospital, University of Toronto, Toronto, ON, CANADA
| | - Nico Papinutto
- Department of Neurology, University of California at San Francisco, San Francisco, CA
| | - Daniel Pelletier
- Department of Neurology, University of Southern California, Los Angeles, CA
| | | | - Praneeta Raza
- Cleveland Clinic Lerner College of Medicine, Cleveland, OH
| | - Marc Ramos
- QMENTA Cloud Platform, QMENTA Inc., Boston, MA, USA
| | | | - Matthew K. Schindler
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | | | - Nancy L. Sicotte
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Andrew J. Solomon
- Department of Neurological Sciences, Larner College of Medicine, The University of Vermont, Burlington, VT
| | - Russell T. Shinohara
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Daniel S. Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Pascal Sati
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Daniel Ontaneda
- Mellen Center for Multiple Sclerosis, Cleveland Clinic, Cleveland, OH
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16
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Emmert BE, Xie K, Conrad EC, Ghosn NJ, Bauman K, Korzun J, Kulick-Soper CV, Naveed O, Hartmann N, LaRocque JJ, Mindy Ganguly T, Gugger JJ, Raghupathi R, Gelfand MA, Davis KA, Sinha SR, Litt B, Shinohara RT, Ellis CA. Alcohol for seizure induction in the epilepsy monitoring unit. Epilepsy Behav 2024; 150:109572. [PMID: 38070406 PMCID: PMC10842723 DOI: 10.1016/j.yebeh.2023.109572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/17/2023] [Accepted: 11/28/2023] [Indexed: 01/14/2024]
Abstract
RATIONALE Seizure induction techniques are used in the epilepsy monitoring unit (EMU) to increase diagnostic yield and reduce length of stay. There are insufficient data on the efficacy of alcohol as an induction technique. METHODS We performed a retrospective cohort study using six years of EMU data at our institution. We compared cases who received alcohol for seizure induction to matched controls who did not. The groups were matched on the following variables: age, reason for admission, length of stay, number of antiseizure medications (ASM) at admission, whether ASMs were tapered during admission, and presence of interictal epileptiform discharges. We used both propensity score and exact matching strategies. We compared the likelihood of epileptic seizures and nonepileptic events in cases versus controls using Kaplan-Meier time-to-event analysis, as well as odds ratios for these outcomes occurring at any time during the admission. RESULTS We analyzed 256 cases who received alcohol (median dose 2.5 standard drinks) and 256 propensity score-matched controls. Cases who received alcohol were no more likely than controls to have an epileptic seizure (X2(1) = 0.01, p = 0.93) or nonepileptic event (X2(1) = 2.1, p = 0.14) in the first 48 h after alcohol administration. For the admission overall, cases were no more likely to have an epileptic seizure (OR 0.89, 95 % CI 0.61-1.28, p = 0.58), nonepileptic event (OR 0.97, CI 0.62-1.53, p = 1.00), nor require rescue benzodiazepine (OR 0.63, CI 0.35-1.12, p = 0.15). Stratified analyses revealed no increased risk of epileptic seizure in any subgroups. Sensitivity analysis using exact matching showed that results were robust to matching strategy. CONCLUSIONS Alcohol was not an effective induction technique in the EMU. This finding has implications for counseling patients with epilepsy about the risks of drinking alcohol in moderation in their daily lives.
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Affiliation(s)
- Brian E Emmert
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia PA, USA.
| | - Kevin Xie
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Center for Neuroengineering & Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Erin C Conrad
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia PA, USA; Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Center for Neuroengineering & Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Nina J Ghosn
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Center for Neuroengineering & Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristie Bauman
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia PA, USA
| | - Jacob Korzun
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia PA, USA
| | - Catherine V Kulick-Soper
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia PA, USA
| | - Omer Naveed
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia PA, USA
| | - Nicole Hartmann
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia PA, USA
| | - Joshua J LaRocque
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia PA, USA
| | - Taneeta Mindy Ganguly
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia PA, USA
| | - James J Gugger
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia PA, USA; Center for Neuroengineering & Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ramya Raghupathi
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia PA, USA
| | - Michael A Gelfand
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia PA, USA
| | - Kathryn A Davis
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia PA, USA; Center for Neuroengineering & Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Saurabh R Sinha
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia PA, USA
| | - Brian Litt
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia PA, USA; Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Center for Neuroengineering & Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA; Center for Biomedical Image Computing and Analytics, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Colin A Ellis
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia PA, USA
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17
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Yang Z, Wen J, Erus G, Govindarajan ST, Melhem R, Mamourian E, Cui Y, Srinivasan D, Abdulkadir A, Parmpi P, Wittfeld K, Grabe HJ, Bülow R, Frenzel S, Tosun D, Bilgel M, An Y, Yi D, Marcus DS, LaMontagne P, Benzinger TL, Heckbert SR, Austin TR, Waldstein SR, Evans MK, Zonderman AB, Launer LJ, Sotiras A, Espeland MA, Masters CL, Maruff P, Fripp J, Toga A, O’Bryant S, Chakravarty MM, Villeneuve S, Johnson SC, Morris JC, Albert MS, Yaffe K, Völzke H, Ferrucci L, Bryan NR, Shinohara RT, Fan Y, Habes M, Lalousis PA, Koutsouleris N, Wolk DA, Resnick SM, Shou H, Nasrallah IM, Davatzikos C. Five dominant dimensions of brain aging are identified via deep learning: associations with clinical, lifestyle, and genetic measures. medRxiv 2023:2023.12.29.23300642. [PMID: 38234857 PMCID: PMC10793523 DOI: 10.1101/2023.12.29.23300642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Brain aging is a complex process influenced by various lifestyle, environmental, and genetic factors, as well as by age-related and often co-existing pathologies. MRI and, more recently, AI methods have been instrumental in understanding the neuroanatomical changes that occur during aging in large and diverse populations. However, the multiplicity and mutual overlap of both pathologic processes and affected brain regions make it difficult to precisely characterize the underlying neurodegenerative profile of an individual from an MRI scan. Herein, we leverage a state-of-the art deep representation learning method, Surreal-GAN, and present both methodological advances and extensive experimental results that allow us to elucidate the heterogeneity of brain aging in a large and diverse cohort of 49,482 individuals from 11 studies. Five dominant patterns of neurodegeneration were identified and quantified for each individual by their respective (herein referred to as) R-indices. Significant associations between R-indices and distinct biomedical, lifestyle, and genetic factors provide insights into the etiology of observed variances. Furthermore, baseline R-indices showed predictive value for disease progression and mortality. These five R-indices contribute to MRI-based precision diagnostics, prognostication, and may inform stratification into clinical trials.
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Affiliation(s)
- Zhijian Yang
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Graduate Group in Applied Mathematics and Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Junhao Wen
- Laboratory of AI and Biomedical Science (LABS), Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, USA
| | - Guray Erus
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sindhuja T. Govindarajan
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Randa Melhem
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth Mamourian
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuhan Cui
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dhivya Srinivasan
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ahmed Abdulkadir
- Laboratory for Research in Neuroimaging, Department of Clinical Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Paraskevi Parmpi
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katharina Wittfeld
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Germany
| | - Hans J. Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Germany
- German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, Germany
| | - Robin Bülow
- Institute of Diagnostic Radiology and Neuroradiology, University of Greifswald, Germany
| | - Stefan Frenzel
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Germany
| | - Duygu Tosun
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, USA
| | - Murat Bilgel
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Yang An
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Dahyun Yi
- Institute of Human Behavioral Medicine, Medical Research Center Seoul National University, Seoul, Republic of Korea
| | - Daniel S. Marcus
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Pamela LaMontagne
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Tammie L.S. Benzinger
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Susan R. Heckbert
- Cardiovascular Health Research Unit and Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Thomas R. Austin
- Cardiovascular Health Research Unit and Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Shari R. Waldstein
- Department of Psychology, University of Maryland, Baltimore County, Catonsville, MD, USA
| | - Michele K. Evans
- Health Disparities Research Section, Laboratory of Epidemiology and Population Sciences, NIA/NIH/IRP, Baltimore, MD, USA
| | - Alan B. Zonderman
- Health Disparities Research Section, Laboratory of Epidemiology and Population Sciences, NIA/NIH/IRP, Baltimore, MD, USA
| | - Lenore J. Launer
- Neuroepidemiology Section, Intramural Research Program, National Institute on Aging, Bethesda, Maryland, USA
| | - Aristeidis Sotiras
- Department of Radiology and Institute of Informatics, Washington University in St. Luis, St. Luis, MO63110, USA
| | - Mark A. Espeland
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Colin L. Masters
- Florey Institute, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Paul Maruff
- Florey Institute, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Jurgen Fripp
- CSIRO Health and Biosecurity, Australian e-Health Research Centre CSIRO, Brisbane, Queensland, Australia
| | - Arthur Toga
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, USA
| | - Sid O’Bryant
- Institute for Translational Research University of North Texas Health Science Center Fort Worth Texas USA
| | - Mallar M. Chakravarty
- Computational Brain Anatomy (CoBrA) Laboratory, Cerebral Imaging Center, Douglas Mental Health University Institute, McGill University, Verdun, Quebec, Canada
| | - Sylvia Villeneuve
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Sterling C. Johnson
- Wisconsin Alzheimer’s Institute, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - John C. Morris
- Knight Alzheimer Disease Research Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Marilyn S. Albert
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kristine Yaffe
- Departments of Neurology, Psychiatry and Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Luigi Ferrucci
- Translational Gerontology Branch, Longitudinal Studies Section, National Institute on Aging, National Institutes of Health, MedStar Harbor Hospital, 3001 S. Hanover Street, Baltimore, MD, USA
| | - Nick R. Bryan
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Russell T. Shinohara
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, & Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Yong Fan
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mohamad Habes
- Biggs Alzheimer’s Institute, University of Texas San Antonio Health Science Center, USA
| | - Paris Alexandros Lalousis
- Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Nikolaos Koutsouleris
- Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
- Section for Precision Psychiatry, Department of Psychiatry and Psychotherapy, Ludwig-Maximilian-University Munich, Munich, Germany
| | - David A. Wolk
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Susan M. Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Haochang Shou
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, & Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ilya M. Nasrallah
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Christos Davatzikos
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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18
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Lucas A, Campbell Arnold T, Okar SV, Vadali C, Kawatra KD, Ren Z, Cao Q, Shinohara RT, Schindler MK, Davis KA, Litt B, Reich DS, Stein JM. Multi-contrast high-field quality image synthesis for portable low-field MRI using generative adversarial networks and paired data. medRxiv 2023:2023.12.28.23300409. [PMID: 38234785 PMCID: PMC10793526 DOI: 10.1101/2023.12.28.23300409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Introduction Portable low-field strength (64mT) MRI scanners promise to increase access to neuroimaging for clinical and research purposes, however these devices produce lower quality images compared to high-field scanners. In this study, we developed and evaluated a deep learning architecture to generate high-field quality brain images from low-field inputs using a paired dataset of multiple sclerosis (MS) patients scanned at 64mT and 3T. Methods A total of 49 MS patients were scanned on portable 64mT and standard 3T scanners at Penn (n=25) or the National Institutes of Health (NIH, n=24) with T1-weighted, T2-weighted and FLAIR acquisitions. Using this paired data, we developed a generative adversarial network (GAN) architecture for low- to high-field image translation (LowGAN). We then evaluated synthesized images with respect to image quality, brain morphometry, and white matter lesions. Results Synthetic high-field images demonstrated visually superior quality compared to low-field inputs and significantly higher normalized cross-correlation (NCC) to actual high-field images for T1 (p=0.001) and FLAIR (p<0.001) contrasts. LowGAN generally outperformed the current state-of-the-art for low-field volumetrics. For example, thalamic, lateral ventricle, and total cortical volumes in LowGAN outputs did not differ significantly from 3T measurements. Synthetic outputs preserved MS lesions and captured a known inverse relationship between total lesion volume and thalamic volume. Conclusions LowGAN generates synthetic high-field images with comparable visual and quantitative quality to actual high-field scans. Enhancing portable MRI image quality could add value and boost clinician confidence, enabling wider adoption of this technology.
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Affiliation(s)
- Alfredo Lucas
- Perelman School of Medicine, University of Pennsylvania
- Center for Neuroengineering and Therapeutics, Departments of Bioengineering and Neurology, University of Pennsylvania
| | - T Campbell Arnold
- Center for Neuroengineering and Therapeutics, Departments of Bioengineering and Neurology, University of Pennsylvania
| | - Serhat V Okar
- National Institute of Neurological Disorders and Stroke, National Institutes of Health
| | - Chetan Vadali
- Center for Neuroengineering and Therapeutics, Departments of Bioengineering and Neurology, University of Pennsylvania
- Department of Radiology, University of Pennsylvania
| | - Karan D Kawatra
- National Institute of Neurological Disorders and Stroke, National Institutes of Health
| | - Zheng Ren
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania
| | - Quy Cao
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania
| | - Matthew K Schindler
- Perelman School of Medicine, University of Pennsylvania
- Department of Neurology, University of Pennsylvania
| | - Kathryn A Davis
- Perelman School of Medicine, University of Pennsylvania
- Center for Neuroengineering and Therapeutics, Departments of Bioengineering and Neurology, University of Pennsylvania
- Department of Neurology, University of Pennsylvania
| | - Brian Litt
- Perelman School of Medicine, University of Pennsylvania
- Center for Neuroengineering and Therapeutics, Departments of Bioengineering and Neurology, University of Pennsylvania
- Department of Neurology, University of Pennsylvania
| | - Daniel S Reich
- National Institute of Neurological Disorders and Stroke, National Institutes of Health
| | - Joel M Stein
- Perelman School of Medicine, University of Pennsylvania
- Center for Neuroengineering and Therapeutics, Departments of Bioengineering and Neurology, University of Pennsylvania
- Department of Radiology, University of Pennsylvania
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19
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Wen J, Nasrallah IM, Abdulkadir A, Satterthwaite TD, Yang Z, Erus G, Robert-Fitzgerald T, Singh A, Sotiras A, Boquet-Pujadas A, Mamourian E, Doshi J, Cui Y, Srinivasan D, Skampardoni I, Chen J, Hwang G, Bergman M, Bao J, Veturi Y, Zhou Z, Yang S, Dazzan P, Kahn RS, Schnack HG, Zanetti MV, Meisenzahl E, Busatto GF, Crespo-Facorro B, Pantelis C, Wood SJ, Zhuo C, Shinohara RT, Gur RC, Gur RE, Koutsouleris N, Wolf DH, Saykin AJ, Ritchie MD, Shen L, Thompson PM, Colliot O, Wittfeld K, Grabe HJ, Tosun D, Bilgel M, An Y, Marcus DS, LaMontagne P, Heckbert SR, Austin TR, Launer LJ, Espeland M, Masters CL, Maruff P, Fripp J, Johnson SC, Morris JC, Albert MS, Bryan RN, Resnick SM, Fan Y, Habes M, Wolk D, Shou H, Davatzikos C. Genomic loci influence patterns of structural covariance in the human brain. Proc Natl Acad Sci U S A 2023; 120:e2300842120. [PMID: 38127979 PMCID: PMC10756284 DOI: 10.1073/pnas.2300842120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 10/31/2023] [Indexed: 12/23/2023] Open
Abstract
Normal and pathologic neurobiological processes influence brain morphology in coordinated ways that give rise to patterns of structural covariance (PSC) across brain regions and individuals during brain aging and diseases. The genetic underpinnings of these patterns remain largely unknown. We apply a stochastic multivariate factorization method to a diverse population of 50,699 individuals (12 studies and 130 sites) and derive data-driven, multi-scale PSCs of regional brain size. PSCs were significantly correlated with 915 genomic loci in the discovery set, 617 of which are newly identified, and 72% were independently replicated. Key pathways influencing PSCs involve reelin signaling, apoptosis, neurogenesis, and appendage development, while pathways of breast cancer indicate potential interplays between brain metastasis and PSCs associated with neurodegeneration and dementia. Using support vector machines, multi-scale PSCs effectively derive imaging signatures of several brain diseases. Our results elucidate genetic and biological underpinnings that influence structural covariance patterns in the human brain.
