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Royer J, Kebets V, Piguet C, Chen J, Ooi LQR, Kirschner M, Siffredi V, Misic B, Yeo BTT, Bernhardt BC. MULTIMODAL NEURAL CORRELATES OF CHILDHOOD PSYCHOPATHOLOGY. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.02.530821. [PMID: 39185226 PMCID: PMC11343159 DOI: 10.1101/2023.03.02.530821] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Complex structural and functional changes occurring in typical and atypical development necessitate multidimensional approaches to better understand the risk of developing psychopathology. Here, we simultaneously examined structural and functional brain network patterns in relation to dimensions of psychopathology in the Adolescent Brain Cognitive Development dataset. Several components were identified, recapitulating the psychopathology hierarchy, with the general psychopathology (p) factor explaining most covariance with multimodal imaging features, while the internalizing, externalizing, and neurodevelopmental dimensions were each associated with distinct morphological and functional connectivity signatures. Connectivity signatures associated with the p factor and neurodevelopmental dimensions followed the sensory-to-transmodal axis of cortical organization, which is related to the emergence of complex cognition and risk for psychopathology. Results were consistent in two separate data subsamples, supporting generalizability, and robust to variations in analytical parameters. Our findings help in better understanding biological mechanisms underpinning dimensions of psychopathology, and could provide brain-based vulnerability markers.
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Affiliation(s)
- Jessica Royer
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Valeria Kebets
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
- Centre for Sleep and Cognition & Centre for Translational MR Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore
- N.1 Institute for Health & Institute for Digital Medicine, National University of Singapore, Singapore
| | - Camille Piguet
- Young Adult Unit, Psychiatric Specialities Division, Geneva University Hospitals and Department of Psychiatry, Faculty of Medicine, University of Geneva, Switzerland
- Adolescent Unit, Division of General Paediatric, Department of Paediatrics, Gynaecology and Obstetrics, Geneva University Hospitals
| | - Jianzhong Chen
- Centre for Sleep and Cognition & Centre for Translational MR Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore
- N.1 Institute for Health & Institute for Digital Medicine, National University of Singapore, Singapore
| | - Leon Qi Rong Ooi
- Centre for Sleep and Cognition & Centre for Translational MR Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore
- N.1 Institute for Health & Institute for Digital Medicine, National University of Singapore, Singapore
| | - Matthias Kirschner
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
- Division of Adult Psychiatry, Department of Psychiatry, Geneva University Hospitals, Geneva, Switzerland
| | - Vanessa Siffredi
- Division of Development and Growth, Department of Paediatrics, Gynaecology and Obstetrics, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
- Neuro-X Institute, Ecole Polytechnique Fédérale de Lausanne, Geneva, Switzerland
- Department of Radiology and Medical Informatics, Faculty of Medicine, University of Geneva, Switzerland
| | - Bratislav Misic
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - B T Thomas Yeo
- Centre for Sleep and Cognition & Centre for Translational MR Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore
- N.1 Institute for Health & Institute for Digital Medicine, National University of Singapore, Singapore
- Integrative Sciences and Engineering Programme, National University Singapore, Singapore
- Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
| | - Boris C Bernhardt
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
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2
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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. Biostatistics 2024:kxae026. [PMID: 39140988 DOI: 10.1093/biostatistics/kxae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 07/05/2024] [Accepted: 07/08/2024] [Indexed: 08/15/2024] Open
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 preprocessing 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, 423 Guardian Drive, University of Pennsylvania, Philadelphia, PA, 19104, United States
| | - Julia Wrobel
- Department of Biostatistics and Bioinformatics, 1518 Clifton Rd. NE, Emory University, Atlanta, GA, 30322, United States
| | - Theodore D Satterthwaite
- Department of Psychiatry, 3700 Hamilton Walk, Perelman School of Medicine, Philadelphia, PA, 19104, United States
- Penn Lifespan Informatics and Neuroimaging Center, 3700 Hamilton Walk, Philadelphia, PA, 19104, United States
| | - Jeff Goldsmith
- Department of Biostatistics, 722 W. 168th St, Columbia University, New York, NY, 10032, United States
| | - Ruben C Gur
- Department of Psychiatry, 3700 Hamilton Walk, Perelman School of Medicine, Philadelphia, PA, 19104, United States
- The Penn Medicine-CHOP Lifespan Brain Institute, 3700 Hamilton Walk, Philadelphia, PA, 19104, United States
| | - Raquel E Gur
- Department of Psychiatry, 3700 Hamilton Walk, Perelman School of Medicine, Philadelphia, PA, 19104, United States
- The Penn Medicine-CHOP Lifespan Brain Institute, 3700 Hamilton Walk, Philadelphia, PA, 19104, United States
| | - Jan Gertheiss
- Department of Mathematics and Statistics, School of Economics and Social Sciences, Holstenhofweg 85, Helmut Schmidt University, 22043 Hamburg, Germany
| | - Dani S Bassett
- Department of Bioengineering, 210 S 33rd St, University of Pennsylvania, Philadelphia, PA, 19104, United States
- Department of Physics and Astronomy, 209 S 33rd St, University of Pennsylvania, Philadelphia, PA, 19104, United States
- Department of Electrical and Systems Engineering, 200 S 33rd St, University of Pennsylvania, Philadelphia, PA, 19104, United States
- Department of Neurology, 3400 Spruce St, University of Pennsylvania, Philadelphia, PA, 19104, United States
| | - Russell T Shinohara
- The Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, 423 Guardian Drive, University of Pennsylvania, Philadelphia, PA, 19104, United States
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3
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Hubbard NA, Bauer CCC, Siless V, Auerbach RP, Elam JS, Frosch IR, Henin A, Hofmann SG, Hodge MR, Jones R, Lenzini P, Lo N, Park AT, Pizzagalli DA, Vaz-DeSouza F, Gabrieli JDE, Whitfield-Gabrieli S, Yendiki A, Ghosh SS. The Human Connectome Project of adolescent anxiety and depression dataset. Sci Data 2024; 11:837. [PMID: 39095370 PMCID: PMC11297143 DOI: 10.1038/s41597-024-03629-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 07/09/2024] [Indexed: 08/04/2024] Open
Abstract
This article describes primary data and resources available from the Boston Adolescent Neuroimaging of Depression and Anxiety (BANDA) study, a novel arm of the Human Connectome Project (HCP). Data were collected from 215 adolescents (14-17 years old), 152 of whom had current diagnoses of anxiety and/or depressive disorders at study intake. Data include cross-sectional structural (T1- and T2-weighted), functional (resting state and three tasks), and diffusion-weighted magnetic resonance images. Both unprocessed and HCP minimally-preprocessed imaging data are available within the data release packages. Adolescent and parent clinical interview data, as well as cognitive and neuropsychological data are also included within these packages. Release packages additionally provide data collected from self-report measures assessing key features of adolescent psychopathology, including: anxious and depressive symptom dimensions, behavioral inhibition/activation, exposure to stressful life events, and risk behaviors. Finally, the release packages include 6- and 12-month longitudinal data acquired from clinical measures. Data are publicly accessible through the National Institute of Mental Health Data Archive (ID: #2505).
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Affiliation(s)
- N A Hubbard
- Department of Psychology, University of Nebraska-Lincoln, Lincoln, NE, USA.
- Center for Brain, Biology, and Behavior, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - C C C Bauer
- Department of Psychology, Northeastern University, Boston, MA, USA
- Department of Brain and Cognitive Sciences and McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - V Siless
- Harvard Medical School, Boston, MA, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
| | - R P Auerbach
- Department of Psychiatry, Columbia University, New York, NY, USA
| | - J S Elam
- Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - I R Frosch
- Department of Brain and Cognitive Sciences and McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - A Henin
- Harvard Medical School, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - S G Hofmann
- Department of Psychology, Philipps University of Marburg, DEU, Germany
| | - M R Hodge
- Department of Radiology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - R Jones
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
| | - P Lenzini
- Department of Radiology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - N Lo
- Department of Brain and Cognitive Sciences and McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - A T Park
- Department of Brain and Cognitive Sciences and McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - D A Pizzagalli
- Harvard Medical School, Boston, MA, USA
- Center for Depression, Anxiety, and Stress Research, McLean Hospital, Belmont, MA, USA
| | - F Vaz-DeSouza
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - J D E Gabrieli
- Department of Brain and Cognitive Sciences and McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - S Whitfield-Gabrieli
- Department of Psychology, Northeastern University, Boston, MA, USA
- Department of Brain and Cognitive Sciences and McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - A Yendiki
- Harvard Medical School, Boston, MA, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
| | - S S Ghosh
- Department of Brain and Cognitive Sciences and McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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4
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Karl V, Engen H, Beck D, Norbom LB, Ferschmann L, Aksnes ER, Kjelkenes R, Voldsbekk I, Andreassen OA, Alnæs D, Ladouceur CD, Westlye LT, Tamnes CK. The role of functional emotion circuits in distinct dimensions of psychopathology in youth. Transl Psychiatry 2024; 14:317. [PMID: 39095355 PMCID: PMC11297301 DOI: 10.1038/s41398-024-03036-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 07/17/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
Several mental disorders emerge during childhood or adolescence and are often characterized by socioemotional difficulties, including alterations in emotion perception. Emotional facial expressions are processed in discrete functional brain modules whose connectivity patterns encode emotion categories, but the involvement of these neural circuits in psychopathology in youth is poorly understood. This study examined the associations between activation and functional connectivity patterns in emotion circuits and psychopathology during development. We used task-based fMRI data from the Philadelphia Neurodevelopmental Cohort (PNC, N = 1221, 8-23 years) and conducted generalized psycho-physiological interaction (gPPI) analyses. Measures of psychopathology were derived from an independent component analysis of questionnaire data. The results showed positive associations between identifying fearful, sad, and angry faces and depressive symptoms, and a negative relationship between sadness recognition and positive psychosis symptoms. We found a positive main effect of depressive symptoms on BOLD activation in regions overlapping with the default mode network, while individuals reporting higher levels of norm-violating behavior exhibited emotion-specific lower functional connectivity within regions of the salience network and between modules that overlapped with the salience and default mode network. Our findings illustrate the relevance of functional connectivity patterns underlying emotion processing for behavioral problems in children and adolescents.