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Affiliation(s)
- Junhao Wen
- Laboratory of AI and Biomedical Science, Department of Neurology, Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA90033
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Ilya M. Nasrallah
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Radiology, University of Pennsylvania, Philadelphia, PA19104
| | - Ahmed Abdulkadir
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Theodore D. Satterthwaite
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Zhijian Yang
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Guray Erus
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Timothy Robert-Fitzgerald
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Ashish Singh
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Aristeidis Sotiras
- Department of Radiology, Washington University School of Medicine, St. Louis, MO63110
| | - Aleix Boquet-Pujadas
- Biomedical Imaging Group, Department of Biomedical Engineering, École Polytechnique Fédérale de Lausanne, Lausanne1015, Switzerland
| | - Elizabeth Mamourian
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Jimit Doshi
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Yuhan Cui
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Dhivya Srinivasan
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Ioanna Skampardoni
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Jiong Chen
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Gyujoon Hwang
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Mark Bergman
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Jingxuan Bao
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA19104
| | - Yogasudha Veturi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Zhen Zhou
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Shu Yang
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA19104
| | - Paola Dazzan
- Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, LondonWC2R 2LS, United Kingdom
| | - Rene S. Kahn
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Hugo G. Schnack
- Department of Psychiatry, University Medical Center Utrecht, Utrecht 3584 CX Ut, Netherlands
| | - Marcus V. Zanetti
- Institute of Psychiatry, Department of Psychiatry, Faculty of Medicine, University of São Paulo, São Paulo05508-070, Brazil
| | - Eva Meisenzahl
- Department of Psychiatry and Psychotherapy, Heinrich Heine University, Düsseldorf40204, Germany
| | - Geraldo F. Busatto
- Institute of Psychiatry, Department of Psychiatry, Faculty of Medicine, University of São Paulo, São Paulo05508-070, Brazil
| | - Benedicto Crespo-Facorro
- Hospital Universitario Virgen del Rocio, School of Medicine, University of Sevilla,Sevilla41004, Spain
| | - Christos Pantelis
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Stephen J. Wood
- Orygen and the Centre for Youth Mental Health, Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Chuanjun Zhuo
- Key Laboratory of Real Tine Tracing of Brain Circuits in Psychiatry and Neurology, Department of Psychiatry, Tianjin Medical University, Tianjin300070, China
| | - Russell T. Shinohara
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Ruben C. Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Raquel E. Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Nikolaos Koutsouleris
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian University, Munich 80539, Germany
| | - Daniel H. Wolf
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Andrew J. Saykin
- Indiana Alzheimer’s Disease Research Center, Department of Radiology, Indiana University School of Medicine, Indianapolis, IN46202-3082
| | - Marylyn D. Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Li Shen
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA19104
| | - Paul M. Thompson
- Imaging Genetics Center, Department of Neurology, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA90033
| | - Olivier Colliot
- Institut du Cerveau, Sorbonne Université, Paris75013, France
| | - Katharina Wittfeld
- Department of Psychiatry and Psychotherapy, German Center for Neurodegenerative Diseases, University Medicine Greifswald, Greifswald17475, Germany
| | - Hans J. Grabe
- Department of Psychiatry and Psychotherapy, German Center for Neurodegenerative Diseases, University Medicine Greifswald, Greifswald17475, Germany
| | - Duygu Tosun
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA 94143
| | - Murat Bilgel
- Laboratory of Behavioral Neuroscience, National Institute on Aging, NIH, Baltimore21224, MD
| | - Yang An
- Laboratory of Behavioral Neuroscience, National Institute on Aging, NIH, Baltimore21224, MD
| | - Daniel S. Marcus
- Department of Radiology, Washington University School of Medicine, St. Louis, MO63110
| | - Pamela LaMontagne
- Department of Radiology, Washington University School of Medicine, St. Louis, MO63110
| | - Susan R. Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA98195
| | - Thomas R. Austin
- Department of Epidemiology, University of Washington, Seattle, WA98195
| | - Lenore J. Launer
- Neuroepidemiology Section, Intramural Research Program, National Institute on Aging, Washington, MD20817
| | - Mark Espeland
- Sticht Center for Healthy Aging and Alzheimer’s Prevention, Divisions of Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC27101
| | - Colin L. Masters
- Florey Institute of Neuroscience and Mental Health, Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC3010, Australia
| | - Paul Maruff
- Florey Institute of Neuroscience and Mental Health, Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC3010, Australia
| | - Jurgen Fripp
- Health and Biosecurity, Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, Brisbane, QLD4029, Australia
| | - Sterling C. Johnson
- Wisconsin Alzheimer's Institute, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI53792
| | - John C. Morris
- Knight Alzheimer Disease Research Center, Department of Neurology, Washington University in St. Louis, St. Louis, MO63110
| | - Marilyn S. Albert
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - R. Nick Bryan
- Department of Radiology, University of Pennsylvania, Philadelphia, PA19104
| | - Susan M. Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, NIH, Baltimore21224, MD
| | - Yong Fan
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Mohamad Habes
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, Department of Radiology, University of Texas Health Science Center at San Antonio, San Antonio, TX78229
| | - David Wolk
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Neurology, University of Pennsylvania, Philadelphia, PA19104
| | - Haochang Shou
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Christos Davatzikos
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
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20
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Keller AS, Pines AR, Shanmugan S, Sydnor VJ, Cui Z, Bertolero MA, Barzilay R, Alexander-Bloch AF, Byington N, Chen A, Conan GM, Davatzikos C, Feczko E, Hendrickson TJ, Houghton A, Larsen B, Li H, Miranda-Dominguez O, Roalf DR, Perrone A, Shetty A, Shinohara RT, Fan Y, Fair DA, Satterthwaite TD. Personalized functional brain network topography is associated with individual differences in youth cognition. Nat Commun 2023; 14:8411. [PMID: 38110396 PMCID: PMC10728159 DOI: 10.1038/s41467-023-44087-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/29/2023] [Indexed: 12/20/2023] Open
Abstract
Individual differences in cognition during childhood are associated with important social, physical, and mental health outcomes in adolescence and adulthood. Given that cortical surface arealization during development reflects the brain's functional prioritization, quantifying variation in the topography of functional brain networks across the developing cortex may provide insight regarding individual differences in cognition. We test this idea by defining personalized functional networks (PFNs) that account for interindividual heterogeneity in functional brain network topography in 9-10 year olds from the Adolescent Brain Cognitive Development℠ Study. Across matched discovery (n = 3525) and replication (n = 3447) samples, the total cortical representation of fronto-parietal PFNs positively correlates with general cognition. Cross-validated ridge regressions trained on PFN topography predict cognition in unseen data across domains, with prediction accuracy increasing along the cortex's sensorimotor-association organizational axis. These results establish that functional network topography heterogeneity is associated with individual differences in cognition before the critical transition into adolescence.
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Affiliation(s)
- Arielle S Keller
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Adam R Pines
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sheila Shanmugan
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Valerie J Sydnor
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zaixu Cui
- Chinese Institute for Brain Research, Beijing, China
| | - Maxwell A Bertolero
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ran Barzilay
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Aaron F Alexander-Bloch
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nora Byington
- Masonic Institute for the Developing Brain, Institute of Child Development, College of Education and Human Development, Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN, 55414, USA
| | - Andrew Chen
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gregory M Conan
- Masonic Institute for the Developing Brain, Institute of Child Development, College of Education and Human Development, Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN, 55414, USA
| | - Christos Davatzikos
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Eric Feczko
- Masonic Institute for the Developing Brain, Institute of Child Development, College of Education and Human Development, Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN, 55414, USA
| | - Timothy J Hendrickson
- Masonic Institute for the Developing Brain, Institute of Child Development, College of Education and Human Development, Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN, 55414, USA
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, MN, 55414, USA
| | - Audrey Houghton
- Masonic Institute for the Developing Brain, Institute of Child Development, College of Education and Human Development, Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN, 55414, USA
| | - Bart Larsen
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hongming Li
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Oscar Miranda-Dominguez
- Masonic Institute for the Developing Brain, Institute of Child Development, College of Education and Human Development, Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN, 55414, USA
| | - David R Roalf
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Anders Perrone
- Masonic Institute for the Developing Brain, Institute of Child Development, College of Education and Human Development, Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN, 55414, USA
| | - Alisha Shetty
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yong Fan
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Damien A Fair
- Masonic Institute for the Developing Brain, Institute of Child Development, College of Education and Human Development, Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN, 55414, USA
| | - Theodore D Satterthwaite
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Child and Adolescent Psychiatry and Behavioral Science, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
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21
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Tu D, Mahony B, Moore TM, Bertolero MA, Alexander-Bloch AF, Gur R, Bassett DS, Satterthwaite TD, Raznahan A, Shinohara RT. CoCoA: conditional correlation models with association size. Biostatistics 2023; 25:154-170. [PMID: 35939558 PMCID: PMC10724258 DOI: 10.1093/biostatistics/kxac032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/14/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Many scientific questions can be formulated as hypotheses about conditional correlations. For instance, in tests of cognitive and physical performance, the trade-off between speed and accuracy motivates study of the two variables together. A natural question is whether speed-accuracy coupling depends on other variables, such as sustained attention. Classical regression techniques, which posit models in terms of covariates and outcomes, are insufficient to investigate the effect of a third variable on the symmetric relationship between speed and accuracy. In response, we propose a conditional correlation model with association size, a likelihood-based statistical framework to estimate the conditional correlation between speed and accuracy as a function of additional variables. We propose novel measures of the association size, which are analogous to effect sizes on the correlation scale while adjusting for confound variables. In simulation studies, we compare likelihood-based estimators of conditional correlation to semiparametric estimators adapted from genomic studies and find that the former achieves lower bias and variance under both ideal settings and model assumption misspecification. Using neurocognitive data from the Philadelphia Neurodevelopmental Cohort, we demonstrate that greater sustained attention is associated with stronger speed-accuracy coupling in a complex reasoning task while controlling for age. By highlighting conditional correlations as the outcome of interest, our model provides complementary insights to traditional regression modeling and partitioned correlation analyses.
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Affiliation(s)
- Danni Tu
- The Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, 423 Guardian Drive, Philadelphia, PA, 19104, USA
| | - Bridget Mahony
- Section on Developmental Neurogenomics, National Institutes of Mental Health, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Tyler M Moore
- Department of Psychiatry, Perelman School of Medicine, 3400 Spruce Street, Philadelphia, PA, 19104, USA
| | - Maxwell A Bertolero
- Department of Psychiatry, Perelman School of Medicine, Philadelphia, PA, USA and Penn Lifespan Informatics and Neuroimaging Center, 3700 Hamilton Walk, Philadelphia, PA, 19104, USA
| | | | - Ruben Gur
- Department of Psychiatry, Perelman School of Medicine, Philadelphia, PA, USA
| | - Dani S Bassett
- Department of Bioengineering, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA, 19104, USA, Department of Physics and Astronomy, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA, 19104, USA, Department of Electrical and Systems Engineering, University of Pennsylvania, 200 South 33rd Street, Philadelphia, PA, 19104, USA and Department of Neurology, University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA, 19104, USA
| | - Theodore D Satterthwaite
- Department of Psychiatry, Perelman School of Medicine, Philadelphia, PA, USA and Penn Lifespan Informatics and Neuroimaging Center, Philadelphia, PA, USA
| | - Armin Raznahan
- Section on Developmental Neurogenomics, National Institutes of Mental Health, Bethesda, MD, USA
| | - Russell T Shinohara
- The Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, USA
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22
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Vandekar SN, Kang K, Woodward ND, Huang A, McHugo M, Garbett S, Stephens J, Shinohara RT, Schwartzman A, Blume J. Evaluation of resampling-based inference for topological features of neuroimages. bioRxiv 2023:2023.12.12.571377. [PMID: 38168311 PMCID: PMC10760090 DOI: 10.1101/2023.12.12.571377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Many recent studies have demonstrated the inflated type 1 error rate of the original Gaussian random field (GRF) methods for inference of neuroimages and identified resampling (permutation and bootstrapping) methods that have better performance. There has been no evaluation of resampling procedures when using robust (sandwich) statistical images with different topological features (TF) used for neuroimaging inference. Here, we consider estimation of distributions TFs of a statistical image and evaluate resampling procedures that can be used when exchangeability is violated. We compare the methods using realistic simulations and study sex differences in life-span age-related changes in gray matter volume in the Nathan Kline Institute Rockland sample. We find that our proposed wild bootstrap and the commonly used permutation procedure perform well in sample sizes above 50 under realistic simulations with heteroskedasticity. The Rademacher wild bootstrap has fewer assumptions than the permutation and performs similarly in samples of 100 or more, so is valid in a broader range of conditions. We also evaluate the GRF-based pTFCE method and show that it has inflated error rates in samples less than 200. Our R package, pbj , is available on Github and allows the user to reproducibly implement various resampling-based group level neuroimage analyses.
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23
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Chen AA, Weinstein SM, Adebimpe A, Gur RC, Gur RE, Merikangas KR, Satterthwaite TD, Shinohara RT, Shou H. Similarity-based multimodal regression. Biostatistics 2023:kxad033. [PMID: 38058018 DOI: 10.1093/biostatistics/kxad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 10/07/2023] [Accepted: 11/06/2023] [Indexed: 12/08/2023] Open
Abstract
To better understand complex human phenotypes, large-scale studies have increasingly collected multiple data modalities across domains such as imaging, mobile health, and physical activity. The properties of each data type often differ substantially and require either separate analyses or extensive processing to obtain comparable features for a combined analysis. Multimodal data fusion enables certain analyses on matrix-valued and vector-valued data, but it generally cannot integrate modalities of different dimensions and data structures. For a single data modality, multivariate distance matrix regression provides a distance-based framework for regression accommodating a wide range of data types. However, no distance-based method exists to handle multiple complementary types of data. We propose a novel distance-based regression model, which we refer to as Similarity-based Multimodal Regression (SiMMR), that enables simultaneous regression of multiple modalities through their distance profiles. We demonstrate through simulation, imaging studies, and longitudinal mobile health analyses that our proposed method can detect associations between clinical variables and multimodal data of differing properties and dimensionalities, even with modest sample sizes. We perform experiments to evaluate several different test statistics and provide recommendations for applying our method across a broad range of scenarios.
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Affiliation(s)
- Andrew A Chen
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Sarah M Weinstein
- Department of Epidemiology and Biostatistics, Temple University College of Public Health, Philadelphia, PA 19122, USA
| | - Azeez Adebimpe
- Penn Lifespan Informatics & Neuroimaging Center, Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ruben C Gur
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute Penn Medicine and CHOP, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Raquel E Gur
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute Penn Medicine and CHOP, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathleen R Merikangas
- Genetic Epidemiology Research Branch, Intramural Research Program, National Institute of Mental Health, Bethesda, MD 20892, USA
| | - Theodore D Satterthwaite
- Penn Lifespan Informatics & Neuroimaging Center, Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Haochang Shou
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, PA 19104, USA
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24
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Lemley BA, Wu L, Roberts AL, Shinohara RT, Quarshie WO, Qureshi AM, Smith CL, Dori Y, Gillespie MJ, Rome JJ, Glatz AC, Amaral S, O'Byrne ML. Trends in Ductus Arteriosus Stent Versus Blalock-Taussig-Thomas Shunt Use and Comparison of Cost, Length of Stay, and Short-Term Outcomes in Neonates With Ductal-Dependent Pulmonary Blood Flow: An Observational Study Using the Pediatric Health Information Systems Database. J Am Heart Assoc 2023; 12:e030575. [PMID: 38038172 PMCID: PMC10727347 DOI: 10.1161/jaha.123.030575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 10/09/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND The modified Blalock-Taussig-Thomas shunt is the gold standard palliation for securing pulmonary blood flow in infants with ductal-dependent pulmonary blood flow. Recently, the ductus arteriosus stent (DAS) has become a viable alternative. METHODS AND RESULTS This was a retrospective multicenter study of neonates ≤30 days undergoing DAS or Blalock-Taussig-Thomas shunt placement between January 1, 2017 and December 31, 2020 at hospitals reporting to the Pediatric Health Information Systems database. We performed generalized linear mixed-effects modeling to evaluate trends in intervention and intercenter variation, propensity score adjustment and inverse probability weighting with linear mixed-effects modeling to analyze length of stay and cost of hospitalization, and generalized linear mixed modeling to analyze differences in 30-day outcomes. There were 1874 subjects (58% male, 61% White) from 45 centers (29% DAS). Odds of DAS increased with time (odds ratio [OR] 1.23, annually, P<0.01 [95% CI, 1.10-1.38]) with significant intercenter variation (median OR, 3.81 [95% CI, 2.74-5.91]). DAS was associated with shorter hospital length of stay (ratio of geometric means, 0.76 [95% CI, 0.63-0.91]), shorter intensive care unit length of stay (ratio of geometric means, 0.77 [95% CI, 0.61-0.97]), and less expensive hospitalization (ratio of geometric means, 0.70 [95% CI, 0.56-0.87]). Intervention was not significantly associated with odds of 30-day transplant-free survival (OR,1.18 [95% CI, 0.70-1.99]) or freedom from catheter reintervention (OR, 1.02 [95% CI, 0.65-1.58]), but DAS was associated with 30-day freedom from composite adverse outcome (OR, 1.51 [95% CI, 1.11-2.05]). CONCLUSIONS Use of DAS is increasing, but there is variability across centers. Though odds of transplant-free survival and reintervention were not significantly different after DAS, and DAS was associated with shorter length of stay and lower in-hospital costs.