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Affiliation(s)
- Valerie Karl
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- PROMENTA Research Center, Department of Psychology, University of Oslo, Oslo, Norway.
| | - Haakon Engen
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
- Institute of Military Psychiatry Norwegian Armed Forces Joint Medical Services, Oslo, Norway
| | - Dani Beck
- PROMENTA Research Center, Department of Psychology, University of Oslo, Oslo, Norway
- Division of Mental Health and Substance Abuse, Diakonhjemmet Hospital, Oslo, Norway
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Linn B Norbom
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- PROMENTA Research Center, Department of Psychology, University of Oslo, Oslo, Norway
| | - Lia Ferschmann
- PROMENTA Research Center, Department of Psychology, University of Oslo, Oslo, Norway
| | - Eira R Aksnes
- PROMENTA Research Center, Department of Psychology, University of Oslo, Oslo, Norway
- Division of Mental Health and Substance Abuse, Diakonhjemmet Hospital, Oslo, Norway
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Rikka Kjelkenes
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
| | - Irene Voldsbekk
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
| | - Ole A Andreassen
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - Dag Alnæs
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Cecile D Ladouceur
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Psychology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lars T Westlye
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - Christian K Tamnes
- PROMENTA Research Center, Department of Psychology, University of Oslo, Oslo, Norway
- Division of Mental Health and Substance Abuse, Diakonhjemmet Hospital, Oslo, Norway
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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5
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Rosenblatt M, Tejavibulya L, Sun H, Camp CC, Khaitova M, Adkinson BD, Jiang R, Westwater ML, Noble S, Scheinost D. Power and reproducibility in the external validation of brain-phenotype predictions. Nat Hum Behav 2024:10.1038/s41562-024-01931-7. [PMID: 39085406 DOI: 10.1038/s41562-024-01931-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 06/18/2024] [Indexed: 08/02/2024]
Abstract
Brain-phenotype predictive models seek to identify reproducible and generalizable brain-phenotype associations. External validation, or the evaluation of a model in external datasets, is the gold standard in evaluating the generalizability of models in neuroimaging. Unlike typical studies, external validation involves two sample sizes: the training and the external sample sizes. Thus, traditional power calculations may not be appropriate. Here we ran over 900 million resampling-based simulations in functional and structural connectivity data to investigate the relationship between training sample size, external sample size, phenotype effect size, theoretical power and simulated power. Our analysis included a wide range of datasets: the Healthy Brain Network, the Adolescent Brain Cognitive Development Study, the Human Connectome Project (Development and Young Adult), the Philadelphia Neurodevelopmental Cohort, the Queensland Twin Adolescent Brain Project, and the Chinese Human Connectome Project; and phenotypes: age, body mass index, matrix reasoning, working memory, attention problems, anxiety/depression symptoms and relational processing. High effect size predictions achieved adequate power with training and external sample sizes of a few hundred individuals, whereas low and medium effect size predictions required hundreds to thousands of training and external samples. In addition, most previous external validation studies used sample sizes prone to low power, and theoretical power curves should be adjusted for the training sample size. Furthermore, model performance in internal validation often informed subsequent external validation performance (Pearson's r difference <0.2), particularly for well-harmonized datasets. These results could help decide how to power future external validation studies.
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Affiliation(s)
- Matthew Rosenblatt
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
| | - Link Tejavibulya
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT, USA
| | - Huili Sun
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Chris C Camp
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT, USA
| | - Milana Khaitova
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - Brendan D Adkinson
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT, USA
| | - Rongtao Jiang
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - Margaret L Westwater
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - Stephanie Noble
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Psychology, Northeastern University, Boston, MA, USA
| | - Dustin Scheinost
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT, USA
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
- Child Study Center, Yale School of Medicine, New Haven, CT, USA
- Department of Statistics and Data Science, Yale University, New Haven, CT, USA
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6
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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. A network control theory pipeline for studying the dynamics of the structural connectome. Nat Protoc 2024:10.1038/s41596-024-01023-w. [PMID: 39075309 DOI: 10.1038/s41596-024-01023-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 05/16/2024] [Indexed: 07/31/2024]
Abstract
Network control theory (NCT) is a simple and powerful tool for studying how network topology informs and constrains the dynamics of a system. 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 the dynamics of a system in a desired way. An interesting development for NCT in the neuroscience field is its application to study behavior and mental health symptoms. To date, NCT has been validated to study different aspects of the human structural connectome. NCT outputs can be monitored throughout developmental stages to study the effects of connectome topology on neural dynamics and, separately, to test the coherence of empirical datasets with brain function and stimulation. Here, we provide a comprehensive pipeline for applying NCT to structural connectomes by following two procedures. The main procedure focuses on computing the control energy associated with the transitions between specific neural activity states. The second procedure focuses on computing average controllability, which indexes nodes' general capacity to control the dynamics of the system. We provide recommendations for comparing NCT outputs against null network models, and we further support this approach with a Python-based software package called 'network control theory for python'. The procedures in this protocol are appropriate for users with a background in network neuroscience and experience in dynamical systems theory.
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Affiliation(s)
- Linden Parkes
- Department of Psychiatry, Rutgers University, Piscataway, NJ, USA.
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Jason Z Kim
- Department of Physics, Cornell University, Ithaca, NY, USA
| | - Jennifer Stiso
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Julia K Brynildsen
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew Cieslak
- Lifespan Informatics and Neuroimaging Center (PennLINC), 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 Research Institute, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sydney Covitz
- Lifespan Informatics and Neuroimaging Center (PennLINC), 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 Research Institute, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Raquel E Gur
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ruben C Gur
- Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Fabio Pasqualetti
- Department of Mechanical Engineering, University of California, Riverside, Riverside, CA, USA
| | - Russell T Shinohara
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, Philadelphia, PA, USA
- Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dale Zhou
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Theodore D Satterthwaite
- Lifespan Informatics and Neuroimaging Center (PennLINC), 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 Research Institute, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA, USA
| | - Dani S Bassett
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Neurology, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, USA
- Santa Fe Institute, Santa Fe, NM, USA
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7
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Bartnik A, Singh S, Sum C, Smith M, Bergsland N, Zivadinov R, Dwyer MG. An Automated Tool to Classify and Transform Unstructured MRI Data into BIDS Datasets. Neuroinformatics 2024; 22:229-238. [PMID: 38530566 DOI: 10.1007/s12021-024-09659-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2024] [Indexed: 03/28/2024]
Abstract
The increasing use of neuroimaging in clinical research has driven the creation of many large imaging datasets. However, these datasets often rely on inconsistent naming conventions in image file headers to describe acquisition, and time-consuming manual curation is necessary. Therefore, we sought to automate the process of classifying and organizing magnetic resonance imaging (MRI) data according to acquisition types common to the clinical routine, as well as automate the transformation of raw, unstructured images into Brain Imaging Data Structure (BIDS) datasets. To do this, we trained an XGBoost model to classify MRI acquisition types using relatively few acquisition parameters that are automatically stored by the MRI scanner in image file metadata, which are then mapped to the naming conventions prescribed by BIDS to transform the input images to the BIDS structure. The model recognizes MRI types with 99.475% accuracy, as well as a micro/macro-averaged precision of 0.9995/0.994, a micro/macro-averaged recall of 0.9995/0.989, and a micro/macro-averaged F1 of 0.9995/0.991. Our approach accurately and quickly classifies MRI types and transforms unstructured data into standardized structures with little-to-no user intervention, reducing the barrier of entry for clinical scientists and increasing the accessibility of existing neuroimaging data.
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Affiliation(s)
- Alexander Bartnik
- Buffalo Neuroimaging Analysis Center, Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, 77 Goodell St, Buffalo, NY, 14203, USA
| | - Sujal Singh
- Buffalo Neuroimaging Analysis Center, Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, 77 Goodell St, Buffalo, NY, 14203, USA
| | - Conan Sum
- Buffalo Neuroimaging Analysis Center, Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, 77 Goodell St, Buffalo, NY, 14203, USA
| | - Mackenzie Smith
- Buffalo Neuroimaging Analysis Center, Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, 77 Goodell St, Buffalo, NY, 14203, USA
| | - Niels Bergsland
- Buffalo Neuroimaging Analysis Center, Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, 77 Goodell St, Buffalo, NY, 14203, USA
| | - Robert Zivadinov
- Buffalo Neuroimaging Analysis Center, Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, 77 Goodell St, Buffalo, NY, 14203, USA
| | - Michael G Dwyer
- Buffalo Neuroimaging Analysis Center, Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, 77 Goodell St, Buffalo, NY, 14203, USA.
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8
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Weinstein SM, Tu D, Hu F, Pan R, Zhang R, Vandekar SN, Baller EB, Gur RC, Gur RE, Alexander-Bloch AF, Satterthwaite TD, Park JY. Mapping Individual Differences in Intermodal Coupling in Neurodevelopment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600817. [PMID: 38979274 PMCID: PMC11230458 DOI: 10.1101/2024.06.26.600817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Within-individual coupling between measures of brain structure and function evolves in development and may underlie differential risk for neuropsychiatric disorders. Despite increasing interest in the development of structure-function relationships, rigorous methods to quantify and test individual differences in coupling remain nascent. In this article, we explore and address gaps in approaches for testing and spatially localizing individual differences in intermodal coupling. We propose a new method, called CIDeR, which is designed to simultaneously perform hypothesis testing in a way that limits false positive results and improve detection of true positive results. Through a comparison across different approaches to testing individual differences in intermodal coupling, we delineate subtle differences in the hypotheses they test, which may ultimately lead researchers to arrive at different results. Finally, we illustrate the utility of CIDeR in two applications to brain development using data from the Philadelphia Neurodevelopmental Cohort.
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Affiliation(s)
- Sarah M. Weinstein
- Department of Epidemiology and Biostatistics, Temple University College of Public Health, Philadelphia, PA, USA
| | - Danni Tu
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Fengling Hu
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ruyi Pan
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
- Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Rongqian Zhang
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
| | - Simon N. Vandekar
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Erica B. Baller
- Department of Psychiatry, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn Lifespan Informatics and Neuroimaging Center, Philadelphia, PA, USA
| | - Ruben C. Gur
- Department of Psychiatry, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn-CHOP Lifespan Brain Institute (LiBI), Philadelphia, PA, USA
| | - Raquel E. Gur
- Department of Psychiatry, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn-CHOP Lifespan Brain Institute (LiBI), Philadelphia, PA, USA
| | - Aaron F. Alexander-Bloch
- Department of Psychiatry, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn-CHOP Lifespan Brain Institute (LiBI), Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Theodore D. Satterthwaite
- Department of Psychiatry, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn Lifespan Informatics and Neuroimaging Center, Philadelphia, PA, USA
- Penn-CHOP Lifespan Brain Institute (LiBI), Philadelphia, PA, USA
| | - Jun Young Park
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
- Department of Psychology, University of Toronto, Toronto, ON, Canada
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9
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Sydnor VJ, Bagautdinova J, Larsen B, Arcaro MJ, Barch DM, Bassett DS, Alexander-Bloch AF, Cook PA, Covitz S, Franco AR, Gur RE, Gur RC, Mackey AP, Mehta K, Meisler SL, Milham MP, Moore TM, Müller EJ, Roalf DR, Salo T, Schubiner G, Seidlitz J, Shinohara RT, Shine JM, Yeh FC, Cieslak M, Satterthwaite TD. A sensorimotor-association axis of thalamocortical connection development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598749. [PMID: 38915591 PMCID: PMC11195180 DOI: 10.1101/2024.06.13.598749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Human cortical development follows a sensorimotor-to-association sequence during childhood and adolescence1-6. The brain's capacity to enact this sequence over decades indicates that it relies on intrinsic mechanisms to regulate inter-regional differences in the timing of cortical maturation, yet regulators of human developmental chronology are not well understood. Given evidence from animal models that thalamic axons modulate windows of cortical plasticity7-12, here we evaluate the overarching hypothesis that structural connections between the thalamus and cortex help to coordinate cortical maturational heterochronicity during youth. We first introduce, cortically annotate, and anatomically validate a new atlas of human thalamocortical connections using diffusion tractography. By applying this atlas to three independent youth datasets (ages 8-23 years; total N = 2,676), we reproducibly demonstrate that thalamocortical connections develop along a maturational gradient that aligns with the cortex's sensorimotor-association axis. Associative cortical regions with thalamic connections that take longest to mature exhibit protracted expression of neurochemical, structural, and functional markers indicative of higher circuit plasticity as well as heightened environmental sensitivity. This work highlights a central role for the thalamus in the orchestration of hierarchically organized and environmentally sensitive windows of cortical developmental malleability.
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Affiliation(s)
- Valerie J. Sydnor
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joëlle Bagautdinova
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, 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), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, USA
| | - Michael J. Arcaro
- Department of Psychology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Deanna M. Barch
- Department of Psychiatry, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
- Department of Psychological & Brain Sciences, Washington University in St Louis, St Louis, Missouri, USA
| | - Dani S. Bassett
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Electrical & Systems Engineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physics & Astronomy, University of Pennsylvania, Philadelphia, PA, USA
- The Santa Fe Institute, Santa Fe, NM, USA
| | - Aaron F. Alexander-Bloch
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Lifespan Brain Institute (LiBI), Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Philip A. Cook
- Penn Image Computing and Science Lab (PICSL), Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Sydney Covitz
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Stanford, CA, USA
| | - Alexandre R. Franco
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, USA
- Strategic Data Initiatives, Child Mind Institute, New York, NY, USA
- Department of Psychiatry, NYU Grossman School of Medicine, New York, NY, USA
| | - Raquel E. Gur
- Lifespan Brain Institute (LiBI), Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Neurodevelopment and Psychosis Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ruben C. Gur
- Lifespan Brain Institute (LiBI), Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Brain Behavior Laboratory, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Allyson P. Mackey
- Department of Psychology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Kahini Mehta
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Steven L. Meisler
- Program in Speech and Hearing Bioscience and Technology, Harvard University, Division of Medical Sciences, Cambridge, MA, USA
| | - Michael P. Milham
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, USA
- Center for the Developing Brain, Child Mind Institute, New York, NY, USA
| | - Tyler M. Moore
- Lifespan Brain Institute (LiBI), Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Brain Behavior Laboratory, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eli J. Müller
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - David R. Roalf
- Lifespan Brain Institute (LiBI), Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Brain Behavior Laboratory, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Taylor Salo
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, 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
- Lifespan Brain Institute (LiBI), Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Russell T. Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, & Informatics, Philadelphia, PA, USA
- Center for Biomedical Image Computing and Analytics, Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - James M. Shine
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Fang-Cheng Yeh
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew Cieslak
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Lifespan Brain Institute (LiBI), Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - Theodore D. Satterthwaite
- Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Lifespan Brain Institute (LiBI), Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Center for Biomedical Image Computing and Analytics, Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
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10
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Tetereva A, Pat N. Brain age has limited utility as a biomarker for capturing fluid cognition in older individuals. eLife 2024; 12:RP87297. [PMID: 38869938 PMCID: PMC11175613 DOI: 10.7554/elife.87297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024] Open
Abstract
One well-known biomarker candidate that supposedly helps capture fluid cognition is Brain Age, or a predicted value based on machine-learning models built to predict chronological age from brain MRI. To formally evaluate the utility of Brain Age for capturing fluid cognition, we built 26 age-prediction models for Brain Age based on different combinations of MRI modalities, using the Human Connectome Project in Aging (n=504, 36-100 years old). First, based on commonality analyses, we found a large overlap between Brain Age and chronological age: Brain Age could uniquely add only around 1.6% in explaining variation in fluid cognition over and above chronological age. Second, the age-prediction models that performed better at predicting chronological age did NOT necessarily create better Brain Age for capturing fluid cognition over and above chronological age. Instead, better-performing age-prediction models created Brain Age that overlapped larger with chronological age, up to around 29% out of 32%, in explaining fluid cognition. Third, Brain Age missed around 11% of the total variation in fluid cognition that could have been explained by the brain variation. That is, directly predicting fluid cognition from brain MRI data (instead of relying on Brain Age and chronological age) could lead to around a 1/3-time improvement of the total variation explained. Accordingly, we demonstrated the limited utility of Brain Age as a biomarker for fluid cognition and made some suggestions to ensure the utility of Brain Age in explaining fluid cognition and other phenotypes of interest.
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Affiliation(s)
- Alina Tetereva
- Department of Psychology, University of OtagoDunedinNew Zealand
| | - Narun Pat
- Department of Psychology, University of OtagoDunedinNew Zealand
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11
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Luppi AI, Gellersen HM, Liu ZQ, Peattie ARD, Manktelow AE, Adapa R, Owen AM, Naci L, Menon DK, Dimitriadis SI, Stamatakis EA. Systematic evaluation of fMRI data-processing pipelines for consistent functional connectomics. Nat Commun 2024; 15:4745. [PMID: 38834553 PMCID: PMC11150439 DOI: 10.1038/s41467-024-48781-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 05/10/2024] [Indexed: 06/06/2024] Open
Abstract
Functional interactions between brain regions can be viewed as a network, enabling neuroscientists to investigate brain function through network science. Here, we systematically evaluate 768 data-processing pipelines for network reconstruction from resting-state functional MRI, evaluating the effect of brain parcellation, connectivity definition, and global signal regression. Our criteria seek pipelines that minimise motion confounds and spurious test-retest discrepancies of network topology, while being sensitive to both inter-subject differences and experimental effects of interest. We reveal vast and systematic variability across pipelines' suitability for functional connectomics. Inappropriate choice of data-processing pipeline can produce results that are not only misleading, but systematically so, with the majority of pipelines failing at least one criterion. However, a set of optimal pipelines consistently satisfy all criteria across different datasets, spanning minutes, weeks, and months. We provide a full breakdown of each pipeline's performance across criteria and datasets, to inform future best practices in functional connectomics.
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Affiliation(s)
- Andrea I Luppi
- Division of Anaesthesia, University of Cambridge, Cambridge, UK.
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.
- St John's College, University of Cambridge, Cambridge, UK.
- Montreal Neurological Institute, McGill University, Montreal, Canada.
| | - Helena M Gellersen
- German Center for Neurodegenerative Diseases, Magdeburg, Germany
- Department of Psychology, University of Cambridge, Cambridge, UK
| | - Zhen-Qi Liu
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Alexander R D Peattie
- Division of Anaesthesia, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Anne E Manktelow
- Division of Anaesthesia, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Ram Adapa
- Division of Anaesthesia, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Adrian M Owen
- Department of Psychology, Western Institute for Neuroscience (WIN), Western University, London, ON, Canada
- Department of Physiology and Pharmacology, Western Institute for Neuroscience (WIN), Western University, London, ON, Canada
| | - Lorina Naci
- Trinity College Institute of Neuroscience, School of Psychology, Trinity College Dublin, Dublin, Ireland
| | - David K Menon
- Division of Anaesthesia, University of Cambridge, Cambridge, UK
| | - Stavros I Dimitriadis
- Department of Clinical Psychology and Psychobiology, University of Barcelona, Barcelona, Spain
- Institut de Neurociències, University of Barcelona, Barcelona, Spain
- Neuroinformatics Group, Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, College of Biomedical and Life Sciences, Cardiff, Wales, UK
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Cardiff, Wales, UK
- Neuroscience and Mental Health Research Institute, School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Cardiff, Wales, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Cardiff, Wales, UK
- Integrative Neuroimaging Lab, Thessaloniki, Greece
| | - Emmanuel A Stamatakis
- Division of Anaesthesia, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
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12
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Weinstein SM, Vandekar SN, Li B, 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. Hum Brain Mapp 2024; 45:e26714. [PMID: 38878300 PMCID: PMC11179683 DOI: 10.1002/hbm.26714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 04/08/2024] [Accepted: 05/04/2024] [Indexed: 06/19/2024] Open
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 spatial properties 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 genetics 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 enrichment of 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 BiostatisticsTemple University College of Public HealthPhiladelphiaPennsylvaniaUSA
| | - Simon N. Vandekar
- Department of BiostatisticsVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Bin Li
- Department of Computer and Information SciencesTemple University College of Science and TechnologyPhiladelphiaPennsylvaniaUSA
| | - Aaron F. Alexander‐Bloch
- Department of PsychiatryUniversity of Pennsylvania, Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
- Department of Child and Adolescent Psychiatry and Behavioral ScienceChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | - Armin Raznahan
- Section on Developmental NeurogenomicsNational Institute of Mental Health Intramural Research ProgramBethesdaMarylandUSA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology, and InformaticsUniversity of Pennsylvania, Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
| | - Raquel E. Gur
- Department of PsychiatryUniversity of Pennsylvania, Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
| | - Ruben C. Gur
- Department of PsychiatryUniversity of Pennsylvania, Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
| | - David R. Roalf
- Department of PsychiatryUniversity of Pennsylvania, Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
| | - Min Tae M. Park
- Department of Psychiatry, Temerty Faculty of MedicineUniversity of TorontoTorontoOntarioCanada
- Integrated Program in NeuroscienceMcGill UniversityQCCanada
| | - Mallar Chakravarty
- Department of PsychiatryMcGill UniversityQCCanada
- Cerebral Imaging Centre, Douglas Research Centre, McGill UniversityQCCanada
| | - Erica B. Baller
- Department of PsychiatryUniversity of Pennsylvania, Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
| | - Kristin A. Linn
- Department of Biostatistics, Epidemiology, and InformaticsUniversity of Pennsylvania, Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
| | - Theodore D. Satterthwaite
- Department of PsychiatryUniversity of Pennsylvania, Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
| | - Russell T. Shinohara
- Department of Biostatistics, Epidemiology, and InformaticsUniversity of Pennsylvania, Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
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13
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Fattal J, Giljen M, Vargas T, Damme KSF, Calkins ME, Pinkham AE, Mittal VA. A Developmental Perspective on Early and Current Motor Abnormalities and Psychotic-Like Symptoms. Schizophr Bull 2024:sbae062. [PMID: 38728386 DOI: 10.1093/schbul/sbae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
BACKGROUND AND HYPOTHESIS Psychotic-like experiences (PLEs) are prevalent in the general population and, because they represent a lower end of the psychosis vulnerability spectrum, may be useful in informing mechanistic understanding. Although it is well-understood that motor signs characterize formal psychotic disorders, the developmental trajectory of these features and their relationships with PLEs are less well-understood. STUDY DESIGN Data from 7559 adolescents and young adults (age 11-21) in the Philadelphia Neurodevelopmental Cohort were used to investigate whether early-life milestone-attainment delays relate to current adolescent sensorimotor functioning and positive and negative PLEs. Current sensorimotor functioning was assessed using the Computerized Finger Tapping task (assessing motor slowing) and Mouse Practice task (assessing sensorimotor planning). STUDY RESULTS Early developmental abnormalities were related to current adolescent-aged motor slowing (t(7415.3) = -7.74, corrected-P < .001) and impaired sensorimotor planning (t(7502.5) = 5.57, corrected-P < .001). There was a significant interaction between developmental delays and current sensorimotor functioning on positive and negative PLEs (t = 1.67-4.51), such that individuals with early developmental delays had a stronger positive relationship between sensorimotor dysfunction and PLEs. Importantly, interaction models were significantly better at explaining current PLEs than those treating early and current sensorimotor dysfunction independently (χ2 = 4.89-20.34). CONCLUSIONS These findings suggest a relationship between early developmental delays and current sensorimotor functioning in psychosis proneness and inform an understanding of heterotypic continuity as well as a neurodevelopmental perspective of motor circuits. Furthermore, results indicate that motor signs are a clear factor in the psychosis continuum, suggesting that they may represent a core feature of psychosis vulnerability.