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Affiliation(s)
- Bethan A. Lemley
- Division of CardiologyLurie Children’s HospitalChicagoILUSA
- Department of PediatricsFeinberg School of Medicine Northwestern UniversityChicagoILUSA
| | - Lezhou Wu
- Department of Biomedical and Health InformaticsChildren’s Hospital of PhiladelphiaPhiladelphiaPAUSA
| | - Amy L. Roberts
- Division of CardiologyThe Children’s Hospital of PhiladelphiaPhiladelphiaPAUSA
- Department of Pediatrics Perelman School of Medicine at The University of PennsylvaniaPhiladelphiaPAUSA
| | - Russell T. Shinohara
- Department of Biostatistics, Epidemiology, and InformaticsPerelman School of Medicine at the University of PennsylvaniaPhiladelphiaPAUSA
| | - William O. Quarshie
- Division of CardiologyThe Children’s Hospital of PhiladelphiaPhiladelphiaPAUSA
- Department of Pediatrics Perelman School of Medicine at The University of PennsylvaniaPhiladelphiaPAUSA
| | - Athar M. Qureshi
- Division of CardiologyTexas Children’s HospitalHoustonTXUSA
- Department of Pediatrics Baylor College of MedicineHoustonTXUSA
| | - Christopher L. Smith
- Division of CardiologyThe Children’s Hospital of PhiladelphiaPhiladelphiaPAUSA
- Department of Pediatrics Perelman School of Medicine at The University of PennsylvaniaPhiladelphiaPAUSA
| | - Yoav Dori
- Division of CardiologyThe Children’s Hospital of PhiladelphiaPhiladelphiaPAUSA
- Department of Pediatrics Perelman School of Medicine at The University of PennsylvaniaPhiladelphiaPAUSA
| | - Matthew J. Gillespie
- Division of CardiologyThe Children’s Hospital of PhiladelphiaPhiladelphiaPAUSA
- Department of Pediatrics Perelman School of Medicine at The University of PennsylvaniaPhiladelphiaPAUSA
| | - Jonathan J. Rome
- Division of CardiologyThe Children’s Hospital of PhiladelphiaPhiladelphiaPAUSA
- Department of Pediatrics Perelman School of Medicine at The University of PennsylvaniaPhiladelphiaPAUSA
| | - Andrew C. Glatz
- Division of CardiologySt. Louis Children’s HospitalSt. LouisMOUSA
- Department of PediatricsWashington University School of MedicineSt. LouisMOUSA
| | - Sandra Amaral
- Division of NephrologyThe Children’s Hospital of PhiladelphiaPhiladelphiaPAUSA
- Department of PediatricsPerelman School of Medicine at The University of PennsylvaniaPhiladelphiaPAUSA
| | - Michael L. O'Byrne
- Division of CardiologyThe Children’s Hospital of PhiladelphiaPhiladelphiaPAUSA
- Department of Pediatrics Perelman School of Medicine at The University of PennsylvaniaPhiladelphiaPAUSA
- Clinical Futures, The Children’s Hospital of Philadelphia and Leonard Davis Institute and Cardiovascular Outcomes, Quality, and Evaluative Research CenterPerelman School of Medicine at The University of PennsylvaniaPhiladelphiaPAUSA
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25
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Mehta K, Salo T, Madison T, Adebimpe A, Bassett DS, Bertolero M, Cieslak M, Covitz S, Houghton A, Keller AS, Luo A, Miranda-Dominguez O, Nelson SM, Shafiei G, Shanmugan S, Shinohara RT, Sydnor VJ, Feczko E, Fair DA, Satterthwaite TD. XCP-D: A Robust Pipeline for the post-processing of fMRI data. bioRxiv 2023:2023.11.20.567926. [PMID: 38045258 PMCID: PMC10690221 DOI: 10.1101/2023.11.20.567926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Functional neuroimaging is an essential tool for neuroscience research. Pre-processing pipelines produce standardized, minimally pre-processed data to support a range of potential analyses. However, post-processing is not similarly standardized. While several options for post-processing exist, they tend not to support output from disparate pre-processing pipelines, may have limited documentation, and may not follow BIDS best practices. Here we present XCP-D, which presents a solution to these issues. XCP-D is a collaborative effort between PennLINC at the University of Pennsylvania and the DCAN lab at the University at Minnesota. XCP-D uses an open development model on GitHub and incorporates continuous integration testing; it is distributed as a Docker container or Singularity image. XCP-D generates denoised BOLD images and functional derivatives from resting-state data in either NifTI or CIFTI files, following pre-processing with fMRIPrep, HCP, and ABCD-BIDS pipelines. Even prior to its official release, XCP-D has been downloaded >3,000 times from DockerHub. Together, XCP-D facilitates robust, scalable, and reproducible post-processing of fMRI data.
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Affiliation(s)
- Kahini Mehta
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Taylor Salo
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Thomas Madison
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55454, USA
| | - Azeez Adebimpe
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Danielle S Bassett
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, PA 19104, USA
- Department of Electrical & Systems Engineering, University of Pennsylvania, PA 19104, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Physics & Astronomy, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Santa Fe Institute, Santa Fe, NM, 87051, USA
| | - Max Bertolero
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew Cieslak
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sydney Covitz
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Audrey Houghton
- Masonic Institute for the Developing Brain, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Arielle S Keller
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Audrey Luo
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Oscar Miranda-Dominguez
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55454, USA
- Masonic Institute for the Developing Brain, University of Minnesota Medical School, Minneapolis, MN, USA
- Institute of Child Development, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Steve M Nelson
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55454, USA
| | - Golia Shafiei
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sheila Shanmugan
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Biomedical Image Computing and Analytics, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Valerie J Sydnor
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eric Feczko
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55454, USA
| | - Damien A Fair
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55454, USA
- Masonic Institute for the Developing Brain, University of Minnesota Medical School, Minneapolis, MN, USA
- Institute of Child Development, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Theodore D Satterthwaite
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Biomedical Image Computing and Analytics, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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26
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Baller EB, Sweeney EM, Cieslak M, Robert-Fitzgerald T, Covitz SC, Martin ML, Schindler MK, Bar-Or A, Elahi A, Larsen BS, Manning AR, Markowitz CE, Perrone CM, Rautman V, Seitz MM, Detre JA, Fox MD, Shinohara RT, Satterthwaite TD. Mapping the Relationship of White Matter Lesions to Depression in Multiple Sclerosis. Biol Psychiatry 2023:S0006-3223(23)01722-5. [PMID: 37981178 DOI: 10.1016/j.biopsych.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/27/2023] [Accepted: 11/11/2023] [Indexed: 11/21/2023]
Abstract
BACKGROUND Multiple sclerosis (MS) is an immune-mediated neurological disorder, and up to 50% of patients experience depression. We investigated how white matter network disruption is related to depression in MS. METHODS Using electronic health records, 380 participants with MS were identified. Depressed individuals (MS+Depression group; n = 232) included persons who had an ICD-10 depression diagnosis, had a prescription for antidepressant medication, or screened positive via Patient Health Questionnaire (PHQ)-2 or PHQ-9. Age- and sex-matched nondepressed individuals with MS (MS-Depression group; n = 148) included persons who had no prior depression diagnosis, had no psychiatric medication prescriptions, and were asymptomatic on PHQ-2 or PHQ-9. Research-quality 3T structural magnetic resonance imaging was obtained as part of routine care. We first evaluated whether lesions were preferentially located within the depression network compared with other brain regions. Next, we examined if MS+Depression patients had greater lesion burden and if this was driven by lesions in the depression network. Primary outcome measures were the burden of lesions (e.g., impacted fascicles) within a network and across the brain. RESULTS MS lesions preferentially affected fascicles within versus outside the depression network (β = 0.09, 95% CI = 0.08 to 0.10, p < .001). MS+Depression patients had more lesion burden (β = 0.06, 95% CI = 0.01 to 0.10, p = .015); this was driven by lesions within the depression network (β = 0.02, 95% CI = 0.003 to 0.040, p = .020). CONCLUSIONS We demonstrated that lesion location and burden may contribute to depression comorbidity in MS. MS lesions disproportionately impacted fascicles in the depression network. MS+Depression patients had more disease than MS-Depression patients, which was driven by disease within the depression network. Future studies relating lesion location to personalized depression interventions are warranted.
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Affiliation(s)
- Erica B Baller
- Penn Lifespan Informatics and Neuroimaging Center, Philadelphia, Pennsylvania; Department of Psychiatry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Elizabeth M Sweeney
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Matthew Cieslak
- Penn Lifespan Informatics and Neuroimaging Center, Philadelphia, Pennsylvania; Department of Psychiatry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Timothy Robert-Fitzgerald
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sydney C Covitz
- Penn Lifespan Informatics and Neuroimaging Center, Philadelphia, Pennsylvania; Department of Psychiatry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Melissa L Martin
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Matthew K Schindler
- Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania; Center for Neuroinflammation and Neurotherapeutics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Amit Bar-Or
- Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania; Center for Neuroinflammation and Neurotherapeutics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ameena Elahi
- Department of Information Services, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Bart S Larsen
- Penn Lifespan Informatics and Neuroimaging Center, Philadelphia, Pennsylvania; Department of Psychiatry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Abigail R Manning
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Clyde E Markowitz
- Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania; Center for Neuroinflammation and Neurotherapeutics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Christopher M Perrone
- Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania; Center for Neuroinflammation and Neurotherapeutics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Victoria Rautman
- Department of Information Services, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Madeleine M Seitz
- Penn Lifespan Informatics and Neuroimaging Center, Philadelphia, Pennsylvania; Department of Psychiatry, University of Pennsylvania, Philadelphia, Pennsylvania; Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - John A Detre
- Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michael D Fox
- Center for Brain Circuit Therapeutics, Department of Neurology, Psychiatry, and Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania; Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Theodore D Satterthwaite
- Penn Lifespan Informatics and Neuroimaging Center, Philadelphia, Pennsylvania; Department of Psychiatry, University of Pennsylvania, Philadelphia, Pennsylvania; Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, Pennsylvania.
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27
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Weinstein SM, Vandekar SN, Alexander-Bloch AF, Raznahan A, Li M, Gur RE, Gur RC, Roalf DR, Park MTM, Chakravarty M, Baller EB, Linn KA, Satterthwaite TD, Shinohara RT. Network Enrichment Significance Testing in Brain-Phenotype Association Studies. bioRxiv 2023:2023.11.10.566593. [PMID: 38014137 PMCID: PMC10680593 DOI: 10.1101/2023.11.10.566593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Functional networks often guide our interpretation of spatial maps of brain-phenotype associations. However, methods for assessing enrichment of associations within networks of interest have varied in terms of both scientific rigor and underlying assumptions. While some approaches have relied on subjective interpretations, others have made unrealistic assumptions about the spatial structure of imaging data, leading to inflated false positive rates. We seek to address this gap in existing methodology by borrowing insight from a method widely used in genomics research for testing enrichment of associations between a set of genes and a phenotype of interest. We propose Network Enrichment Significance Testing (NEST), a flexible framework for testing the specificity of brain-phenotype associations to functional networks or other sub-regions of the brain. We apply NEST to study phenotype associations with structural and functional brain imaging data from a large-scale neurodevelopmental cohort study.
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Affiliation(s)
- Sarah M. Weinstein
- Department of Epidemiology and Biostatistics, Temple University College of Public Health, Philadelphia, PA, USA
| | - Simon N. Vandekar
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Aaron F. Alexander-Bloch
- Department of Psychiatry, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Armin Raznahan
- Section on Developmental Neurogenomics, National Institute of Mental Health Intramural Research Program, Bethesda, MD, USA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Raquel E. Gur
- Department of Psychiatry, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ruben C. Gur
- Department of Psychiatry, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - David R. Roalf
- Department of Psychiatry, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Min Tae M. Park
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada
| | - Mallar Chakravarty
- Department of Psychiatry, McGill University, Montreal, QC, Canada
- Cerebral Imaging Centre, Douglas Research Centre, McGill University, Montreal, QC, Canada
| | - Erica B. Baller
- Department of Psychiatry, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Kristin A. Linn
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Theodore D. Satterthwaite
- Department of Psychiatry, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Russell T. Shinohara
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
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28
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Clark KA, O’Donnell CM, Elliott MA, Tauhid S, Dewey BE, Chu R, Khalil S, Nair G, Sati P, DuVal A, Pellegrini N, Bar-Or A, Markowitz C, Schindler MK, Zurawski J, Calabresi PA, Reich DS, Bakshi R, Shinohara RT. Intersite brain MRI volumetric biases persist even in a harmonized multisubject study of multiple sclerosis. J Neuroimaging 2023; 33:941-952. [PMID: 37587544 PMCID: PMC10981935 DOI: 10.1111/jon.13147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND AND PURPOSE Multicenter study designs involving a variety of MRI scanners have become increasingly common. However, these present the issue of biases in image-based measures due to scanner or site differences. To assess these biases, we imaged 11 volunteers with multiple sclerosis (MS) with scan and rescan data at four sites. METHODS Images were acquired on Siemens or Philips scanners at 3 Tesla. Automated white matter lesion detection and whole-brain, gray and white matter, and thalamic volumetry were performed, as well as expert manual delineations of T1 magnetization-prepared rapid acquisition gradient echo and T2 fluid-attenuated inversion recovery lesions. Random-effect and permutation-based nonparametric modeling was performed to assess differences in estimated volumes within and across sites. RESULTS Random-effect modeling demonstrated model assumption violations for most comparisons of interest. Nonparametric modeling indicated that site explained >50% of the variation for most estimated volumes. This expanded to >75% when data from both Siemens and Philips scanners were included. Permutation tests revealed significant differences between average inter- and intrasite differences in most estimated brain volumes (P < .05). The automatic activation of spine coil elements during some acquisitions resulted in a shading artifact in these images. Permutation tests revealed significant differences between thalamic volume measurements from acquisitions with and without this artifact. CONCLUSION Differences in brain volumetry persisted across MR scanners despite protocol harmonization. These differences were not well explained by variance component modeling; however, statistical innovations for mitigating intersite differences show promise in reducing biases in multicenter studies of MS.