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Affiliation(s)
- Jessica Fattal
- Department of Psychology, Northwestern University, Evanston, IL, USA
| | - Maksim Giljen
- Department of Psychological Science, University of California, Irvine, Irvine, CA, USA
| | - Teresa Vargas
- Department of Psychology, Harvard University, Cambridge, MA, USA
| | | | - Monica E Calkins
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amy E Pinkham
- Department of Psychology, University of Texas at Dallas, Richardson, TX, USA
| | - Vijay A Mittal
- Department of Psychology, Northwestern University, Evanston, IL, USA
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14
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Dafflon J, Moraczewski D, Earl E, Nielson DM, Loewinger G, McClure P, Thomas AG, Pereira F. Reliability and predictability of phenotype information from functional connectivity in large imaging datasets. ARXIV 2024:arXiv:2405.00255v1. [PMID: 38745697 PMCID: PMC11092871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
One of the central objectives of contemporary neuroimaging research is to create predictive models that can disentangle the connection between patterns of functional connectivity across the entire brain and various behavioral traits. Previous studies have shown that models trained to predict behavioral features from the individual's functional connectivity have modest to poor performance. In this study, we trained models that predict observable individual traits (phenotypes) and their corresponding singular value decomposition (SVD) representations - herein referred to as latent phenotypes from resting state functional connectivity. For this task, we predicted phenotypes in two large neuroimaging datasets: the Human Connectome Project (HCP) and the Philadelphia Neurodevelopmental Cohort (PNC). We illustrate the importance of regressing out confounds, which could significantly influence phenotype prediction. Our findings reveal that both phenotypes and their corresponding latent phenotypes yield similar predictive performance. Interestingly, only the first five latent phenotypes were reliably identified, and using just these reliable phenotypes for predicting phenotypes yielded a similar performance to using all latent phenotypes. This suggests that the predictable information is present in the first latent phenotypes, allowing the remainder to be filtered out without any harm in performance. This study sheds light on the intricate relationship between functional connectivity and the predictability and reliability of phenotypic information, with potential implications for enhancing predictive modeling in the realm of neuroimaging research.
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Affiliation(s)
- Jessica Dafflon
- Data Science & Sharing Team, National Institute of Mental Health, Bethesda, MD, USA
- Machine Learning Team, National Institute of Mental Health, Bethesda, MD, USA
| | - Dustin Moraczewski
- Data Science & Sharing Team, National Institute of Mental Health, Bethesda, MD, USA
| | - Eric Earl
- Data Science & Sharing Team, National Institute of Mental Health, Bethesda, MD, USA
| | - Dylan M Nielson
- Machine Learning Team, National Institute of Mental Health, Bethesda, MD, USA
| | - Gabriel Loewinger
- Machine Learning Team, National Institute of Mental Health, Bethesda, MD, USA
| | | | - Adam G Thomas
- Data Science & Sharing Team, National Institute of Mental Health, Bethesda, MD, USA
| | - Francisco Pereira
- Machine Learning Team, National Institute of Mental Health, Bethesda, MD, USA
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15
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Qu G, Orlichenko A, Wang J, Zhang G, Xiao L, Zhang K, Wilson TW, Stephen JM, Calhoun VD, Wang YP. Interpretable Cognitive Ability Prediction: A Comprehensive Gated Graph Transformer Framework for Analyzing Functional Brain Networks. IEEE TRANSACTIONS ON MEDICAL IMAGING 2024; 43:1568-1578. [PMID: 38109241 PMCID: PMC11090410 DOI: 10.1109/tmi.2023.3343365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Graph convolutional deep learning has emerged as a promising method to explore the functional organization of the human brain in neuroscience research. This paper presents a novel framework that utilizes the gated graph transformer (GGT) model to predict individuals' cognitive ability based on functional connectivity (FC) derived from fMRI. Our framework incorporates prior spatial knowledge and uses a random-walk diffusion strategy that captures the intricate structural and functional relationships between different brain regions. Specifically, our approach employs learnable structural and positional encodings (LSPE) in conjunction with a gating mechanism to efficiently disentangle the learning of positional encoding (PE) and graph embeddings. Additionally, we utilize the attention mechanism to derive multi-view node feature embeddings and dynamically distribute propagation weights between each node and its neighbors, which facilitates the identification of significant biomarkers from functional brain networks and thus enhances the interpretability of the findings. To evaluate our proposed model in cognitive ability prediction, we conduct experiments on two large-scale brain imaging datasets: the Philadelphia Neurodevelopmental Cohort (PNC) and the Human Connectome Project (HCP). The results show that our approach not only outperforms existing methods in prediction accuracy but also provides superior explainability, which can be used to identify important FCs underlying cognitive behaviors.
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16
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Gottschewsky N, Kraft D, Kaufmann T. Menarche, pubertal timing and the brain: female-specific patterns of brain maturation beyond age-related development. Biol Sex Differ 2024; 15:25. [PMID: 38532493 DOI: 10.1186/s13293-024-00604-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Puberty depicts a period of profound and multifactorial changes ranging from social to biological factors. While brain development in youths has been studied mostly from an age perspective, recent evidence suggests that pubertal measures may be more sensitive to study adolescent neurodevelopment, however, studies on pubertal timing in relation to brain development are still scarce. METHODS We investigated if pre- vs. post-menarche status can be classified using machine learning on cortical and subcortical structural magnetic resonance imaging (MRI) data from strictly age-matched adolescent females from the Adolescent Brain Cognitive Development (ABCD) cohort. For comparison of the identified menarche-related patterns to age-related patterns of neurodevelopment, we trained a brain age prediction model on data from the Philadelphia Neurodevelopmental Cohort and applied it to the same ABCD data, yielding differences between predicted and chronological age referred to as brain age gaps. We tested the sensitivity of both these frameworks to measures of pubertal maturation, specifically age at menarche and puberty status. RESULTS The machine learning model achieved moderate but statistically significant accuracy in the menarche classification task, yielding for each subject a class probability ranging from 0 (pre-) to 1 (post- menarche). Comparison to brain age predictions revealed shared and distinct patterns of neurodevelopment captured by both approaches. Continuous menarche class probabilities were positively associated with brain age gaps, but only the menarche class probabilities-not the brain age gaps-were associated with age at menarche. CONCLUSIONS This study demonstrates the use of a machine learning model to classify menarche status from structural MRI data while accounting for age-related neurodevelopment. Given its sensitivity towards measures of puberty timing, our work suggests that menarche class probabilities may be developed toward an objective brain-based marker of pubertal development.
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Affiliation(s)
- Nina Gottschewsky
- Department of Psychiatry and Psychotherapy, Tübingen Center for Mental Health, University of Tübingen, Tübingen, Germany.
- Max Planck School of Cognition, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.
| | - Dominik Kraft
- Department of Psychiatry and Psychotherapy, Tübingen Center for Mental Health, University of Tübingen, Tübingen, Germany
| | - Tobias Kaufmann
- Department of Psychiatry and Psychotherapy, Tübingen Center for Mental Health, University of Tübingen, Tübingen, Germany.
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- German Center for Mental Health (DZPG), Partner Site Tübingen, Tübingen, Germany.
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Hyde LW, Bezek JL, Michael C. The future of neuroscience in developmental psychopathology. Dev Psychopathol 2024:1-16. [PMID: 38444150 DOI: 10.1017/s0954579424000233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Developmental psychopathology started as an intersection of fields and is now a field itself. As we contemplate the future of this field, we consider the ways in which a newer, interdisciplinary field - human developmental neuroscience - can inform, and be informed by, developmental psychopathology. To do so, we outline principles of developmental psychopathology and how they are and/or can be implemented in developmental neuroscience. In turn, we highlight how the collaboration between these fields can lead to richer models and more impactful translation. In doing so, we describe the ways in which models from developmental psychopathology can enrich developmental neuroscience and future directions for developmental psychopathology.
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Affiliation(s)
- Luke W Hyde
- Department of Psychology, Survey Research Center at the Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Jessica L Bezek
- Department of Psychology, University of Michigan, Ann Arbor, MI, USA
| | - Cleanthis Michael
- Department of Psychology, University of Michigan, Ann Arbor, MI, USA
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18
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Dickie EW, Ameis SH, Boileau I, Diaconescu AO, Felsky D, Goldstein BI, Gonçalves V, Griffiths JD, Haltigan JD, Husain MO, Rubin-Kahana DS, Iftikhar M, Jani M, Lai MC, Lin HY, MacIntosh BJ, Wheeler AL, Vasdev N, Vieira E, Ahmadzadeh G, Heyland L, Mohan A, Ogunsanya F, Oliver LD, Zhu C, Wong JKY, Charlton C, Truong J, Yu L, Kelly R, Cleverley K, Courtney DB, Foussias G, Hawke LD, Hill S, Kozloff N, Polillo A, Rotenberg M, Quilty LC, Tempelaar W, Wang W, Nikolova YS, Voineskos AN. Neuroimaging and Biosample Collection in the Toronto Adolescent and Youth Cohort Study: Rationale, Methods, and Early Data. BIOLOGICAL PSYCHIATRY. COGNITIVE NEUROSCIENCE AND NEUROIMAGING 2024; 9:275-284. [PMID: 37979944 DOI: 10.1016/j.bpsc.2023.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 11/20/2023]
Abstract
BACKGROUND The Toronto Adolescent and Youth (TAY) Cohort Study will characterize the neurobiological trajectories of psychosis spectrum symptoms, functioning, and suicidality (i.e., suicidal thoughts and behaviors) in youth seeking mental health care. Here, we present the neuroimaging and biosample component of the protocol. We also present feasibility and quality control metrics for the baseline sample collected thus far. METHODS The current study includes youths (ages 11-24 years) who were referred to child and youth mental health services within a large tertiary care center in Toronto, Ontario, Canada, with target recruitment of 1500 participants. Participants were offered the opportunity to provide any or all of the following: 1) 1-hour magnetic resonance imaging (MRI) scan (electroencephalography if ineligible for or declined MRI), 2) blood sample for genomic and proteomic data (or saliva if blood collection was declined or not feasible) and urine sample, and 3) heart rate recording to assess respiratory sinus arrhythmia. RESULTS Of the first 417 participants who consented to participate between May 4, 2021, and February 2, 2023, 412 agreed to participate in the imaging and biosample protocol. Of these, 334 completed imaging, 341 provided a biosample, 338 completed respiratory sinus arrhythmia, and 316 completed all 3. Following quality control, data usability was high (MRI: T1-weighted 99%, diffusion-weighted imaging 99%, arterial spin labeling 90%, resting-state functional MRI 95%, task functional MRI 90%; electroencephalography: 83%; respiratory sinus arrhythmia: 99%). CONCLUSIONS The high consent rates, good completion rates, and high data usability reported here demonstrate the feasibility of collecting and using brain imaging and biosamples in a large clinical cohort of youths seeking mental health care.
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Affiliation(s)
- Erin W Dickie
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie H Ameis
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Isabelle Boileau
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Andreea O Diaconescu
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Daniel Felsky
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin I Goldstein
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Vanessa Gonçalves
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - John D Griffiths
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - John D Haltigan
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Muhammad O Husain
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Dafna S Rubin-Kahana
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Myera Iftikhar
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Melanie Jani
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Meng-Chuan Lai
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom; National Taiwan University Hospital and College of Medicine, Taiwan
| | - Hsiang-Yuan Lin
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Bradley J MacIntosh
- Sunnybrook Research Institute, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Oslo University Hospital, Oslo, Norway
| | - Anne L Wheeler
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Hospital for Sick Children, Neurosciences and Mental Health, Toronto, Ontario, Canada; Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Neil Vasdev
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Erica Vieira
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ghazaleh Ahmadzadeh
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Lindsay Heyland
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Acadia University, Wolfville, Nova Scotia, Canada
| | - Akshay Mohan
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Feyi Ogunsanya
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychology, Western University, London, Ontario, Canada
| | - Lindsay D Oliver
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Cherrie Zhu
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute at Sinai Health, Toronto, Ontario, Canada
| | - Jimmy K Y Wong
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Colleen Charlton
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Jennifer Truong
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Lujia Yu
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Rachel Kelly
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Kristin Cleverley
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Darren B Courtney
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - George Foussias
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lisa D Hawke
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Sean Hill
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Nicole Kozloff
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Alexia Polillo
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Martin Rotenberg
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lena C Quilty
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Wanda Tempelaar
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Wei Wang
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Yuliya S Nikolova
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Aristotle N Voineskos
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
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Rosenblatt M, Tejavibulya L, Jiang R, Noble S, Scheinost D. Data leakage inflates prediction performance in connectome-based machine learning models. Nat Commun 2024; 15:1829. [PMID: 38418819 PMCID: PMC10901797 DOI: 10.1038/s41467-024-46150-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
Predictive modeling is a central technique in neuroimaging to identify brain-behavior relationships and test their generalizability to unseen data. However, data leakage undermines the validity of predictive models by breaching the separation between training and test data. Leakage is always an incorrect practice but still pervasive in machine learning. Understanding its effects on neuroimaging predictive models can inform how leakage affects existing literature. Here, we investigate the effects of five forms of leakage-involving feature selection, covariate correction, and dependence between subjects-on functional and structural connectome-based machine learning models across four datasets and three phenotypes. Leakage via feature selection and repeated subjects drastically inflates prediction performance, whereas other forms of leakage have minor effects. Furthermore, small datasets exacerbate the effects of leakage. Overall, our results illustrate the variable effects of leakage and underscore the importance of avoiding data leakage to improve the validity and reproducibility of predictive modeling.
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Affiliation(s)
- Matthew Rosenblatt
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
| | - Link Tejavibulya
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT, USA
| | - Rongtao Jiang
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - Stephanie Noble
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Psychology, Northeastern University, Boston, MA, USA
| | - Dustin Scheinost
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT, USA
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
- Child Study Center, Yale School of Medicine, New Haven, CT, USA
- Department of Statistics & Data Science, Yale University, New Haven, CT, USA
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20
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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21
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Adkinson BD, Rosenblatt M, Dadashkarimi J, Tejavibulya L, Jiang R, Noble S, Scheinost D. Brain-phenotype predictions can survive across diverse real-world data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576916. [PMID: 38328100 PMCID: PMC10849571 DOI: 10.1101/2024.01.23.576916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Recent work suggests that machine learning models predicting psychiatric treatment outcomes based on clinical data may fail when applied to unharmonized samples. Neuroimaging predictive models offer the opportunity to incorporate neurobiological information, which may be more robust to dataset shifts. Yet, among the minority of neuroimaging studies that undertake any form of external validation, there is a notable lack of attention to generalization across dataset-specific idiosyncrasies. Research settings, by design, remove the between-site variations that real-world and, eventually, clinical applications demand. Here, we rigorously test the ability of a range of predictive models to generalize across three diverse, unharmonized samples: the Philadelphia Neurodevelopmental Cohort (n=1291), the Healthy Brain Network (n=1110), and the Human Connectome Project in Development (n=428). These datasets have high inter-dataset heterogeneity, encompassing substantial variations in age distribution, sex, racial and ethnic minority representation, recruitment geography, clinical symptom burdens, fMRI tasks, sequences, and behavioral measures. We demonstrate that reproducible and generalizable brain-behavior associations can be realized across diverse dataset features with sample sizes in the hundreds. Results indicate the potential of functional connectivity-based predictive models to be robust despite substantial inter-dataset variability. Notably, for the HCPD and HBN datasets, the best predictions were not from training and testing in the same dataset (i.e., cross-validation) but across datasets. This result suggests that training on diverse data may improve prediction in specific cases. Overall, this work provides a critical foundation for future work evaluating the generalizability of neuroimaging predictive models in real-world scenarios and clinical settings.
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Affiliation(s)
- Brendan D Adkinson
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Matthew Rosenblatt
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA
| | - Javid Dadashkarimi
- Department of Radiology, Athinoula. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, 02129, USA
- Department of Radiology, Harvard Medical School, Boston, MA, 02129, USA
| | - Link Tejavibulya
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Rongtao Jiang
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Stephanie Noble
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT, 06510, USA
- Department of Bioengineering, Northeastern University, Boston, MA, 02120, USA
- Department of Psychology, Northeastern University, Boston, MA, 02115, USA
| | - Dustin Scheinost
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT, 06510, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT, 06510, USA
- Department of Statistics & Data Science, Yale University, New Haven, CT, 06520, USA
- Child Study Center, Yale School of Medicine, New Haven, CT, 06510, USA
- Wu Tsai Institute, Yale University, New Haven, CT, 06510, USA
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22
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Parikh K, Quintero Reis A, Wendt FR. Association between suicidal ideation and tandem repeats in contactins. Front Psychiatry 2024; 14:1236540. [PMID: 38239902 PMCID: PMC10794671 DOI: 10.3389/fpsyt.2023.1236540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/13/2023] [Indexed: 01/22/2024] Open
Abstract
Background Death by suicide is one of the leading causes of death among adolescents. Genome-wide association studies (GWAS) have identified loci that associate with suicidal ideation and related behaviours. One such group of loci are the six contactin genes (CNTN1-6) that are critical to neurodevelopment through regulating neurite structure. Because single nucleotide polymorphisms (SNPs) detected by GWAS often map to non-coding intergenic regions, we investigated whether repetitive variants in CNTNs associated with suicidality in a young cohort aged 8 to 21. Understanding the genetic liability of suicidal thought and behavior in this age group will promote early intervention and treatment. Methods Genotypic and phenotypic data were obtained from the Philadelphia Neurodevelopment Cohort (PNC). Across six CNTNs, 232 short tandem repeats (STRs) were analyzed in up to 4,595 individuals of European ancestry who expressed current, previous, or no suicidal ideation. STRs were imputed into SNP arrays using a phased SNP-STR haplotype reference panel from the 1000 Genomes Project. We tested several additive and interactive models of locus-level burden (i.e., sum of STR alleles) with respect to suicidal ideation. Additive models included sex, birth year, developmental stage ("DevStage"), and the first 10 principal components of ancestry as covariates; interactive models assessed the effect of STR-by-DevStage considering all other covariates. Results CNTN1-[T]N interacted with DevStage to increase risk for current suicidal ideation (CNTN1-[T]N-by-DevStage; p = 0.00035). Compared to the youngest age group, the middle (OR = 1.80, p = 0.0514) and oldest (OR = 3.82, p = 0.0002) participant groups had significantly higher odds of suicidal ideation as their STR length expanded; this result was independent of polygenic scores for suicidal ideation. Discussion These findings highlight diversity in the genetic effects (i.e., SNP and STR) acting on suicidal thoughts and behavior and advance our understanding of suicidal ideation across childhood and adolescence.