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Affiliation(s)
- Kelly A. Clark
- Penn Statistics in Imaging and Visualization Endeavor, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Carly M. O’Donnell
- Penn Statistics in Imaging and Visualization Endeavor, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Mark A. Elliott
- Department of Radiology, University of Pennsylvania, Philadelphia, PA
| | - Shahamat Tauhid
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Blake E. Dewey
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Renxin Chu
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Samar Khalil
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Govind Nair
- Quantitative MRI core facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Pascal Sati
- Neuroimaging Program, Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Anna DuVal
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Nicole Pellegrini
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Amit Bar-Or
- Center for Neuroinflammation and Neurotherapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Clyde Markowitz
- Center for Neuroinflammation and Neurotherapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Matthew K. Schindler
- Center for Neuroinflammation and Neurotherapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jonathan Zurawski
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Peter A. Calabresi
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Daniel S. Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Rohit Bakshi
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Russell T. Shinohara
- Penn Statistics in Imaging and Visualization Endeavor, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Center for Neuroinflammation and Neurotherapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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29
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Sha Z, Warrier V, Bethlehem RA, Schultz LM, Merikangas A, Sun KY, Gur RC, Gur RE, Shinohara RT, Seidlitz J, Almasy L, Andreassen OA, Alexander-Bloch AF. The overlapping genetic architecture of psychiatric disorders and cortical brain structure. bioRxiv 2023:2023.10.05.561040. [PMID: 37873315 PMCID: PMC10592957 DOI: 10.1101/2023.10.05.561040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Both psychiatric vulnerability and cortical structure are shaped by the cumulative effect of common genetic variants across the genome. However, the shared genetic underpinnings between psychiatric disorders and brain structural phenotypes, such as thickness and surface area of the cerebral cortex, remains elusive. In this study, we employed pleiotropy-informed conjunctional false discovery rate analysis to investigate shared loci across genome-wide association scans of regional cortical thickness, surface area, and seven psychiatric disorders in approximately 700,000 individuals of European ancestry. Aggregating regional measures, we identified 50 genetic loci shared between psychiatric disorders and surface area, as well as 26 genetic loci shared with cortical thickness. Risk alleles exhibited bidirectional effects on both cortical thickness and surface area, such that some risk alleles for each disorder increased regional brain size while other risk alleles decreased regional brain size. Due to bidirectional effects, in many cases we observed extensive pleiotropy between an imaging phenotype and a psychiatric disorder even in the absence of a significant genetic correlation between them. The impact of genetic risk for psychiatric disorders on regional brain structure did exhibit a consistent pattern across highly comorbid psychiatric disorders, with 80% of the genetic loci shared across multiple disorders displaying consistent directions of effect. Cortical patterning of genetic overlap revealed a hierarchical genetic architecture, with the association cortex and sensorimotor cortex representing two extremes of shared genetic influence on psychiatric disorders and brain structural variation. Integrating multi-scale functional annotations and transcriptomic profiles, we observed that shared genetic loci were enriched in active genomic regions, converged on neurobiological and metabolic pathways, and showed differential expression in postmortem brain tissue from individuals with psychiatric disorders. Cumulatively, these findings provide a significant advance in our understanding of the overlapping polygenic architecture between psychopathology and cortical brain structure.
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Affiliation(s)
- Zhiqiang Sha
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Varun Warrier
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Department of Psychology, University of Cambridge, Cambridge, UK
| | | | - Laura M. Schultz
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - Alison Merikangas
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kevin Y. Sun
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - Ruben C. Gur
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, 19104, USA
| | - Raquel E. Gur
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, 19104, USA
| | - Russell T. Shinohara
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Dr, Philadelphia, PA 19104, United States
- Center for Biomedical Image Computing and Analytics (CBICA), Department of Radiology, Perelman School of Medicine, United States
| | - Jakob Seidlitz
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - Laura Almasy
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ole A. Andreassen
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Aaron F. Alexander-Bloch
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
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Schabdach JM, Schmitt JE, Sotardi S, Vossough A, Andronikou S, Roberts TP, Huang H, Padmanabhan V, Ortiz-Rosa A, Gardner M, Covitz S, Bedford SA, Mandal AS, Chaiyachati BH, White SR, Bullmore E, Bethlehem RAI, Shinohara RT, Billot B, Iglesias JE, Ghosh S, Gur RE, Satterthwaite TD, Roalf D, Seidlitz J, Alexander-Bloch A. Brain Growth Charts for Quantitative Analysis of Pediatric Clinical Brain MRI Scans with Limited Imaging Pathology. Radiology 2023; 309:e230096. [PMID: 37906015 PMCID: PMC10623207 DOI: 10.1148/radiol.230096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 08/21/2023] [Accepted: 09/12/2023] [Indexed: 11/02/2023]
Abstract
Background Clinically acquired brain MRI scans represent a valuable but underused resource for investigating neurodevelopment due to their technical heterogeneity and lack of appropriate controls. These barriers have curtailed retrospective studies of clinical brain MRI scans compared with more costly prospectively acquired research-quality brain MRI scans. Purpose To provide a benchmark for neuroanatomic variability in clinically acquired brain MRI scans with limited imaging pathology (SLIPs) and to evaluate if growth charts from curated clinical MRI scans differed from research-quality MRI scans or were influenced by clinical indication for the scan. Materials and Methods In this secondary analysis of preexisting data, clinical brain MRI SLIPs from an urban pediatric health care system (individuals aged ≤22 years) were scanned across nine 3.0-T MRI scanners. The curation process included manual review of signed radiology reports and automated and manual quality review of images without gross pathology. Global and regional volumetric imaging phenotypes were measured using two image segmentation pipelines, and clinical brain growth charts were quantitatively compared with charts derived from a large set of research controls in the same age range by means of Pearson correlation and age at peak volume. Results The curated clinical data set included 532 patients (277 male; median age, 10 years [IQR, 5-14 years]; age range, 28 days after birth to 22 years) scanned between 2005 and 2020. Clinical brain growth charts were highly correlated with growth charts derived from research data sets (22 studies, 8346 individuals [4947 male]; age range, 152 days after birth to 22 years) in terms of normative developmental trajectories predicted by the models (median r = 0.979). Conclusion The clinical indication of the scans did not significantly bias the output of clinical brain charts. Brain growth charts derived from clinical controls with limited imaging pathology were highly correlated with brain charts from research controls, suggesting the potential of curated clinical MRI scans to supplement research data sets. © RSNA, 2023 Supplemental material is available for this article. See also the editorial by Ertl-Wagner and Pai in this issue.
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Affiliation(s)
- Jenna M. Schabdach
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - J. Eric Schmitt
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Susan Sotardi
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Arastoo Vossough
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Savvas Andronikou
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Timothy P. Roberts
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Hao Huang
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Viveknarayanan Padmanabhan
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Alfredo Ortiz-Rosa
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Margaret Gardner
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Sydney Covitz
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Saashi A. Bedford
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Ayan S. Mandal
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Barbara H. Chaiyachati
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Simon R. White
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Edward Bullmore
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Richard A. I. Bethlehem
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Russell T. Shinohara
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Benjamin Billot
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - J. Eugenio Iglesias
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Satrajit Ghosh
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Raquel E. Gur
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Theodore D. Satterthwaite
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - David Roalf
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Jakob Seidlitz
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - Aaron Alexander-Bloch
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
| | - for the Lifespan Brain Chart Consortium
- From the Lifespan Brain Institute (LiBI) of the Children’s
Hospital of Philadelphia (CHOP) and Penn Medicine, Philadelphia, Pa (J.M.S.,
A.O.R., M.G., A.S.M., B.H.C., R.E.G., T.D.S., J.S., A.A.B.); Department of Child
and Adolescent Psychiatry and Behavioral Science (J.M.S., J.S., A.A.B.),
Department of Radiology (S.S., A.V., S.A., T.P.R., H.H.), PolicyLab and Clinical
Futures, CHOP Research Institute (B.H.C.), and Department of Biomedical and
Health Informatics (J.E.S., S.S., V.P.), Children’s Hospital of
Philadelphia, Philadelphia, Pa; Department of Psychiatry (J.E.S., R.E.G.,
T.D.S., D.R., J.S., A.A.B.), Department of Radiology (J.E.S., S.S., A.V., S.A.,
T.P.R., H.H.), Lifespan Informatics and Neuroimaging Center (PennLINC),
Department of Psychiatry (S.C., T.D.S.), and Department of Pediatrics (B.H.C.),
Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa;
Departments of Psychiatry (S.A.B., S.R.W., E.B., R.A.I.B.) and Psychology
(R.A.I.B.), University of Cambridge, Cambridge, United Kingdom; Center for
Biomedical Image Computation and Analytics (R.T.S.), Penn Statistics in Imaging
and Visualization Center, Department of Biostatistics, Epidemiology and
Informatics (R.T.S.), and Lifespan Brain Chart Consortium (S.R.W., E.B.,
R.A.I.B., R.T.S., T.D.S., J.S., A.A.B.), University of Pennsylvania,
Philadelphia, Pa; Centre for Medical Image Computing, Department of Medical
Physics and Biomedical Engineering, University College London, London, United
Kingdom (B.B., J.E.I.); Martinos Center for Biomedical Imaging and Department of
Radiology (J.E.I.) and Department of Otolaryngology–Head and Neck Surgery
(S.G.), Massachusetts General Hospital and Harvard Medical School, Boston, Mass;
and McGovern Institute for Brain Research (S.G.) and Computer Science &
Artificial Intelligence Laboratory (B.B., J.E.I.), Massachusetts Institute of
Technology, Cambridge, Mass
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31
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Clark KA, Manning AR, Chen L, Liu F, Cao Q, Bar-Or A, Shinohara RT, Sweeney E, Schindler MK. Early Magnetic Resonance Imaging Features of New Paramagnetic Rim Lesions in Multiple Sclerosis. Ann Neurol 2023; 94:736-744. [PMID: 37345334 PMCID: PMC10543566 DOI: 10.1002/ana.26727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 05/22/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
OBJECTIVE To determine early magnetic resonance imaging (MRI) features of new multiple sclerosis (MS) lesions that will develop into paramagnetic rim lesions (PRLs), which have been associated with progressive tissue injury in MS. METHODS New contrast-enhancing lesions observed on routine clinical MRI were imaged at 7 T within 4 weeks of observation, and 3 and 6 months later. The 6-month MRI was used to classify PRL status (PRL or non-PRL). The relationship between early lesion characteristics and subsequent PRL status was assessed using generalized linear mixed effects models. Random forest classification was performed to classify early predictors of subsequent PRL status. RESULTS From 93 contrast-enhancing lesions in 23 MS patients, 37 lesions developed into a PRL. In lesions that developed into PRLs compared with those that did not, the average lesion T1 on the initial 7 T MRI was 1994 ms compared with 1,670 ms (p-value <0.001), and the average volume was 168.7 mL compared with 44 mL (p-value <0.001) in lesions that did not. These volume differences were also found on 3 T scans (p-value <0.001), and for intensity-normalized T1 -w (p-value = 0.011) and fluid-attenuated inversion recovery (p-value = 0.005). The area under the receiver operating characteristic curve for the random forest classification with leave-one-out cross-validation was found to be 0.86 using initial 7 T features. INTERPRETATION New MS lesions that evolve into PRLs can be identified early in lesion evolution. These findings suggest that biological mechanisms underlying PRL development begin early, which has important implications for clinical trials targeting PRLs development and subsequent therapeutics. ANN NEUROL 2023;94:736-744.
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Affiliation(s)
- Kelly A. Clark
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania
- Penn Statistics in Imaging and Visualization Endeavor, University of Pennsylvania
| | - Abby R. Manning
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania
- Penn Statistics in Imaging and Visualization Endeavor, University of Pennsylvania
| | - Luyun Chen
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania
- Penn Statistics in Imaging and Visualization Endeavor, University of Pennsylvania
| | - Fang Liu
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania
| | - Quy Cao
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania
| | - Amit Bar-Or
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania
| | - Russell T. Shinohara
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania
- Penn Statistics in Imaging and Visualization Endeavor, University of Pennsylvania
- Center for Biomedical Image Computing and Analytics, Department of Radiology, Perelman School of Medicine at the University of Pennsylvania
| | - Elizabeth Sweeney
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania
- Penn Statistics in Imaging and Visualization Endeavor, University of Pennsylvania
| | - Matthew K. Schindler
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania
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32
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Torgersen J, Akers S, Huo Y, Terry JG, Carr JJ, Ruutiainen AT, Skanderson M, Levin W, Lim JK, Taddei TH, So-Armah K, Bhattacharya D, Rentsch CT, Shen L, Carr R, Shinohara RT, McClain M, Freiberg M, Justice AC, Re VL. Performance of an automated deep learning algorithm to identify hepatic steatosis within noncontrast computed tomography scans among people with and without HIV. Pharmacoepidemiol Drug Saf 2023; 32:1121-1130. [PMID: 37276449 PMCID: PMC10527049 DOI: 10.1002/pds.5648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 05/06/2023] [Accepted: 05/31/2023] [Indexed: 06/07/2023]
Abstract
PURPOSE Hepatic steatosis (fatty liver disease) affects 25% of the world's population, particularly people with HIV (PWH). Pharmacoepidemiologic studies to identify medications associated with steatosis have not been conducted because methods to evaluate liver fat within digitized images have not been developed. We determined the accuracy of a deep learning algorithm (automatic liver attenuation region-of-interest-based measurement [ALARM]) to identify steatosis within clinically obtained noncontrast abdominal CT images compared to manual radiologist review and evaluated its performance by HIV status. METHODS We performed a cross-sectional study to evaluate the performance of ALARM within noncontrast abdominal CT images from a sample of patients with and without HIV in the US Veterans Health Administration. We evaluated the ability of ALARM to identify moderate-to-severe hepatic steatosis, defined by mean absolute liver attenuation <40 Hounsfield units (HU), compared to manual radiologist assessment. RESULTS Among 120 patients (51 PWH) who underwent noncontrast abdominal CT, moderate-to-severe hepatic steatosis was identified in 15 (12.5%) persons via ALARM and 12 (10%) by radiologist assessment. Percent agreement between ALARM and radiologist assessment of absolute liver attenuation <40 HU was 95.8%. Sensitivity, specificity, positive predictive value, and negative predictive value of ALARM were 91.7% (95%CI, 51.5%-99.8%), 96.3% (95%CI, 90.8%-99.0%), 73.3% (95%CI, 44.9%-92.2%), and 99.0% (95%CI, 94.8%-100%), respectively. No differences in performance were observed by HIV status. CONCLUSIONS ALARM demonstrated excellent accuracy for moderate-to-severe hepatic steatosis regardless of HIV status. Application of ALARM to radiographic repositories could facilitate real-world studies to evaluate medications associated with steatosis and assess differences by HIV status.
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Affiliation(s)
- Jessie Torgersen
- Department of Medicine, Penn Center for AIDS Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biostatistics, Epidemiology, and Informatics, Center for Clinical Epidemiology and Biostatistics, Center for Real World Effectiveness and Safety of Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Scott Akers
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Yuankai Huo
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - James G. Terry
- Department of Radiology and Radiological Sciences, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - J. Jeffrey Carr
- Department of Radiology and Radiological Sciences, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Melissa Skanderson
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
| | - Woody Levin
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
| | - Joseph K. Lim
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
| | - Tamar H. Taddei
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
| | - Kaku So-Armah
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Debika Bhattacharya
- VA Greater Los Angeles Healthcare System and David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Christopher T. Rentsch
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Li Shen
- Department of Biostatistics, Epidemiology, and Informatics, Center for Clinical Epidemiology and Biostatistics, Center for Real World Effectiveness and Safety of Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rotonya Carr
- Department of Medicine, Division of Gastroenterology, University of Washington, Seattle, WA, USA
| | - Russell T. Shinohara
- Department of Biostatistics, Epidemiology, and Informatics, Center for Clinical Epidemiology and Biostatistics, Center for Real World Effectiveness and Safety of Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Biomedical Image Computing and Analysis (CBICA), Department of Radiology, University of Pennsylvania, Philadelphia, PA, 19104
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, PA, 19104
| | | | - Matthew Freiberg
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Amy C. Justice
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
- Division of Health Policy and Management, Yale School of Public Health, New Haven, CT, USA
| | - Vincent Lo Re
- Department of Medicine, Penn Center for AIDS Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biostatistics, Epidemiology, and Informatics, Center for Clinical Epidemiology and Biostatistics, Center for Real World Effectiveness and Safety of Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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33
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Fotiadis P, Cieslak M, He X, Caciagli L, Ouellet M, Satterthwaite TD, Shinohara RT, Bassett DS. Myelination and excitation-inhibition balance synergistically shape structure-function coupling across the human cortex. Nat Commun 2023; 14:6115. [PMID: 37777569 PMCID: PMC10542365 DOI: 10.1038/s41467-023-41686-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 09/08/2023] [Indexed: 10/02/2023] Open
Abstract
Recent work has demonstrated that the relationship between structural and functional connectivity varies regionally across the human brain, with reduced coupling emerging along the sensory-association cortical hierarchy. The biological underpinnings driving this expression, however, remain largely unknown. Here, we postulate that intracortical myelination and excitation-inhibition (EI) balance mediate the heterogeneous expression of structure-function coupling (SFC) and its temporal variance across the cortical hierarchy. We employ atlas- and voxel-based connectivity approaches to analyze neuroimaging data acquired from two groups of healthy participants. Our findings are consistent across six complementary processing pipelines: 1) SFC and its temporal variance respectively decrease and increase across the unimodal-transmodal and granular-agranular gradients; 2) increased myelination and lower EI-ratio are associated with more rigid SFC and restricted moment-to-moment SFC fluctuations; 3) a gradual shift from EI-ratio to myelination as the principal predictor of SFC occurs when traversing from granular to agranular cortical regions. Collectively, our work delivers a framework to conceptualize structure-function relationships in the human brain, paving the way for an improved understanding of how demyelination and/or EI-imbalances induce reorganization in brain disorders.