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Affiliation(s)
- Kairavi Parikh
- Forensic Science Program, University of Toronto, Mississauga, ON, Canada
| | - Andrea Quintero Reis
- Forensic Science Program, University of Toronto, Mississauga, ON, Canada
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Department of Anthropology, University of Toronto, Mississauga, ON, Canada
| | - Frank R. Wendt
- Forensic Science Program, University of Toronto, Mississauga, ON, Canada
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Department of Anthropology, University of Toronto, Mississauga, ON, Canada
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23
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Caspi A, Houts RM, Fisher HL, Danese A, Moffitt TE. The general factor of psychopathology (p): Choosing among competing models and interpreting p. Clin Psychol Sci 2024; 12:53-82. [PMID: 38236494 PMCID: PMC10794018 DOI: 10.1177/21677026221147872] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 12/04/2022] [Indexed: 01/19/2024]
Abstract
Over the past 10 years, the general factor of psychopathology, p, has attracted interest and scrutiny. We review the history of the idea that all mental disorders share something in common, p; how we arrived at this idea; and how it became conflated with a statistical representation, the Bi-Factor Model. We then leverage the Environmental Risk (E-Risk) longitudinal twin study to examine the properties and nomological network of different statistical representations of p. We find that p performed similarly regardless of how it was modelled, suggesting that if the sample and content are the same the resulting p factor will be similar. We suggest that the meaning of p is not to be found by dueling over statistical models but by conducting well-specified criterion-validation studies and developing new measurement approaches. We outline new directions to refresh research efforts to uncover what all mental disorders have in common.
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Affiliation(s)
- Avshalom Caspi
- Department of Psychology & Neuroscience, Duke University
- PROMENTA, Department of Psychology, University of Oslo
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology, & Neuroscience, King’s College London
| | | | - Helen L. Fisher
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology, & Neuroscience, King’s College London
- ESRC Centre for Society and Mental Health, Kings’ College London
| | - Andrea Danese
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology, & Neuroscience, King’s College London
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology, & Neuroscience, King’s College London
- National and Specialist CAMHS Clinic for Trauma, Anxiety, and Depression, South London and Maudsley NHS Foundation Trust, London, United Kingdom
| | - Terrie E. Moffitt
- Department of Psychology & Neuroscience, Duke University
- PROMENTA, Department of Psychology, University of Oslo
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology, & Neuroscience, King’s College London
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Rosenblatt M, Tejavibulya L, Jiang R, Noble S, Scheinost D. The effects of data leakage on connectome-based machine learning models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544383. [PMID: 38234740 PMCID: PMC10793416 DOI: 10.1101/2023.06.09.544383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Predictive modeling has now become a central technique in neuroimaging to identify complex brain-behavior relationships and test their generalizability to unseen data. However, data leakage, which unintentionally breaches the separation between data used to train and test the model, undermines the validity of predictive models. Previous literature suggests that leakage is generally pervasive in machine learning, but few studies have empirically evaluated the effects of leakage in neuroimaging data. Although leakage is always an incorrect practice, understanding the effects of leakage on neuroimaging predictive models provides insight into the extent to which leakage may affect the literature. Here, we investigated the effects of leakage on machine learning models in two common neuroimaging modalities, functional and structural connectomes. Using over 400 different pipelines spanning four large datasets and three phenotypes, we evaluated five forms of leakage fitting into three broad categories: feature selection, covariate correction, and lack of independence between subjects. As expected, leakage via feature selection and repeated subjects drastically inflated prediction performance. Notably, other forms of leakage had only minor effects (e.g., leaky site correction) or even decreased prediction performance (e.g., leaky covariate regression). In some cases, leakage affected not only prediction performance, but also model coefficients, and thus neurobiological interpretations. Finally, we found that predictive models using small datasets were more sensitive to leakage. Overall, our results illustrate the variable effects of leakage on prediction pipelines and underscore the importance of avoiding data leakage to improve the validity and reproducibility of predictive modeling.
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Affiliation(s)
| | - Link Tejavibulya
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT
| | - Rongtao Jiang
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT
| | - Stephanie Noble
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT
- Department of Bioengineering, Northeastern University, Boston, MA
- Department of Psychology, Northeastern University, Boston, MA
| | - Dustin Scheinost
- Department of Biomedical Engineering, Yale University, New Haven, CT
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT
- Child Study Center, Yale School of Medicine, New Haven, CT
- Department of Statistics & Data Science, Yale University, New Haven, CT
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25
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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] [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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26
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Hoy N, Lynch SJ, Waszczuk MA, Reppermund S, Mewton L. Transdiagnostic biomarkers of mental illness across the lifespan: A systematic review examining the genetic and neural correlates of latent transdiagnostic dimensions of psychopathology in the general population. Neurosci Biobehav Rev 2023; 155:105431. [PMID: 37898444 DOI: 10.1016/j.neubiorev.2023.105431] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/26/2023] [Accepted: 10/21/2023] [Indexed: 10/30/2023]
Abstract
This systematic review synthesizes evidence from research investigating the biological correlates of latent transdiagnostic dimensions of psychopathology (e.g., the p-factor, internalizing, externalizing) across the lifespan. Eligibility criteria captured genomic and neuroimaging studies investigating general and/or specific dimensions in general population samples across all age groups. MEDLINE, Embase, and PsycINFO were searched for relevant studies published up to March 2023 and 46 studies were selected for inclusion. The results revealed several biological correlates consistently associated with transdiagnostic dimensions of psychopathology, including polygenic scores for ADHD and neuroticism, global surface area and global gray matter volume. Shared and unique associations between symptom dimensions are highlighted, as are potential age-specific differences in biological associations. Findings are interpreted with reference to key methodological differences across studies. The included studies provide compelling evidence that the general dimension of psychopathology reflects common underlying genetic and neurobiological vulnerabilities that are shared across diverse manifestations of mental illness. Substantive interpretations of general psychopathology in the context of genetic and neurobiological evidence are discussed.
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Affiliation(s)
- Nicholas Hoy
- The Matilda Centre for Research in Mental Health and Substance Use, University of Sydney, Sydney, Australia; Centre for Healthy Brain Ageing, University of New South Wales, Sydney, Australia.
| | - Samantha J Lynch
- The Matilda Centre for Research in Mental Health and Substance Use, University of Sydney, Sydney, Australia; Department of Psychiatry, Université de Montréal, Montreal, Canada; Research Centre, CHU Sainte-Justine, Montreal, Canada
| | - Monika A Waszczuk
- Department of Psychology, Rosalind Franklin University of Medicine and Science, North Chicago, United States
| | - Simone Reppermund
- Centre for Healthy Brain Ageing, University of New South Wales, Sydney, Australia; Department of Developmental Disability Neuropsychiatry, University of New South Wales, Sydney, Australia
| | - Louise Mewton
- The Matilda Centre for Research in Mental Health and Substance Use, University of Sydney, Sydney, Australia
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27
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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28
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Rosenblatt M, Tejavibulya L, Camp CC, Jiang R, Westwater ML, Noble S, Scheinost D. Power and reproducibility in the external validation of brain-phenotype predictions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.563971. [PMID: 37961654 PMCID: PMC10634903 DOI: 10.1101/2023.10.25.563971] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Identifying reproducible and generalizable brain-phenotype associations is a central goal of neuroimaging. Consistent with this goal, prediction frameworks evaluate brain-phenotype models in unseen data. Most prediction studies train and evaluate a model in the same dataset. However, external validation, or the evaluation of a model in an external dataset, provides a better assessment of robustness and generalizability. Despite the promise of external validation and calls for its usage, the statistical power of such studies has yet to be investigated. In this work, we ran over 60 million simulations across several datasets, phenotypes, and sample sizes to better understand how the sizes of the training and external datasets affect statistical power. We found that prior external validation studies used sample sizes prone to low power, which may lead to false negatives and effect size inflation. Furthermore, increases in the external sample size led to increased simulated power directly following theoretical power curves, whereas changes in the training dataset size offset the simulated power curves. Finally, we compared the performance of a model within a dataset to the external performance. The within-dataset performance was typically within r=0.2 of the cross-dataset performance, which could help decide how to power future external validation studies. Overall, our results illustrate the importance of considering the sample sizes of both the training and external datasets when performing external validation.
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Affiliation(s)
| | - Link Tejavibulya
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT
| | - Chris C. Camp
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT
| | - Rongtao Jiang
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT
| | - Margaret L. Westwater
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT
| | - Stephanie Noble
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT
- Department of Bioengineering, Northeastern University, Boston, MA
- Department of Psychology, Northeastern University, Boston, MA
| | - Dustin Scheinost
- Department of Biomedical Engineering, Yale University, New Haven, CT
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT
- Child Study Center, Yale School of Medicine, New Haven, CT
- Department of Statistics & Data Science, Yale University, New Haven, CT
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29
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Kraft D, Alnæs D, Kaufmann T. Domain adapted brain network fusion captures variance related to pubertal brain development and mental health. Nat Commun 2023; 14:6698. [PMID: 37872174 PMCID: PMC10593774 DOI: 10.1038/s41467-023-41839-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 09/15/2023] [Indexed: 10/25/2023] Open
Abstract
Puberty demarks a period of profound brain dynamics that orchestrates changes to a multitude of neuroimaging-derived phenotypes. This complexity poses a dimensionality problem when attempting to chart an individual's brain development over time. Here, we illustrate that shifts in subject similarity of brain imaging data relate to pubertal maturation in the longitudinal ABCD study. Given that puberty depicts a critical window for emerging mental health issues, we additionally show that our model is capable of capturing variance in the adolescent brain related to psychopathology in a population-based and a clinical cohort. These results suggest that low-dimensional reference spaces based on subject similarities render useful to chart variance in brain development in youths.
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Affiliation(s)
- Dominik Kraft
- Department of Psychiatry and Psychotherapy, Tübingen Center for Mental Health, University of Tübingen, Tübingen, Germany.
| | - Dag Alnæs
- Norwegian Centre for Mental Disorders Research, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Tobias Kaufmann
- Department of Psychiatry and Psychotherapy, Tübingen Center for Mental Health, University of Tübingen, Tübingen, Germany.
- Norwegian Centre for Mental Disorders Research, University of Oslo and Oslo University Hospital, Oslo, Norway.
- German Center for Mental Health (DZPG), partner site Tübingen, Tübingen, Germany.