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Affiliation(s)
- Panagiotis Fotiadis
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Matthew Cieslak
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Xiaosong He
- Department of Psychology, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Lorenzo Caciagli
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mathieu Ouellet
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Theodore D Satterthwaite
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Center for Biomedical Image Computing & Analytics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dani S Bassett
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Electrical & Systems Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Physics & Astronomy, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Santa Fe Institute, Santa Fe, NM, 87501, USA.
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34
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Tu D, Goyal MS, Dworkin JD, Kampondeni S, Vidal L, Biondo-Savin E, Juvvadi S, Raghavan P, Nicholas J, Chetcuti K, Clark K, Robert-Fitzgerald T, Satterthwaite TD, Yushkevich P, Davatzikos C, Erus G, Tustison NJ, Postels DG, Taylor TE, Small DS, Shinohara RT. Automated analysis of low-field brain MRI in cerebral malaria. Biometrics 2023; 79:2417-2429. [PMID: 35731973 PMCID: PMC10267853 DOI: 10.1111/biom.13708] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 06/08/2022] [Indexed: 11/26/2022]
Abstract
A central challenge of medical imaging studies is to extract biomarkers that characterize disease pathology or outcomes. Modern automated approaches have found tremendous success in high-resolution, high-quality magnetic resonance images. These methods, however, may not translate to low-resolution images acquired on magnetic resonance imaging (MRI) scanners with lower magnetic field strength. In low-resource settings where low-field scanners are more common and there is a shortage of radiologists to manually interpret MRI scans, it is critical to develop automated methods that can augment or replace manual interpretation, while accommodating reduced image quality. We present a fully automated framework for translating radiological diagnostic criteria into image-based biomarkers, inspired by a project in which children with cerebral malaria (CM) were imaged using low-field 0.35 Tesla MRI. We integrate multiatlas label fusion, which leverages high-resolution images from another sample as prior spatial information, with parametric Gaussian hidden Markov models based on image intensities, to create a robust method for determining ventricular cerebrospinal fluid volume. We also propose normalized image intensity and texture measurements to determine the loss of gray-to-white matter tissue differentiation and sulcal effacement. These integrated biomarkers have excellent classification performance for determining severe brain swelling due to CM.
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Affiliation(s)
- Danni Tu
- The Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania
| | - Manu S. Goyal
- Mallinckrodt Institute of Radiology, Washington University in St. Louis
| | | | | | - Lorenna Vidal
- Department of Radiology, Children’s Hospital of Philadelphia
| | | | | | - Prashant Raghavan
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine
| | - Jennifer Nicholas
- University Hospitals Cleveland Medical Center, Department of Radiology, Case Western Reserve University
| | - Karen Chetcuti
- Department of Paediatrics and Child Health, Kamuzu University of Health Sciences
| | - Kelly Clark
- The Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania
| | - Timothy Robert-Fitzgerald
- The Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania
| | | | | | | | - Guray Erus
- Center for Biomedical Image Computing and Analysis (CBICA), Department of Radiology, University of Pennsylvania
| | | | - Douglas G. Postels
- Division of Neurology, George Washington University/Children’s National Medical Center
| | - Terrie E. Taylor
- Blantyre Malaria Project, Kamuzu University of Health Sciences
- College of Osteopathic Medicine, Michigan State University
| | | | - Russell T. Shinohara
- The Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania
- Center for Biomedical Image Computing and Analysis (CBICA), Department of Radiology, University of Pennsylvania
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35
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MacDonald DN, Bedford SA, Olafson E, Park MTM, Devenyi GA, Tullo S, Patel R, Anagnostou E, Baron-Cohen S, Bullmore ET, Chura LR, Craig MC, Ecker C, Floris DL, Holt RJ, Lenroot R, Lerch JP, Lombardo MV, Murphy DGM, Raznahan A, Ruigrok ANV, Smith E, Shinohara RT, Spencer MD, Suckling J, Taylor MJ, Thurm A, Lai MC, Chakravarty MM. Characterizing Subcortical Structural Heterogeneity in Autism. bioRxiv 2023:2023.08.28.554882. [PMID: 37693556 PMCID: PMC10491091 DOI: 10.1101/2023.08.28.554882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Autism presents with significant phenotypic and neuroanatomical heterogeneity, and neuroimaging studies of the thalamus, globus pallidus and striatum in autism have produced inconsistent and contradictory results. These structures are critical mediators of functions known to be atypical in autism, including sensory gating and motor function. We examined both volumetric and fine-grained localized shape differences in autism using a large (n=3145, 1045-1318 after strict quality control), cross-sectional dataset of T1-weighted structural MRI scans from 32 sites, including both males and females (assigned-at-birth). We investigated three potentially important sources of neuroanatomical heterogeneity: sex, age, and intelligence quotient (IQ), using a meta-analytic technique after strict quality control to minimize non-biological sources of variation. We observed no volumetric differences in the thalamus, globus pallidus, or striatum in autism. Rather, we identified a variety of localized shape differences in all three structures. Including age, but not sex or IQ, in the statistical model improved the fit for both the pallidum and striatum, but not for the thalamus. Age-centered shape analysis indicated a variety of age-dependent regional differences. Overall, our findings help confirm that the neurodevelopment of the striatum, globus pallidus and thalamus are atypical in autism, in a subtle location-dependent manner that is not reflected in overall structure volumes, and that is highly non-uniform across the lifespan.
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Affiliation(s)
- David N. MacDonald
- Integrated Program in Neuroscience, McGill University
- Cerebral Imaging Centre, Douglas Mental Health University Institute
| | - Saashi A. Bedford
- Integrated Program in Neuroscience, McGill University
- Cerebral Imaging Centre, Douglas Mental Health University Institute
- Autism Research Centre, Department of Psychiatry, University of Cambridge
| | - Emily Olafson
- Cerebral Imaging Centre, Douglas Mental Health University Institute
- Department of Neuroscience, Weill Cornell Graduate School of Medical Sciences
| | - Min Tae M. Park
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto
| | - Gabriel A. Devenyi
- Cerebral Imaging Centre, Douglas Mental Health University Institute
- Department of Psychiatry, McGill University
| | - Stephanie Tullo
- Integrated Program in Neuroscience, McGill University
- Cerebral Imaging Centre, Douglas Mental Health University Institute
| | - Raihaan Patel
- Cerebral Imaging Centre, Douglas Mental Health University Institute
- Department of Biological and Biomedical Engineering, McGill University
| | | | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge
| | | | - Lindsay R. Chura
- Autism Research Centre, Department of Psychiatry, University of Cambridge
| | - Michael C. Craig
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London
- National Autism Unit, Bethlem Royal Hospital, London, UK
| | - Christine Ecker
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, GoetheUniversity
| | - Dorothea L. Floris
- Methods of Plasticity Research, Department of Psychology, University of Zurich, Zurich,Switzerland
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
| | - Rosemary J. Holt
- Autism Research Centre, Department of Psychiatry, University of Cambridge
| | - Rhoshel Lenroot
- Dept.of Psychiatry and Behavioral Sciences, University of New Mexico
| | - Jason P. Lerch
- Program in Neurosciences and Mental Health, The Hospital for Sick Children
- Department of Medical Biophysics, University of Toronto
- Wellcome Centre for Integrative Neuroimaging, University of Oxford
| | - Michael V. Lombardo
- Laboratory for Autism and Neurodevelopmental Disorders, Center for Neuroscience and Cognitive Systems @UniTn, Istituto Italiano di Tecnologia
| | | | - Armin Raznahan
- Developmental Neurogenomics Unit, Human Genetics Branch, National Institute of MentalHealth
| | - Amber N. V. Ruigrok
- Autism Research Centre, Department of Psychiatry, University of Cambridge
- Division of Psychology and Mental Health, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester
| | - Elizabeth Smith
- Division of Behavioral Medicine and Clinical Psychology, Cincinnati Children’s Hospital
| | - Russell T. Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania
- Center for Biomedical Image Computing and Analytics, Department of Radiology, Perelman School of Medicine, University of Pennsylvania
| | - Michael D. Spencer
- Autism Research Centre, Department of Psychiatry, University of Cambridge
| | - John Suckling
- Brain Mapping Unit, Department of Psychiatry, University of Cambridge
| | - Margot J. Taylor
- Program in Neurosciences and Mental Health, The Hospital for Sick Children
- Diagnostic Imaging, The Hospital for Sick Children
| | - Audrey Thurm
- Section on Behavioral Pediatrics, National Institute of Mental Health
| | | | - Meng-Chuan Lai
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto
- Autism Research Centre, Department of Psychiatry, University of Cambridge
- Program in Neurosciences and Mental Health, The Hospital for Sick Children
- The Margaret and Wallace McCain Centre for Child, Youth & Family Mental Health and Azrieli Adult Neurodevelopmental Centre, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine
| | - M. Mallar Chakravarty
- Integrated Program in Neuroscience, McGill University
- Cerebral Imaging Centre, Douglas Mental Health University Institute
- Department of Psychiatry, McGill University
- Department of Biological and Biomedical Engineering, McGill University
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Parkes L, Kim JZ, Stiso J, Brynildsen JK, Cieslak M, Covitz S, Gur RE, Gur RC, Pasqualetti F, Shinohara RT, Zhou D, Satterthwaite TD, Bassett DS. Using network control theory to study the dynamics of the structural connectome. bioRxiv 2023:2023.08.23.554519. [PMID: 37662395 PMCID: PMC10473719 DOI: 10.1101/2023.08.23.554519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Network control theory (NCT) is a simple and powerful tool for studying how network topology informs and constrains dynamics. Compared to other structure-function coupling approaches, the strength of NCT lies in its capacity to predict the patterns of external control signals that may alter dynamics in a desired way. We have extensively developed and validated the application of NCT to the human structural connectome. Through these efforts, we have studied (i) how different aspects of connectome topology affect neural dynamics, (ii) whether NCT outputs cohere with empirical data on brain function and stimulation, and (iii) how NCT outputs vary across development and correlate with behavior and mental health symptoms. In this protocol, we introduce a framework for applying NCT to structural connectomes following two main pathways. Our primary pathway focuses on computing the control energy associated with transitioning between specific neural activity states. Our second pathway focuses on computing average controllability, which indexes nodes' general capacity to control dynamics. We also provide recommendations for comparing NCT outputs against null network models. Finally, we support this protocol with a Python-based software package called network control theory for python (nctpy).
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Affiliation(s)
- Linden Parkes
- Department of Bioengineering, University of Pennsylvania, PA 19104, USA
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Psychiatry, Rutgers University, Piscataway, NJ 08854, USA
| | - Jason Z Kim
- Department of Physics, Cornell University, Ithaca, NY 14853, USA
| | - Jennifer Stiso
- Department of Bioengineering, University of Pennsylvania, PA 19104, USA
| | | | - Matthew Cieslak
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sydney Covitz
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Raquel E Gur
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ruben C Gur
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Fabio Pasqualetti
- Department of Mechanical Engineering, University of California, Riverside, Riverside, CA 92521, USA
| | - Russell T Shinohara
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, Philadelphia, PA 19104, USA
- Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dale Zhou
- Department of Bioengineering, University of Pennsylvania, PA 19104, USA
| | - Theodore D Satterthwaite
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dani S Bassett
- Department of Bioengineering, University of Pennsylvania, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Neurology, Perelman School of Medicine, Philadelphia, PA 19104, USA
- Department of Electrical and Systems Engineering, University of Pennsylvania, PA 19104, USA
- Department of Physics and Astronomy, University of Pennsylvania, PA 19104, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
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37
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Shafiei G, Keller AS, Bertolero M, Shanmugan S, Bassett DS, Chen AA, Covitz S, Houghton A, Luo A, Mehta K, Salo T, Shinohara RT, Fair D, Hallquist MN, Satterthwaite TD. Generalizable links between symptoms of borderline personality disorder and functional connectivity. bioRxiv 2023:2023.08.03.551534. [PMID: 37662311 PMCID: PMC10473667 DOI: 10.1101/2023.08.03.551534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Background | Symptoms of borderline personality disorder (BPD) often manifest in adolescence, yet the underlying relationship between these debilitating symptoms and the development of functional brain networks is not well understood. Here we aimed to investigate how multivariate patterns of functional connectivity are associated with symptoms of BPD in a large sample of young adults and adolescents. Methods | We used high-quality functional Magnetic Resonance Imaging (fMRI) data from young adults from the Human Connectome Project: Young Adults (HCP-YA; N = 870, ages 22-37 years, 457 female) and youth from the Human Connectome Project: Development (HCP-D; N = 223, age range 16-21 years, 121 female). A previously validated BPD proxy score was derived from the NEO Five Factor Inventory (NEO-FFI). A ridge regression model with 10-fold cross-validation and nested hyperparameter tuning was trained and tested in HCP-YA to predict BPD scores in unseen data from regional functional connectivity, while controlling for in-scanner motion, age, and sex. The trained model was further tested on data from HCP-D without further tuning. Finally, we tested how the connectivity patterns associated with BPD aligned with age-related changes in connectivity. Results | Multivariate functional connectivity patterns significantly predicted out-of-sample BPD proxy scores in unseen data in both young adults (HCP-YA; pperm = 0.001) and older adolescents (HCP-D; pperm = 0.001). Predictive capacity of regions was heterogeneous; the most predictive regions were found in functional systems relevant for emotion regulation and executive function, including the ventral attention network. Finally, regional functional connectivity patterns that predicted BPD proxy scores aligned with those associated with development in youth. Conclusion | Individual differences in functional connectivity in developmentally-sensitive regions are associated with the symptoms of BPD.
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Affiliation(s)
- Golia Shafiei
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Arielle S. Keller
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Maxwell Bertolero
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sheila Shanmugan
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dani S. Bassett
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104
- Department of Physics & Astronomy, College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Electrical & Systems Engineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104
- Santa Fe Institute, Santa Fe, NM 87501
| | - Andrew A. Chen
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics,Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sydney Covitz
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Audrey Houghton
- Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN 55414, USA
| | - Audrey Luo
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kahini Mehta
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Taylor Salo
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Russell T. Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics,Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Damien Fair
- Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN 55414, USA
- Institute of Child Development, College of Education and Human Development, Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN 55414, USA
| | - Michael N. Hallquist
- Department of Psychology and Neuroscience, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Theodore D. Satterthwaite
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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Weinstein SM, Davatzikos C, Doshi J, Linn KA, Shinohara RT. Penalized decomposition using residuals (PeDecURe) for feature extraction in the presence of nuisance variables. Biostatistics 2023; 24:653-668. [PMID: 35950944 PMCID: PMC10345990 DOI: 10.1093/biostatistics/kxac031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 07/12/2022] [Accepted: 07/16/2022] [Indexed: 11/13/2022] Open
Abstract
Neuroimaging data are an increasingly important part of etiological studies of neurological and psychiatric disorders. However, mitigating the influence of nuisance variables, including confounders, remains a challenge in image analysis. In studies of Alzheimer's disease, for example, an imbalance in disease rates by age and sex may make it difficult to distinguish between structural patterns in the brain (as measured by neuroimaging scans) attributable to disease progression and those characteristic of typical human aging or sex differences. Concerningly, when not properly accounted for, nuisance variables pose threats to the generalizability and interpretability of findings from these studies. Motivated by this critical issue, in this work, we examine the impact of nuisance variables on feature extraction methods and propose Penalized Decomposition Using Residuals (PeDecURe), a new method for obtaining nuisance variable-adjusted features. PeDecURe estimates primary directions of variation which maximize covariance between partially residualized imaging features and a variable of interest (e.g., Alzheimer's diagnosis) while simultaneously mitigating the influence of nuisance variation through a penalty on the covariance between partially residualized imaging features and those variables. Using features derived using PeDecURe's first direction of variation, we train a highly accurate and generalizable predictive model, as evidenced by its robustness in testing samples with different underlying nuisance variable distributions. We compare PeDecURe to commonly used decomposition methods (principal component analysis (PCA) and partial least squares) as well as a confounder-adjusted variation of PCA. We find that features derived from PeDecURe offer greater accuracy and generalizability and lower correlations with nuisance variables compared with the other methods. While PeDecURe is primarily motivated by challenges that arise in the analysis of neuroimaging data, it is broadly applicable to data sets with highly correlated features, where novel methods to handle nuisance variables are warranted.
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Affiliation(s)
- Sarah M Weinstein
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, Penn Statistics in Imaging and Visualization Center, 108/109B, Blockley Hall, University of Pennsylvania, 423 Guardian Drive, Philadelphia, PA 19104, USA
| | - Christos Davatzikos
- Department of Radiology, Perelman School of Medicine, Center for Biomedical Image Computing and Analytics, 3700 Hamilton Walk, Richards Building 7th Floor, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jimit Doshi
- Department of Radiology, Perelman School of Medicine, Center for Biomedical Image Computing and Analytics, 3700 Hamilton Walk, Richards Building 7th Floor, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristin A Linn
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, Penn Statistics in Imaging and Visualization Center, 2nd Floor, Blockley Hall, University of Pennsylvania, 423 Guardian Drive, Philadelphia, PA 19104, USA and Department of Radiology, Perelman School of Medicine, Center for Biomedical Image Computing and Analytics, 3700 Hamilton Walk, Richards Building 7th Floor, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Russell T Shinohara
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, Penn Statistics in Imaging and Visualization Center, 2nd Floor, Blockley Hall, University of Pennsylvania, 423 Guardian Drive, Philadelphia, PA 19104, USA and Department of Radiology, Perelman School of Medicine, Center for Biomedical Image Computing and Analytics, 3700 Hamilton Walk, Richards Building 7th Floor, University of Pennsylvania, Philadelphia, PA 19104, USA
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39
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Xie K, Gallagher RS, Shinohara RT, Xie SX, Hill CE, Conrad EC, Davis KA, Roth D, Litt B, Ellis CA. Long-term epilepsy outcome dynamics revealed by natural language processing of clinic notes. Epilepsia 2023; 64:1900-1909. [PMID: 37114472 PMCID: PMC10523917 DOI: 10.1111/epi.17633] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 04/29/2023]
Abstract
OBJECTIVE Electronic medical records allow for retrospective clinical research with large patient cohorts. However, epilepsy outcomes are often contained in free text notes that are difficult to mine. We recently developed and validated novel natural language processing (NLP) algorithms to automatically extract key epilepsy outcome measures from clinic notes. In this study, we assessed the feasibility of extracting these measures to study the natural history of epilepsy at our center. METHODS We applied our previously validated NLP algorithms to extract seizure freedom, seizure frequency, and date of most recent seizure from outpatient visits at our epilepsy center from 2010 to 2022. We examined the dynamics of seizure outcomes over time using Markov model-based probability and Kaplan-Meier analyses. RESULTS Performance of our algorithms on classifying seizure freedom was comparable to that of human reviewers (algorithm F1 = .88 vs. human annotatorκ = .86). We extracted seizure outcome data from 55 630 clinic notes from 9510 unique patients written by 53 unique authors. Of these, 30% were classified as seizure-free since the last visit, 48% of non-seizure-free visits contained a quantifiable seizure frequency, and 47% of all visits contained the date of most recent seizure occurrence. Among patients with at least five visits, the probabilities of seizure freedom at the next visit ranged from 12% to 80% in patients having seizures or seizure-free at the prior three visits, respectively. Only 25% of patients who were seizure-free for 6 months remained seizure-free after 10 years. SIGNIFICANCE Our findings demonstrate that epilepsy outcome measures can be extracted accurately from unstructured clinical note text using NLP. At our tertiary center, the disease course often followed a remitting and relapsing pattern. This method represents a powerful new tool for clinical research with many potential uses and extensions to other clinical questions.
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Affiliation(s)
- Kevin Xie
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ryan S. Gallagher
- Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Russell T. Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sharon X. Xie
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Chloe E. Hill
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Erin C. Conrad
- Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kathryn A. Davis
- Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dan Roth
- Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Brian Litt
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Colin A. Ellis
- Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, 19104, USA
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Hu F, Chen AA, Horng H, Bashyam V, Davatzikos C, Alexander-Bloch A, Li M, Shou H, Satterthwaite TD, Yu M, Shinohara RT. Image harmonization: A review of statistical and deep learning methods for removing batch effects and evaluation metrics for effective harmonization. Neuroimage 2023; 274:120125. [PMID: 37084926 PMCID: PMC10257347 DOI: 10.1016/j.neuroimage.2023.120125] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/12/2023] [Accepted: 04/19/2023] [Indexed: 04/23/2023] Open
Abstract
Magnetic resonance imaging and computed tomography from multiple batches (e.g. sites, scanners, datasets, etc.) are increasingly used alongside complex downstream analyses to obtain new insights into the human brain. However, significant confounding due to batch-related technical variation, called batch effects, is present in this data; direct application of downstream analyses to the data may lead to biased results. Image harmonization methods seek to remove these batch effects and enable increased generalizability and reproducibility of downstream results. In this review, we describe and categorize current approaches in statistical and deep learning harmonization methods. We also describe current evaluation metrics used to assess harmonization methods and provide a standardized framework to evaluate newly-proposed methods for effective harmonization and preservation of biological information. Finally, we provide recommendations to end-users to advocate for more effective use of current methods and to methodologists to direct future efforts and accelerate development of the field.
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Affiliation(s)
- Fengling Hu
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Dr, Philadelphia, PA 19104, United States.
| | - Andrew A Chen
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Dr, Philadelphia, PA 19104, United States
| | - Hannah Horng
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Dr, Philadelphia, PA 19104, United States
| | - Vishnu Bashyam
- Center for Biomedical Image Computing and Analytics (CBICA), Perelman School of Medicine, United States
| | - Christos Davatzikos
- Center for Biomedical Image Computing and Analytics (CBICA), Perelman School of Medicine, United States
| | - Aaron Alexander-Bloch
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, United States; Penn-CHOP Lifespan Brain Institute, United States; Department of Child and Adolescent Psychiatry and Behavioral Science, Children's Hospital of Philadelphia, United States
| | - Mingyao Li
- Statistical Center for Single-Cell and Spatial Genomics, Perelman School of Medicine, University of Pennsylvania, United States
| | - Haochang Shou
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Dr, Philadelphia, PA 19104, United States; Center for Biomedical Image Computing and Analytics (CBICA), Perelman School of Medicine, United States
| | - Theodore D Satterthwaite
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, United States; Penn-CHOP Lifespan Brain Institute, United States; The Penn Lifespan Informatics and Neuroimaging Center, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, United States
| | - Meichen Yu
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, United States
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Dr, Philadelphia, PA 19104, United States; Center for Biomedical Image Computing and Analytics (CBICA), Perelman School of Medicine, United States
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Baller EB, Sweeney EM, Cieslak MC, Robert-Fitzgerald T, Covitz SC, Martin ML, Schindler MK, Bar-Or A, Elahi A, Larsen BS, Manning AR, Markowitz CE, Perrone CM, Rautman V, Seitz MM, Detre JA, Fox MD, Shinohara RT, Satterthwaite TD. Mapping the relationship of white matter lesions to depression in multiple sclerosis. medRxiv 2023:2023.06.09.23291080. [PMID: 37398183 PMCID: PMC10312888 DOI: 10.1101/2023.06.09.23291080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Importance Multiple sclerosis (MS) is an immune-mediated neurological disorder that affects nearly one million people in the United States. Up to 50% of patients with MS experience depression. Objective To investigate how white matter network disruption is related to depression in MS. Design Retrospective case-control study of participants who received research-quality 3-tesla neuroimaging as part of MS clinical care from 2010-2018. Analyses were performed from May 1 to September 30, 2022. Setting Single-center academic medical specialty MS clinic. Participants Participants with MS were identified via the electronic health record (EHR). All participants were diagnosed by an MS specialist and completed research-quality MRI at 3T. After excluding participants with poor image quality, 783 were included. Inclusion in the depression group (MS+Depression) required either: 1) ICD-10 depression diagnosis (F32-F34.*); 2) prescription of antidepressant medication; or 3) screening positive via Patient Health Questionnaire-2 (PHQ-2) or -9 (PHQ-9). Age- and sex-matched nondepressed comparators (MS-Depression) included persons with no depression diagnosis, no psychiatric medications, and were asymptomatic on PHQ-2/9. Exposure Depression diagnosis. Main Outcomes and Measures We first evaluated if lesions were preferentially located within the depression network compared to other brain regions. Next, we examined if MS+Depression patients had greater lesion burden, and if this was driven by lesions specifically in the depression network. Outcome measures were the burden of lesions (e.g., impacted fascicles) within a network and across the brain. Secondary measures included between-diagnosis lesion burden, stratified by brain network. Linear mixed-effects models were employed. Results Three hundred-eighty participants met inclusion criteria, (232 MS+Depression: age[SD]=49[12], %females=86; 148 MS-Depression: age[SD]=47[13], %females=79). MS lesions preferentially affected fascicles within versus outside the depression network (β=0.09, 95% CI=0.08-0.10, P<0.001). MS+Depression had more white matter lesion burden (β=0.06, 95% CI=0.01-0.10, P=0.015); this was driven by lesions within the depression network (β=0.02, 95% CI 0.003-0.040, P=0.020). Conclusions and Relevance We provide new evidence supporting a relationship between white matter lesions and depression in MS. MS lesions disproportionately impacted fascicles in the depression network. MS+Depression had more disease than MS-Depression, which was driven by disease within the depression network. Future studies relating lesion location to personalized depression interventions are warranted.
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Affiliation(s)
- Erica B Baller
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Philadelphia, PA USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA USA
| | - Elizabeth M Sweeney
- Penn Statistics in Imaging and Visualization Center (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA USA
| | - Matthew C Cieslak
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Philadelphia, PA USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA USA
| | - Timothy Robert-Fitzgerald
- Penn Statistics in Imaging and Visualization Center (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA USA
| | - Sydney C Covitz
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Philadelphia, PA USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA USA
| | - Melissa L Martin
- Penn Statistics in Imaging and Visualization Center (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA USA
| | - Matthew K Schindler
- Department of Neurology, University of Pennsylvania, Philadelphia, PA USA
- Center for Neuroinflammation and Neurotherapeutics, University of Pennsylvania, Philadelphia, PA USA
| | - Amit Bar-Or
- Department of Neurology, University of Pennsylvania, Philadelphia, PA USA
- Center for Neuroinflammation and Neurotherapeutics, University of Pennsylvania, Philadelphia, PA USA
| | - Ameena Elahi
- Department of Information Services, University of Pennsylvania, Philadelphia, PA USA
| | - Bart S Larsen
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Philadelphia, PA USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA USA
| | - Abigail R Manning
- Penn Statistics in Imaging and Visualization Center (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA USA
| | - Clyde E Markowitz
- Department of Neurology, University of Pennsylvania, Philadelphia, PA USA
- Center for Neuroinflammation and Neurotherapeutics, University of Pennsylvania, Philadelphia, PA USA
| | - Christopher M Perrone
- Department of Neurology, University of Pennsylvania, Philadelphia, PA USA
- Center for Neuroinflammation and Neurotherapeutics, University of Pennsylvania, Philadelphia, PA USA
| | - Victoria Rautman
- Department of Information Services, University of Pennsylvania, Philadelphia, PA USA
| | - Madeleine M Seitz
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Philadelphia, PA USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA USA
- Penn Statistics in Imaging and Visualization Center (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA USA
| | - John A Detre
- Department of Neurology, University of Pennsylvania, Philadelphia, PA USA
| | - Michael D Fox
- Center for Brain Circuit Therapeutics, Department of Neurology, Psychiatry, and Radiology, Brigham and Women's Hospital, Harvard Medical School
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA USA
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, Philadelphia, PA USA
| | - Theodore D Satterthwaite
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Philadelphia, PA USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA USA
- Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, Philadelphia, PA USA
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Zhao C, Tapera TM, Bagautdinova J, Bourque J, Covitz S, Gur RE, Gur RC, Larsen B, Mehta K, Meisler SL, Murtha K, Muschelli J, Roalf DR, Sydnor VJ, Valcarcel AM, Shinohara RT, Cieslak M, Satterthwaite TD. ModelArray: An R package for statistical analysis of fixel-wise data. Neuroimage 2023; 271:120037. [PMID: 36931330 PMCID: PMC10119782 DOI: 10.1016/j.neuroimage.2023.120037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023] Open
Abstract
Diffusion MRI is the dominant non-invasive imaging method used to characterize white matter organization in health and disease. Increasingly, fiber-specific properties within a voxel are analyzed using fixels. While tools for conducting statistical analyses of fixel-wise data exist, currently available tools support only a limited number of statistical models. Here we introduce ModelArray, an R package for mass-univariate statistical analysis of fixel-wise data. At present, ModelArray supports linear models as well as generalized additive models (GAMs), which are particularly useful for studying nonlinear effects in lifespan data. In addition, ModelArray also aims for scalable analysis. With only several lines of code, even large fixel-wise datasets can be analyzed using a standard personal computer. Detailed memory profiling revealed that ModelArray required only limited memory even for large datasets. As an example, we applied ModelArray to fixel-wise data derived from diffusion images acquired as part of the Philadelphia Neurodevelopmental Cohort (n = 938). ModelArray revealed anticipated nonlinear developmental effects in white matter. Moving forward, ModelArray is supported by an open-source software development model that can incorporate additional statistical models and other imaging data types. Taken together, ModelArray provides a flexible and efficient platform for statistical analysis of fixel-wise data.