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30
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Zhu J, Margulies D, Qiu A. White matter functional gradients and their formation in adolescence. Cereb Cortex 2023; 33:10770-10783. [PMID: 37727985 DOI: 10.1093/cercor/bhad319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 09/21/2023] Open
Abstract
It is well known that functional magnetic resonance imaging (fMRI) is a widely used tool for studying brain activity. Recent research has shown that fluctuations in fMRI data can reflect functionally meaningful patterns of brain activity within the white matter. We leveraged resting-state fMRI from an adolescent population to characterize large-scale white matter functional gradients and their formation during adolescence. The white matter showed gray-matter-like unimodal-to-transmodal and sensorimotor-to-visual gradients with specific cognitive associations and a unique superficial-to-deep gradient with nonspecific cognitive associations. We propose two mechanisms for their formation in adolescence. One is a "function-molded" mechanism that may mediate the maturation of the transmodal white matter via the transmodal gray matter. The other is a "structure-root" mechanism that may support the mutual mediation roles of the unimodal and transmodal white matter maturation during adolescence. Thus, the spatial layout of the white matter functional gradients is in concert with the gray matter functional organization. The formation of the white matter functional gradients may be driven by brain anatomical wiring and functional needs.
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Affiliation(s)
- Jingwen Zhu
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore
| | - Daniel Margulies
- Integrative Neuroscience and Cognition Center, Centre National de la Recherche Scientifique (CNRS) and Université de Paris, 45 Rue des Saint-Pères, 75006 Paris, France
| | - Anqi Qiu
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore
- NUS (Suzhou) Research Institute, National University of Singapore, No. 377 Linquan Street, Suzhou 215000, China
- The N.1 Institute for Health, National University of Singapore, 28 Medical Dr, Singapore 117456, Singapore
- Institute of Data Science, National University of Singapore, 3 Research Link, #04-06, Singapore 117602, Singapore
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, 11 Yuk Choi Rd, Kowloon, Hong Kong
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, United States
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31
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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] [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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32
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Hoffmann MS, Moore TM, Axelrud LK, Tottenham N, Rohde LA, Milham MP, Satterthwaite TD, Salum GA. Harmonizing bifactor models of psychopathology between distinct assessment instruments: Reliability, measurement invariance, and authenticity. Int J Methods Psychiatr Res 2023; 32:e1959. [PMID: 36655616 PMCID: PMC10485343 DOI: 10.1002/mpr.1959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/16/2022] [Accepted: 12/30/2022] [Indexed: 01/20/2023] Open
Abstract
OBJECTIVES Model configuration is important for mental health data harmonization. We provide a method to investigate the performance of different bifactor model configurations to harmonize different instruments. METHODS We used data from six samples from the Reproducible Brain Charts initiative (N = 8,606, ages 5-22 years, 41.0% females). We harmonized items from two psychopathology instruments, Child Behavior Checklist (CBCL) and GOASSESS, based on semantic content. We estimated bifactor models using confirmatory factor analysis, and calculated their model fit, factor reliability, between-instrument invariance, and authenticity (i.e., the correlation and factor score difference between the harmonized and original models). RESULTS Five out of 12 model configurations presented acceptable fit and were instrument-invariant. Correlations between the harmonized factor scores and the original full-item models were high for the p-factor (>0.89) and small to moderate (0.12-0.81) for the specific factors. 6.3%-50.9% of participants presented factor score differences between harmonized and original models higher than 0.5 z-score. CONCLUSIONS The CBCL-GOASSESS harmonization indicates that few models provide reliable specific factors and are instrument-invariant. Moreover, authenticity was high for the p-factor and moderate for specific factors. Future studies can use this framework to examine the impact of harmonizing instruments in psychiatric research.
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Affiliation(s)
- Maurício Scopel Hoffmann
- Department of NeuropsychiatryUniversidade Federal de Santa MariaSanta MariaBrazil
- Graduate Program in Psychiatry and Behavioral SciencesUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
- Section on Negative Affect and Social ProcessesHospital de Clínicas de Porto AlegreUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
- Care Policy and Evaluation CentreLondon School of Economics and Political ScienceLondonUK
| | - Tyler Maxwell Moore
- Department of PsychiatryUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Luiza Kvitko Axelrud
- Graduate Program in Psychiatry and Behavioral SciencesUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
- Section on Negative Affect and Social ProcessesHospital de Clínicas de Porto AlegreUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
| | - Nim Tottenham
- Department of PsychologyColumbia UniversityNew YorkNew YorkUSA
| | - Luis Augusto Rohde
- Graduate Program in Psychiatry and Behavioral SciencesUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT‐CNPq)São PauloBrazil
- Department of Psychiatry and Legal MedicineUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
| | - Michael Peter Milham
- Nathan S. Kline Institute for Psychiatric ResearchOrangeburgNew YorkUSA
- Center for the Developing BrainChild Mind InstituteNew YorkNew YorkUSA
| | - Theodore Daniel Satterthwaite
- Department of PsychiatryUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Lifespan Informatics and Neuroimaging CenterPhiladelphiaPennsylvaniaUSA
| | - Giovanni Abrahão Salum
- Graduate Program in Psychiatry and Behavioral SciencesUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
- Section on Negative Affect and Social ProcessesHospital de Clínicas de Porto AlegreUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT‐CNPq)São PauloBrazil
- Department of Psychiatry and Legal MedicineUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
- Center for the Developing BrainChild Mind InstituteNew YorkNew YorkUSA
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Burstein D, Griffen TC, Therrien K, Bendl J, Venkatesh S, Dong P, Modabbernia A, Zeng B, Mathur D, Hoffman G, Sysko R, Hildebrandt T, Voloudakis G, Roussos P. Genome-wide analysis of a model-derived binge eating disorder phenotype identifies risk loci and implicates iron metabolism. Nat Genet 2023; 55:1462-1470. [PMID: 37550530 PMCID: PMC10947608 DOI: 10.1038/s41588-023-01464-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/29/2023] [Indexed: 08/09/2023]
Abstract
Binge eating disorder (BED) is the most common eating disorder, yet its genetic architecture remains largely unknown. Studying BED is challenging because it is often comorbid with obesity, a common and highly polygenic trait, and it is underdiagnosed in biobank data sets. To address this limitation, we apply a supervised machine-learning approach (using 822 cases of individuals diagnosed with BED) to estimate the probability of each individual having BED based on electronic medical records from the Million Veteran Program. We perform a genome-wide association study of individuals of African (n = 77,574) and European (n = 285,138) ancestry while controlling for body mass index to identify three independent loci near the HFE, MCHR2 and LRP11 genes and suggest APOE as a risk gene for BED. We identify shared heritability between BED and several neuropsychiatric traits, and implicate iron metabolism in the pathophysiology of BED. Overall, our findings provide insights into the genetics underlying BED and suggest directions for future translational research.
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Affiliation(s)
- David Burstein
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, New York, NY, USA
| | - Trevor C Griffen
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center of Excellence in Eating and Weight Disorders, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Karen Therrien
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, New York, NY, USA
| | - Jaroslav Bendl
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sanan Venkatesh
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, New York, NY, USA
| | - Pengfei Dong
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Biao Zeng
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Deepika Mathur
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gabriel Hoffman
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robyn Sysko
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center of Excellence in Eating and Weight Disorders, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tom Hildebrandt
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center of Excellence in Eating and Weight Disorders, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Georgios Voloudakis
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, New York, NY, USA.
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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He Q, Keding TJ, Zhang Q, Miao J, Russell JD, Herringa RJ, Lu Q, Travers BG, Li JJ. Neurogenetic mechanisms of risk for ADHD: Examining associations of polygenic scores and brain volumes in a population cohort. J Neurodev Disord 2023; 15:30. [PMID: 37653373 PMCID: PMC10469494 DOI: 10.1186/s11689-023-09498-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 08/21/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND ADHD polygenic scores (PGSs) have been previously shown to predict ADHD outcomes in several studies. However, ADHD PGSs are typically correlated with ADHD but not necessarily reflective of causal mechanisms. More research is needed to elucidate the neurobiological mechanisms underlying ADHD. We leveraged functional annotation information into an ADHD PGS to (1) improve the prediction performance over a non-annotated ADHD PGS and (2) test whether volumetric variation in brain regions putatively associated with ADHD mediate the association between PGSs and ADHD outcomes. METHODS Data were from the Philadelphia Neurodevelopmental Cohort (N = 555). Multiple mediation models were tested to examine the indirect effects of two ADHD PGSs-one using a traditional computation involving clumping and thresholding and another using a functionally annotated approach (i.e., AnnoPred)-on ADHD inattention (IA) and hyperactivity-impulsivity (HI) symptoms, via gray matter volumes in the cingulate gyrus, angular gyrus, caudate, dorsolateral prefrontal cortex (DLPFC), and inferior temporal lobe. RESULTS A direct effect was detected between the AnnoPred ADHD PGS and IA symptoms in adolescents. No indirect effects via brain volumes were detected for either IA or HI symptoms. However, both ADHD PGSs were negatively associated with the DLPFC. CONCLUSIONS The AnnoPred ADHD PGS was a more developmentally specific predictor of adolescent IA symptoms compared to the traditional ADHD PGS. However, brain volumes did not mediate the effects of either a traditional or AnnoPred ADHD PGS on ADHD symptoms, suggesting that we may still be underpowered in clarifying brain-based biomarkers for ADHD using genetic measures.
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Affiliation(s)
- Quanfa He
- Department of Psychology, University of, Wisconsin-Madison, 1202 W. Johnson Street, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, USA
| | | | - Qi Zhang
- Department of Educational Psychology, University of Wisconsin-Madison, Madison, USA
| | - Jiacheng Miao
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, USA
| | - Justin D Russell
- Department of Psychiatry, School of Medicine and Public Health, University of Wisconsin, Madison, USA
| | - Ryan J Herringa
- Department of Psychiatry, School of Medicine and Public Health, University of Wisconsin, Madison, USA
| | - Qiongshi Lu
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, USA
- Center for Demography of Health and Aging, University of Wisconsin-Madison, Madison, USA
- Department of Statistics, University of Wisconsin-Madison, Madison, USA
| | - Brittany G Travers
- Waisman Center, University of Wisconsin-Madison, Madison, USA
- Department of Kinesiology, University of Wisconsin-Madison, Madison, USA
| | - James J Li
- Department of Psychology, University of, Wisconsin-Madison, 1202 W. Johnson Street, Madison, WI, 53706, USA.
- Waisman Center, University of Wisconsin-Madison, Madison, USA.
- Center for Demography of Health and Aging, University of Wisconsin-Madison, Madison, USA.