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Affiliation(s)
- Chenying Zhao
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tinashe M Tapera
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joëlle Bagautdinova
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Josiane Bourque
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sydney Covitz
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Raquel E Gur
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ruben C Gur
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bart Larsen
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kahini Mehta
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Steven L Meisler
- Program in Speech and Hearing Bioscience and Technology, Harvard University, Cambridge, MA 02139, USA
| | - Kristin Murtha
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John Muschelli
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - David R Roalf
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Valerie J Sydnor
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessandra M Valcarcel
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew Cieslak
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Theodore D Satterthwaite
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Lucas A, Cornblath EJ, Sinha N, Hadar P, Caciagli L, Keller SS, Bonilha L, Shinohara RT, Stein JM, Das S, Gleichgerrcht E, Davis KA. Resting state functional connectivity demonstrates increased segregation in bilateral temporal lobe epilepsy. Epilepsia 2023; 64:1305-1317. [PMID: 36855286 DOI: 10.1111/epi.17565] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 03/02/2023]
Abstract
OBJECTIVE Temporal lobe epilepsy (TLE) is the most common type of focal epilepsy. An increasingly identified subset of patients with TLE consists of those who show bilaterally independent temporal lobe seizures. The purpose of this study was to leverage network neuroscience to better understand the interictal whole brain network of bilateral TLE (BiTLE). METHODS In this study, using a multicenter resting state functional magnetic resonance imaging (rs-fMRI) data set, we constructed whole-brain functional networks of 19 patients with BiTLE, and compared them to those of 75 patients with unilateral TLE (UTLE). We quantified resting-state, whole-brain topological properties using metrics derived from network theory, including clustering coefficient, global efficiency, participation coefficient, and modularity. For each metric, we computed an average across all brain regions, and iterated this process across network densities. Curves of network density vs each network metric were compared between groups. Finally, we derived a combined metric, which we term the "integration-segregation axis," by combining whole-brain average clustering coefficient and global efficiency curves, and applying principal component analysis (PCA)-based dimensionality reduction. RESULTS Compared to UTLE, BiTLE had decreased global efficiency (p = .031), and decreased whole brain average participation coefficient across a range of network densities (p = .019). Modularity maximization yielded a larger number of smaller communities in BiTLE than in UTLE (p = .020). Differences in network properties separate BiTLE and UTLE along the integration-segregation axis, with regions within the axis having a specificity of up to 0.87 for BiTLE. Along the integration-segregation axis, UTLE patients with poor surgical outcomes were distributed in the same regions as BiTLE, and network metrics confirmed similar patterns of increased segregation in both BiTLE and poor outcome UTLE. SIGNIFICANCE Increased interictal whole-brain network segregation, as measured by rs-fMRI, is specific to BiTLE, as well as poor surgical outcome UTLE, and may assist in non-invasively identifying this patient population prior to intracranial electroencephalography or device implantation.
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Affiliation(s)
- Alfredo Lucas
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Eli J Cornblath
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nishant Sinha
- Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Peter Hadar
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lorenzo Caciagli
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Simon S Keller
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Leonardo Bonilha
- Department of Neurology, Emory University, Atlanta, Georgia, USA
| | - Russell T Shinohara
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Joel M Stein
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sandhitsu Das
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ezequiel Gleichgerrcht
- Department of Neurology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Kathryn A Davis
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Dwyer DB, Chand GB, Pigoni A, Khuntia A, Wen J, Antoniades M, Hwang G, Erus G, Doshi J, Srinivasan D, Varol E, Kahn RS, Schnack HG, Meisenzahl E, Wood SJ, Zhuo C, Sotiras A, Shinohara RT, Shou H, Fan Y, Schaulfelberger M, Rosa P, Lalousis PA, Upthegrove R, Kaczkurkin AN, Moore TM, Nelson B, Gur RE, Gur RC, Ritchie MD, Satterthwaite TD, Murray RM, Di Forti M, Ciufolini S, Zanetti MV, Wolf DH, Pantelis C, Crespo-Facorro B, Busatto GF, Davatzikos C, Koutsouleris N, Dazzan P. Psychosis brain subtypes validated in first-episode cohorts and related to illness remission: results from the PHENOM consortium. Mol Psychiatry 2023; 28:2008-2017. [PMID: 37147389 PMCID: PMC10575777 DOI: 10.1038/s41380-023-02069-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 03/15/2023] [Accepted: 04/05/2023] [Indexed: 05/07/2023]
Abstract
Using machine learning, we recently decomposed the neuroanatomical heterogeneity of established schizophrenia to discover two volumetric subgroups-a 'lower brain volume' subgroup (SG1) and an 'higher striatal volume' subgroup (SG2) with otherwise normal brain structure. In this study, we investigated whether the MRI signatures of these subgroups were also already present at the time of the first-episode of psychosis (FEP) and whether they were related to clinical presentation and clinical remission over 1-, 3-, and 5-years. We included 572 FEP and 424 healthy controls (HC) from 4 sites (Sao Paulo, Santander, London, Melbourne) of the PHENOM consortium. Our prior MRI subgrouping models (671 participants; USA, Germany, and China) were applied to both FEP and HC. Participants were assigned into 1 of 4 categories: subgroup 1 (SG1), subgroup 2 (SG2), no subgroup membership ('None'), and mixed SG1 + SG2 subgroups ('Mixed'). Voxel-wise analyses characterized SG1 and SG2 subgroups. Supervised machine learning analyses characterized baseline and remission signatures related to SG1 and SG2 membership. The two dominant patterns of 'lower brain volume' in SG1 and 'higher striatal volume' (with otherwise normal neuromorphology) in SG2 were identified already at the first episode of psychosis. SG1 had a significantly higher proportion of FEP (32%) vs. HC (19%) than SG2 (FEP, 21%; HC, 23%). Clinical multivariate signatures separated the SG1 and SG2 subgroups (balanced accuracy = 64%; p < 0.0001), with SG2 showing higher education but also greater positive psychosis symptoms at first presentation, and an association with symptom remission at 1-year, 5-year, and when timepoints were combined. Neuromorphological subtypes of schizophrenia are already evident at illness onset, separated by distinct clinical presentations, and differentially associated with subsequent remission. These results suggest that the subgroups may be underlying risk phenotypes that could be targeted in future treatment trials and are critical to consider when interpreting neuroimaging literature.
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Affiliation(s)
- Dominic B Dwyer
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian University, Munich, Germany.
- Centre for Youth Mental Health, University of Melbourne, Melbourne, VIC, Australia.
- Orygen, Melbourne, VIC, Australia.
| | - Ganesh B Chand
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Radiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Alessandro Pigoni
- Department of Neurosciences and Mental Health, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Social and Affective Neuroscience Group, MoMiLab, IMT School for Advanced Studies Lucca, Lucca, Italy
| | - Adyasha Khuntia
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian University, Munich, Germany
- Max-Planck Institute of Psychiatry, Munich, Germany
| | - Junhao Wen
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mathilde Antoniades
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gyujoon Hwang
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guray Erus
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jimit Doshi
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dhivya Srinivasan
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erdem Varol
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Statistics, Zuckerman Institute, Columbia University, New York, NY, USA
| | - Rene S Kahn
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hugo G Schnack
- Department of Psychiatry, University Medical Center Utrecht, Utrecht, Netherlands
| | - Eva Meisenzahl
- LVR-Klinikum Düsseldorf, Kliniken der Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Stephen J Wood
- Centre for Youth Mental Health, University of Melbourne, Melbourne, VIC, Australia
- Orygen, Melbourne, VIC, Australia
- University of Birmingham, Edgbaston, UK
| | - Chuanjun Zhuo
- Department of Psychiatric-Neuroimaging-Genetics and Co-morbidity Laboratory (PNGC-Lab), Nankai University Affiliated Tianjin Anding Hospital; Department of Psychiatry, Tianjin Medical University, Tianjin, China
| | - Aristeidis Sotiras
- Department of Radiology and Institute for Informatics, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Russell T Shinohara
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Haochang Shou
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yong Fan
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Pedro Rosa
- Institute of Psychiatry, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Paris A Lalousis
- Institute for Mental Health and Centre for Brain Health, University of Birmingham, Birmingham, UK
| | - Rachel Upthegrove
- Institute for Mental Health and Centre for Brain Health, University of Birmingham, Birmingham, UK
- Early Intervention Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | | | - Tyler M Moore
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Barnaby Nelson
- Centre for Youth Mental Health, University of Melbourne, Melbourne, VIC, Australia
- Orygen, Melbourne, VIC, Australia
| | - Raquel E Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ruben C Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Theodore D Satterthwaite
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Robin M Murray
- Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Marta Di Forti
- Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Simone Ciufolini
- Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Marcus V Zanetti
- Institute of Psychiatry, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
- Hospital Sírio-Libanês, São Paulo, Brazil
| | - Daniel H Wolf
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christos Pantelis
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, University of Melbourne and Melbourne Health, Carlton South, VIC, Australia
| | - Benedicto Crespo-Facorro
- Mental Health Service, Hospital Universitario Virgen del Rocío, Seville, Spain
- Centro de Investigación Biomédica en Red de Salud Mental, Instituto de Salud Carlos III (CIBERSAM), Madrid, Spain
- Instituto de Biomedicina de Sevilla (IBiS), Seville, Spain
- Department of Psychiatry, Universidad de Sevilla, Seville, Spain
| | - Geraldo F Busatto
- Institute of Psychiatry, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Christos Davatzikos
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nikolaos Koutsouleris
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian University, Munich, Germany.
- Max-Planck Institute of Psychiatry, Munich, Germany.
- Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK.
| | - Paola Dazzan
- Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK.
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Hu F, Lucas A, Chen AA, Coleman K, Horng H, Ng RW, Tustison NJ, Davis KA, Shou H, Li M, Shinohara RT. DeepComBat: A Statistically Motivated, Hyperparameter-Robust, Deep Learning Approach to Harmonization of Neuroimaging Data. bioRxiv 2023:2023.04.24.537396. [PMID: 37163042 PMCID: PMC10168207 DOI: 10.1101/2023.04.24.537396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Neuroimaging data from multiple batches (i.e. acquisition sites, scanner manufacturer, datasets, etc.) are increasingly necessary to gain new insights into the human brain. However, multi-batch data, as well as extracted radiomic features, exhibit pronounced technical artifacts across batches. These batch effects introduce confounding into the data and can obscure biological effects of interest, decreasing the generalizability and reproducibility of findings. This is especially true when multi-batch data is used alongside complex downstream analysis models, such as machine learning methods. Image harmonization methods seeking to remove these batch effects are important for mitigating these issues; however, significant multivariate batch effects remain in the data following harmonization by current state-of-the-art statistical and deep learning methods. We present DeepCombat, a deep learning harmonization method based on a conditional variational autoencoder architecture and the ComBat harmonization model. DeepCombat learns and removes subject-level batch effects by accounting for the multivariate relationships between features. Additionally, DeepComBat relaxes a number of strong assumptions commonly made by previous deep learning harmonization methods and is empirically robust across a wide range of hyperparameter choices. We apply this method to neuroimaging data from a large cognitive-aging cohort and find that DeepCombat outperforms existing methods, as assessed by a battery of machine learning methods, in removing scanner effects from cortical thickness measurements while preserving biological heterogeneity. Additionally, DeepComBat provides a new perspective for statistically-motivated deep learning harmonization methods.
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Affiliation(s)
- Fengling Hu
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania
| | - Alfredo Lucas
- Center for Neuroengineering and Therapeutics, Department of Engineering, University of Pennsylvania
| | - Andrew A. Chen
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania
| | - Kyle Coleman
- Statistical Center for Single-Cell and Spatial Genomics, Perelman School of Medicine, University of Pennsylvania
| | - Hannah Horng
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania
| | | | | | - Kathryn A. Davis
- Center for Neuroengineering and Therapeutics, Department of Engineering, University of Pennsylvania
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania
| | - Haochang Shou
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania
- Center for Biomedical Image Computing and Analytics (CBICA), Perelman School of Medicine
| | - Mingyao Li
- Statistical Center for Single-Cell and Spatial Genomics, Perelman School of Medicine, University of Pennsylvania
| | - Russell T. Shinohara
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania
- Center for Biomedical Image Computing and Analytics (CBICA), Perelman School of Medicine
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Pines A, Keller AS, Larsen B, Bertolero M, Ashourvan A, Bassett DS, Cieslak M, Covitz S, Fan Y, Feczko E, Houghton A, Rueter AR, Saggar M, Shafiei G, Tapera TM, Vogel J, Weinstein SM, Shinohara RT, Williams LM, Fair DA, Satterthwaite TD. Development of top-down cortical propagations in youth. Neuron 2023; 111:1316-1330.e5. [PMID: 36803653 PMCID: PMC10121821 DOI: 10.1016/j.neuron.2023.01.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 12/08/2022] [Accepted: 01/18/2023] [Indexed: 02/19/2023]
Abstract
Hierarchical processing requires activity propagating between higher- and lower-order cortical areas. However, functional neuroimaging studies have chiefly quantified fluctuations within regions over time rather than propagations occurring over space. Here, we leverage advances in neuroimaging and computer vision to track cortical activity propagations in a large sample of youth (n = 388). We delineate cortical propagations that systematically ascend and descend a cortical hierarchy in all individuals in our developmental cohort, as well as in an independent dataset of densely sampled adults. Further, we demonstrate that top-down, descending hierarchical propagations become more prevalent with greater demands for cognitive control as well as with development in youth. These findings emphasize that hierarchical processing is reflected in the directionality of propagating cortical activity and suggest top-down propagations as a potential mechanism of neurocognitive maturation in youth.
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Affiliation(s)
- Adam Pines
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94304, USA; The Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, Neurodevelopment & Psychosis Section, University of Pennsylvania, Philadelphia, PA, USA
| | - Arielle S Keller
- The Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, Neurodevelopment & Psychosis Section, University of Pennsylvania, Philadelphia, PA, USA
| | - Bart Larsen
- The Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, Neurodevelopment & Psychosis Section, University of Pennsylvania, Philadelphia, PA, USA
| | - Maxwell Bertolero
- The Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, Neurodevelopment & Psychosis Section, University of Pennsylvania, Philadelphia, PA, USA
| | - Arian Ashourvan
- Department of Psychology, The University of Kansas, Lawrence, KS 66045, USA
| | - Dani S Bassett
- Department of Psychiatry, Neurodevelopment & Psychosis Section, University of Pennsylvania, Philadelphia, PA, USA; Departments of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Electrical & Systems Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Physics & Astronomy, The University of Pennsylvania, Philadelphia, PA 19104, USA; Santa Fe Institute, Santa Fe, NM 87051, USA
| | - Matthew Cieslak
- The Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, Neurodevelopment & Psychosis Section, University of Pennsylvania, Philadelphia, PA, USA
| | - Sydney Covitz
- The Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, Neurodevelopment & Psychosis Section, University of Pennsylvania, Philadelphia, PA, USA
| | - Yong Fan
- Department of Radiology, The University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eric Feczko
- Masonic Institute for the Developing Brain, Institute of Child Development, College of Education and Human Development, Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN 55414, USA
| | - Audrey Houghton
- Masonic Institute for the Developing Brain, Institute of Child Development, College of Education and Human Development, Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN 55414, USA
| | - Amanda R Rueter
- Masonic Institute for the Developing Brain, Institute of Child Development, College of Education and Human Development, Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN 55414, USA
| | - Manish Saggar
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94304, USA
| | - Golia Shafiei
- The Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, Neurodevelopment & Psychosis Section, University of Pennsylvania, Philadelphia, PA, USA
| | - Tinashe M Tapera
- The Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, Neurodevelopment & Psychosis Section, University of Pennsylvania, Philadelphia, PA, USA
| | - Jacob Vogel
- The Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, Neurodevelopment & Psychosis Section, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah M Weinstein
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Russell T Shinohara
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leanne M Williams
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94304, USA
| | - Damien A Fair
- Masonic Institute for the Developing Brain, Institute of Child Development, College of Education and Human Development, Department of Pediatrics, Medical School, University of Minnesota, Minneapolis, MN 55414, USA
| | - Theodore D Satterthwaite
- The Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, Neurodevelopment & Psychosis Section, University of Pennsylvania, Philadelphia, PA, USA.
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Hwang G, Wen J, Sotardi S, Brodkin ES, Chand GB, Dwyer DB, Erus G, Doshi J, Singhal P, Srinivasan D, Varol E, Sotiras A, Dazzan P, Kahn RS, Schnack HG, Zanetti MV, Meisenzahl E, Busatto GF, Crespo-Facorro B, Pantelis C, Wood SJ, Zhuo C, Shinohara RT, Shou H, Fan Y, Di Martino A, Koutsouleris N, Gur RE, Gur RC, Satterthwaite TD, Wolf DH, Davatzikos C. Assessment of Neuroanatomical Endophenotypes of Autism Spectrum Disorder and Association With Characteristics of Individuals With Schizophrenia and the General Population. JAMA Psychiatry 2023; 80:498-507. [PMID: 37017948 PMCID: PMC10157419 DOI: 10.1001/jamapsychiatry.2023.0409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Importance Autism spectrum disorder (ASD) is associated with significant clinical, neuroanatomical, and genetic heterogeneity that limits precision diagnostics and treatment. Objective To assess distinct neuroanatomical dimensions of ASD using novel semisupervised machine learning methods and to test whether the dimensions can serve as endophenotypes also in non-ASD populations. Design, Setting, and Participants This cross-sectional study used imaging data from the publicly available Autism Brain Imaging Data Exchange (ABIDE) repositories as the discovery cohort. The ABIDE sample included individuals diagnosed with ASD aged between 16 and 64 years and age- and sex-match typically developing individuals. Validation cohorts included individuals with schizophrenia from the Psychosis Heterogeneity Evaluated via Dimensional Neuroimaging (PHENOM) consortium and individuals from the UK Biobank to represent the general population. The multisite discovery cohort included 16 internationally distributed imaging sites. Analyses were performed between March 2021 and March 2022. Main Outcomes and Measures The trained semisupervised heterogeneity through discriminative analysis models were tested for reproducibility using extensive cross-validations. It was then applied to individuals from the PHENOM and the UK Biobank. It was hypothesized that neuroanatomical dimensions of ASD would display distinct clinical and genetic profiles and would be prominent also in non-ASD populations. Results Heterogeneity through discriminative analysis models trained on T1-weighted brain magnetic resonance images of 307 individuals with ASD (mean [SD] age, 25.4 [9.8] years; 273 [88.9%] male) and 362 typically developing control individuals (mean [SD] age, 25.8 [8.9] years; 309 [85.4%] male) revealed that a 3-dimensional scheme was optimal to capture the ASD neuroanatomy. The first dimension (A1: aginglike) was associated with smaller brain volume, lower cognitive function, and aging-related genetic variants (FOXO3; Z = 4.65; P = 1.62 × 10-6). The second dimension (A2: schizophrenialike) was characterized by enlarged subcortical volumes, antipsychotic medication use (Cohen d = 0.65; false discovery rate-adjusted P = .048), partially overlapping genetic, neuroanatomical characteristics to schizophrenia (n = 307), and significant genetic heritability estimates in the general population (n = 14 786; mean [SD] h2, 0.71 [0.04]; P < 1 × 10-4). The third dimension (A3: typical ASD) was distinguished by enlarged cortical volumes, high nonverbal cognitive performance, and biological pathways implicating brain development and abnormal apoptosis (mean [SD] β, 0.83 [0.02]; P = 4.22 × 10-6). Conclusions and Relevance This cross-sectional study discovered 3-dimensional endophenotypic representation that may elucidate the heterogeneous neurobiological underpinnings of ASD to support precision diagnostics. The significant correspondence between A2 and schizophrenia indicates a possibility of identifying common biological mechanisms across the 2 mental health diagnoses.
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Affiliation(s)
- Gyujoon Hwang
- AI 2 D Center for Data Science for Integrated Diagnostics, and Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Junhao Wen
- AI 2 D Center for Data Science for Integrated Diagnostics, and Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
- Laboratory of AI & Biomedical Science (LABS), Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Marina del Rey
| | - Susan Sotardi
- Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Edward S Brodkin
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Ganesh B Chand
- AI 2 D Center for Data Science for Integrated Diagnostics, and Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
- Department of Radiology, School of Medicine, Washington University in St Louis, St Louis, Missouri
| | - Dominic B Dwyer
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian University, Munich, Germany
| | - Guray Erus
- AI 2 D Center for Data Science for Integrated Diagnostics, and Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Jimit Doshi
- AI 2 D Center for Data Science for Integrated Diagnostics, and Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Pankhuri Singhal
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Dhivya Srinivasan
- AI 2 D Center for Data Science for Integrated Diagnostics, and Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Erdem Varol
- AI 2 D Center for Data Science for Integrated Diagnostics, and Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
- Department of Statistics, Zuckerman Institute, Columbia University, New York, New York
| | - Aristeidis Sotiras
- AI 2 D Center for Data Science for Integrated Diagnostics, and Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
- Department of Radiology, School of Medicine, Washington University in St Louis, St Louis, Missouri
| | - Paola Dazzan
- Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Rene S Kahn
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Hugo G Schnack
- Department of Psychiatry, University Medical Center Utrecht, Utrecht, Netherlands
| | - Marcus V Zanetti
- Institute of Psychiatry, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
- Hospital Sírio-Libanês, São Paulo, Brazil
| | - Eva Meisenzahl
- LVR-Klinikum Düsseldorf, Kliniken der Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Geraldo F Busatto
- Institute of Psychiatry, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Benedicto Crespo-Facorro
- University Hospital Virgen del Rocio, Department of Psychiatry, School of Medicine, IBiS-CIBERSAM, University of Sevilla, Seville, Spain
| | - Christos Pantelis
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, University of Melbourne and Melbourne Health, Carlton South, Victoria, Australia
| | - Stephen J Wood
- Orygen, Melbourne, Victoria, Australia
- Centre for Youth Mental Health, University of Melbourne, Melbourne, Victoria, Australia
- School of Psychology, University of Birmingham, Edgbaston, UK
| | - Chuanjun Zhuo
- Department of Psychiatric-Neuroimaging-Genetics and Co-morbidity Laboratory, Tianjin Anding Hospital, Tianjin, China
- Department of Psychiatry, Tianjin Medical University, Tianjin, China
| | - Russell T Shinohara
- AI 2 D Center for Data Science for Integrated Diagnostics, and Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Haochang Shou
- AI 2 D Center for Data Science for Integrated Diagnostics, and Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Yong Fan
- AI 2 D Center for Data Science for Integrated Diagnostics, and Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Adriana Di Martino
- Phyllis Green and Randolph Cowen Institute for Pediatric Neuroscience at the New York University Child Study Center, New York
| | - Nikolaos Koutsouleris
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian University, Munich, Germany
| | - Raquel E Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Ruben C Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Theodore D Satterthwaite
- AI 2 D Center for Data Science for Integrated Diagnostics, and Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Daniel H Wolf
- AI 2 D Center for Data Science for Integrated Diagnostics, and Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Christos Davatzikos
- AI 2 D Center for Data Science for Integrated Diagnostics, and Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
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Sydnor VJ, Larsen B, Seidlitz J, Adebimpe A, Alexander-Bloch AF, Bassett DS, Bertolero MA, Cieslak M, Covitz S, Fan Y, Gur RE, Gur RC, Mackey AP, Moore TM, Roalf DR, Shinohara RT, Satterthwaite TD. Intrinsic activity development unfolds along a sensorimotor-association cortical axis in youth. Nat Neurosci 2023; 26:638-649. [PMID: 36973514 PMCID: PMC10406167 DOI: 10.1038/s41593-023-01282-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/15/2023] [Indexed: 03/29/2023]
Abstract
Animal studies of neurodevelopment have shown that recordings of intrinsic cortical activity evolve from synchronized and high amplitude to sparse and low amplitude as plasticity declines and the cortex matures. Leveraging resting-state functional MRI (fMRI) data from 1,033 youths (ages 8-23 years), we find that this stereotyped refinement of intrinsic activity occurs during human development and provides evidence for a cortical gradient of neurodevelopmental change. Declines in the amplitude of intrinsic fMRI activity were initiated heterochronously across regions and were coupled to the maturation of intracortical myelin, a developmental plasticity regulator. Spatiotemporal variability in regional developmental trajectories was organized along a hierarchical, sensorimotor-association cortical axis from ages 8 to 18. The sensorimotor-association axis furthermore captured variation in associations between youths' neighborhood environments and intrinsic fMRI activity; associations suggest that the effects of environmental disadvantage on the maturing brain diverge most across this axis during midadolescence. These results uncover a hierarchical neurodevelopmental axis and offer insight into the progression of cortical plasticity in humans.
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Affiliation(s)
- Valerie J Sydnor
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bart Larsen
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jakob Seidlitz
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Penn-CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Azeez Adebimpe
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Aaron F Alexander-Bloch
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Penn-CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dani S Bassett
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Department of Electrical and Systems Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physics and Astronomy, College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Santa Fe Institute, Santa Fe, NM, USA
| | - Maxwell A Bertolero
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew Cieslak
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sydney Covitz
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yong Fan
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, PA, USA
| | - Raquel E Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Penn-CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ruben C Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Allyson P Mackey
- Department of Psychology, University of Pennsylvania, Philadelphia, PA, USA
| | - Tyler M Moore
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - David R Roalf
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Russell T Shinohara
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Theodore D Satterthwaite
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Penn-CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Okar SV, Hu F, Shinohara RT, Beck ES, Reich DS, Ineichen BV. The etiology and evolution of magnetic resonance imaging-visible perivascular spaces: Systematic review and meta-analysis. Front Neurosci 2023; 17:1038011. [PMID: 37065926 PMCID: PMC10098201 DOI: 10.3389/fnins.2023.1038011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 03/15/2023] [Indexed: 04/03/2023] Open
Abstract
ObjectivesPerivascular spaces have been involved in neuroinflammatory and neurodegenerative diseases. Upon a certain size, these spaces can become visible on magnetic resonance imaging (MRI), referred to as enlarged perivascular spaces (EPVS) or MRI-visible perivascular spaces (MVPVS). However, the lack of systematic evidence on etiology and temporal dynamics of MVPVS hampers their diagnostic utility as MRI biomarker. Thus, the goal of this systematic review was to summarize potential etiologies and evolution of MVPVS.MethodsIn a comprehensive literature search, out of 1,488 unique publications, 140 records assessing etiopathogenesis and dynamics of MVPVS were eligible for a qualitative summary. 6 records were included in a meta-analysis to assess the association between MVPVS and brain atrophy.ResultsFour overarching and partly overlapping etiologies of MVPVS have been proposed: (1) Impairment of interstitial fluid circulation, (2) Spiral elongation of arteries, (3) Brain atrophy and/or perivascular myelin loss, and (4) Immune cell accumulation in the perivascular space. The meta-analysis in patients with neuroinflammatory diseases did not support an association between MVPVS and brain volume measures [R: −0.15 (95%-CI −0.40–0.11)]. Based on few and mostly small studies in tumefactive MVPVS and in vascular and neuroinflammatory diseases, temporal evolution of MVPVS is slow.ConclusionCollectively, this study provides high-grade evidence for MVPVS etiopathogenesis and temporal dynamics. Although several potential etiologies for MVPVS emergence have been proposed, they are only partially supported by data. Advanced MRI methods should be employed to further dissect etiopathogenesis and evolution of MVPVS. This can benefit their implementation as an imaging biomarker.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/display_record.php?RecordID=346564, identifier CRD42022346564.
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Affiliation(s)
- Serhat V. Okar
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Fengling Hu
- Department of Biostatistics, Epidemiology, and Informatics, Penn Statistics in Imaging and Visualization Center, University of Pennsylvania, Philadelphia, PA, United States
| | - Russell T. Shinohara
- Department of Biostatistics, Epidemiology, and Informatics, Penn Statistics in Imaging and Visualization Center, University of Pennsylvania, Philadelphia, PA, United States
| | - Erin S. Beck
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Daniel S. Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Benjamin V. Ineichen
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
- Department of Neuroradiology, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Center for Reproducible Science, University of Zurich, Zurich, Switzerland
- *Correspondence: Benjamin V. Ineichen, , ; orcid.org/0000-0003-1362-4819
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50
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Shapira N, Donovan K, Mei K, Geagan M, Roshkovan L, Gang GJ, Abed M, Linna NB, Cranston CP, O'Leary CN, Dhanaliwala AH, Kontos D, Litt HI, Stayman JW, Shinohara RT, Noël PB. Three-dimensional printing of patient-specific computed tomography lung phantoms: a reader study. PNAS Nexus 2023; 2:pgad026. [PMID: 36909822 PMCID: PMC9992761 DOI: 10.1093/pnasnexus/pgad026] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/20/2022] [Accepted: 01/17/2023] [Indexed: 02/04/2023]
Abstract
In modern clinical decision-support algorithms, heterogeneity in image characteristics due to variations in imaging systems and protocols hinders the development of reproducible quantitative measures including for feature extraction pipelines. With the help of a reader study, we investigate the ability to provide consistent ground-truth targets by using patient-specific 3D-printed lung phantoms. PixelPrint was developed for 3D-printing lifelike computed tomography (CT) lung phantoms by directly translating clinical images into printer instructions that control density on a voxel-by-voxel basis. Data sets of three COVID-19 patients served as input for 3D-printing lung phantoms. Five radiologists rated patient and phantom images for imaging characteristics and diagnostic confidence in a blinded reader study. Effect sizes of evaluating phantom as opposed to patient images were assessed using linear mixed models. Finally, PixelPrint's production reproducibility was evaluated. Images of patients and phantoms had little variation in the estimated mean (0.03-0.29, using a 1-5 scale). When comparing phantom images to patient images, effect size analysis revealed that the difference was within one-third of the inter- and intrareader variabilities. High correspondence between the four phantoms created using the same patient images was demonstrated by PixelPrint's production repeatability tests, with greater similarity scores between high-dose acquisitions of the phantoms than between clinical-dose acquisitions of a single phantom. We demonstrated PixelPrint's ability to produce lifelike CT lung phantoms reliably. These phantoms have the potential to provide ground-truth targets for validating the generalizability of inference-based decision-support algorithms between different health centers and imaging protocols and for optimizing examination protocols with realistic patient-based phantoms. Classification: CT lung phantoms, reader study.
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Affiliation(s)
- Nadav Shapira
- Department of Radiology, Perelman School of Medicine of the University of Pennsylvania, 3400 Civic Center, Philadelphia, PA 19104, USA
| | - Kevin Donovan
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, 423 Guardian Drive, Philadelphia, PA 19104, USA
| | - Kai Mei
- Department of Radiology, Perelman School of Medicine of the University of Pennsylvania, 3400 Civic Center, Philadelphia, PA 19104, USA
| | - Michael Geagan
- Department of Radiology, Perelman School of Medicine of the University of Pennsylvania, 3400 Civic Center, Philadelphia, PA 19104, USA
| | - Leonid Roshkovan
- Department of Radiology, Perelman School of Medicine of the University of Pennsylvania, 3400 Civic Center, Philadelphia, PA 19104, USA
| | - Grace J Gang
- Department of Biomedical Engineering, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
| | - Mohammed Abed
- Department of Radiology, Perelman School of Medicine of the University of Pennsylvania, 3400 Civic Center, Philadelphia, PA 19104, USA
- Department of Radiology, College of Medicine, Ibn Sina University of Medical and Pharmaceutical Sciences, 79G3+3RR Qadisaya Expy, Baghdad, Iraq
| | - Nathaniel B Linna
- Department of Radiology, Perelman School of Medicine of the University of Pennsylvania, 3400 Civic Center, Philadelphia, PA 19104, USA
| | - Coulter P Cranston
- Department of Radiology, Perelman School of Medicine of the University of Pennsylvania, 3400 Civic Center, Philadelphia, PA 19104, USA
| | - Cathal N O'Leary
- Department of Radiology, Perelman School of Medicine of the University of Pennsylvania, 3400 Civic Center, Philadelphia, PA 19104, USA
| | - Ali H Dhanaliwala
- Department of Radiology, Perelman School of Medicine of the University of Pennsylvania, 3400 Civic Center, Philadelphia, PA 19104, USA
| | - Despina Kontos
- Department of Radiology, Perelman School of Medicine of the University of Pennsylvania, 3400 Civic Center, Philadelphia, PA 19104, USA
| | - Harold I Litt
- Department of Radiology, Perelman School of Medicine of the University of Pennsylvania, 3400 Civic Center, Philadelphia, PA 19104, USA
| | - J Webster Stayman
- Department of Biomedical Engineering, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, 423 Guardian Drive, Philadelphia, PA 19104, USA
- Center for Biomedical Image Computing and Analytics (CBICA), Perelman School of Medicine of the University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA 19104, USA
| | - Peter B Noël
- Department of Radiology, Perelman School of Medicine of the University of Pennsylvania, 3400 Civic Center, Philadelphia, PA 19104, USA
- Department of Diagnostic and Interventional Radiology, School of Medicine and Klinikum rechts der Isar, Technical University of Munich, Arcisstraße 21, 80333 München, Germany
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