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Andreou C, Eickhoff S, Heide M, de Bock R, Obleser J, Borgwardt S. Predictors of transition in patients with clinical high risk for psychosis: an umbrella review. Transl Psychiatry 2023; 13:286. [PMID: 37640731 PMCID: PMC10462748 DOI: 10.1038/s41398-023-02586-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023] Open
Abstract
Diagnosis of a clinical high-risk (CHR) state enables timely treatment of individuals at risk for a psychotic disorder, thereby contributing to improving illness outcomes. However, only a minority of patients diagnosed with CHR will make the transition to overt psychosis. To identify patients most likely to benefit from early intervention, several studies have investigated characteristics that distinguish CHR patients who will later develop a psychotic disorder from those who will not. We aimed to summarize evidence from systematic reviews and meta-analyses on predictors of transition to psychosis in CHR patients, among characteristics and biomarkers assessed at baseline. A systematic search was conducted in Pubmed, Scopus, PsychInfo and Cochrane databases to identify reviews and meta-analyses of studies that investigated specific baseline predictors or biomarkers for transition to psychosis in CHR patients using a cross-sectional or longitudinal design. Non-peer-reviewed publications, gray literature, narrative reviews and publications not written in English were excluded from analyses. We provide a narrative synthesis of results from all included reviews and meta-analyses. For each included publication, we indicate the number of studies cited in each domain and its quality rating. A total of 40 publications (21 systematic reviews and 19 meta-analyses) that reviewed a total of 272 original studies qualified for inclusion. Baseline predictors most consistently associated with later transition included clinical characteristics such as attenuated psychotic and negative symptoms and functioning, verbal memory deficits and the electrophysiological marker of mismatch negativity. Few predictors reached a level of evidence sufficient to inform clinical practice, reflecting generalizability issues in a field characterized by studies with small, heterogeneous samples and relatively few transition events. Sample pooling and harmonization of methods across sites and projects are necessary to overcome these limitations.
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Affiliation(s)
- Christina Andreou
- Translational Psychiatry, Department of Psychiatry and Psychotherapy, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
- Center of Brain, Behavior, and Metabolism (CBBM), University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Sofia Eickhoff
- Translational Psychiatry, Department of Psychiatry and Psychotherapy, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Marco Heide
- Translational Psychiatry, Department of Psychiatry and Psychotherapy, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Renate de Bock
- University Psychiatric Clinics Basel, Wilhelm Klein-Strasse 27, 4002, Basel, Switzerland
| | - Jonas Obleser
- Center of Brain, Behavior, and Metabolism (CBBM), University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
- Department of Psychology, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Stefan Borgwardt
- Translational Psychiatry, Department of Psychiatry and Psychotherapy, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.
- Center of Brain, Behavior, and Metabolism (CBBM), University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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Ray B, Chen J, Fu Z, Suresh P, Thapaliya B, Farahdel B, Calhoun VD, Liu J. Replication and Refinement of Brain Age Model for adolescent development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553472. [PMID: 37645839 PMCID: PMC10462059 DOI: 10.1101/2023.08.16.553472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The discrepancy between chronological age and estimated brain age, known as the brain age gap, may serve as a biomarker to reveal brain development and neuropsychiatric problems. This has motivated many studies focusing on the accurate estimation of brain age using different features and models, of which the generalizability is yet to be tested. Our recent study has demonstrated that conventional machine learning models can achieve high accuracy on brain age prediction during development using only a small set of selected features from multimodal brain imaging data. In the current study, we tested the replicability of various brain age models on the Adolescent Brain Cognitive Development (ABCD) cohort. We proposed a new refined model to improve the robustness of brain age prediction. The direct replication test for existing brain age models derived from the age range of 8-22 years onto the ABCD participants at baseline (9 to 10 years old) and year-two follow-up (11 to 12 years old) indicate that pre-trained models could capture the overall mean age failed precisely estimating brain age variation within a narrow range. The refined model, which combined broad prediction of the pre-trained model and granular information with the narrow age range, achieved the best performance with a mean absolute error of 0.49 and 0.48 years on the baseline and year-two data, respectively. The brain age gap yielded by the refined model showed significant associations with the participants' information processing speed and verbal comprehension ability on baseline data.
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Affiliation(s)
- Bhaskar Ray
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS) Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, USA
- Department of Computer Science, Georgia State University, Atlanta, USA
| | - Jiayu Chen
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS) Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, USA
| | - Zening Fu
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS) Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, USA
| | - Pranav Suresh
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS) Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, USA
- Department of Computer Science, Georgia State University, Atlanta, USA
| | - Bishal Thapaliya
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS) Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, USA
- Department of Computer Science, Georgia State University, Atlanta, USA
| | - Britny Farahdel
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS) Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, USA
- Department of Computer Science, Georgia State University, Atlanta, USA
| | - Vince D. Calhoun
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS) Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, USA
- Department of Computer Science, Georgia State University, Atlanta, USA
| | - Jingyu Liu
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS) Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, USA
- Department of Computer Science, Georgia State University, Atlanta, USA
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Rosenblatt M, Rodriguez RX, Westwater ML, Dai W, Horien C, Greene AS, Constable RT, Noble S, Scheinost D. Connectome-based machine learning models are vulnerable to subtle data manipulations. PATTERNS (NEW YORK, N.Y.) 2023; 4:100756. [PMID: 37521052 PMCID: PMC10382940 DOI: 10.1016/j.patter.2023.100756] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/10/2023] [Accepted: 04/24/2023] [Indexed: 08/01/2023]
Abstract
Neuroimaging-based predictive models continue to improve in performance, yet a widely overlooked aspect of these models is "trustworthiness," or robustness to data manipulations. High trustworthiness is imperative for researchers to have confidence in their findings and interpretations. In this work, we used functional connectomes to explore how minor data manipulations influence machine learning predictions. These manipulations included a method to falsely enhance prediction performance and adversarial noise attacks designed to degrade performance. Although these data manipulations drastically changed model performance, the original and manipulated data were extremely similar (r = 0.99) and did not affect other downstream analysis. Essentially, connectome data could be inconspicuously modified to achieve any desired prediction performance. Overall, our enhancement attacks and evaluation of existing adversarial noise attacks in connectome-based models highlight the need for counter-measures that improve the trustworthiness to preserve the integrity of academic research and any potential translational applications.
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Affiliation(s)
- Matthew Rosenblatt
- Department of Biomedical Engineering, Yale School of Engineering and Applied Science, New Haven, CT 06510, USA
| | - Raimundo X. Rodriguez
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, USA
| | - Margaret L. Westwater
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT 06510, USA
| | - Wei Dai
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA
| | - Corey Horien
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, USA
| | - Abigail S. Greene
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, USA
| | - R. Todd Constable
- Department of Biomedical Engineering, Yale School of Engineering and Applied Science, New Haven, CT 06510, USA
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA
| | - Stephanie Noble
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT 06510, USA
| | - Dustin Scheinost
- Department of Biomedical Engineering, Yale School of Engineering and Applied Science, New Haven, CT 06510, USA
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Statistics & Data Science, Yale University, New Haven, CT 06510, USA
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
- Wu Tsai Institute, Yale University, New Haven, CT 06510, USA
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Rai B, Naylor PE, Siqueiros-Sanchez M, Wintermark M, Raman MM, Jo B, Reiss AL, Green T. Novel effects of Ras-MAPK pathogenic variants on the developing human brain and their link to gene expression and inhibition abilities. Transl Psychiatry 2023; 13:245. [PMID: 37407569 DOI: 10.1038/s41398-023-02504-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/27/2023] [Accepted: 06/01/2023] [Indexed: 07/07/2023] Open
Abstract
The RASopathies are genetic syndromes associated with pathogenic variants causing dysregulation of the Ras/mitogen-activated protein kinase (Ras-MAPK) pathway, essential for brain development, and increased risk for neurodevelopmental disorders. Yet, the effects of most pathogenic variants on the human brain are unknown. We examined: (1) How Ras-MAPK activating variants of PTPN11/SOS1 protein-coding genes affect brain anatomy. (2) The relationship between PTPN11 gene expression levels and brain anatomy, and (3) The relevance of subcortical anatomy to attention and memory skills affected in the RASopathies. We collected structural brain MRI and cognitive-behavioral data from 40 pre-pubertal children with Noonan syndrome (NS), caused by PTPN11 (n = 30) or SOS1 (n = 10) variants (age 8.53 ± 2.15, 25 females), and compared them to 40 age- and sex-matched typically developing controls (9.24 ± 1.62, 27 females). We identified widespread effects of NS on cortical and subcortical volumes and on determinants of cortical gray matter volume, surface area (SA), and cortical thickness (CT). In NS, we observed smaller volumes of bilateral striatum, precentral gyri, and primary visual area (d's < -0.8), and extensive effects on SA (d's > |0.8|) and CT (d's > |0.5|) relative to controls. Further, SA effects were associated with increasing PTPN11 gene expression, most prominently in the temporal lobe. Lastly, PTPN11 variants disrupted normative relationships between the striatum and inhibition functioning. We provide evidence for the effects of Ras-MAPK pathogenic variants on striatal and cortical anatomy as well as links between PTPN11 gene expression and cortical SA increases, and striatal volume and inhibition skills. These findings provide essential translational information on the Ras-MAPK pathway's effect on human brain development and function.
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Affiliation(s)
- Bhavana Rai
- Division of Interdisciplinary Brain Sciences, Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
- University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Paige E Naylor
- Department of Clinical Psychology, Palo Alto University, Palo Alto, CA, USA
- Department of Neurology, Medical College of Wisconsin, Wauwatosa, WI, USA
| | - Monica Siqueiros-Sanchez
- Division of Interdisciplinary Brain Sciences, Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Max Wintermark
- Department of Neuroradiology, University of Texas MD Anderson Center, Houston, TX, USA
| | - Mira M Raman
- Division of Interdisciplinary Brain Sciences, Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Booil Jo
- Division of Interdisciplinary Brain Sciences, Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Allan L Reiss
- Division of Interdisciplinary Brain Sciences, Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Radiology and Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Tamar Green
- Division of Interdisciplinary Brain Sciences, Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA.
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Nakua H, Hawco C, Forde NJ, Joseph M, Grillet M, Johnson D, Jacobs GR, Hill S, Voineskos A, Wheeler AL, Lai MC, Szatmari P, Georgiades S, Nicolson R, Schachar R, Crosbie J, Anagnostou E, Lerch JP, Arnold PD, Ameis SH. Systematic comparisons of different quality control approaches applied to three large pediatric neuroimaging datasets. Neuroimage 2023; 274:120119. [PMID: 37068719 DOI: 10.1016/j.neuroimage.2023.120119] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 03/22/2023] [Accepted: 04/14/2023] [Indexed: 04/19/2023] Open
Abstract
INTRODUCTION Poor quality T1-weighted brain scans systematically affect the calculation of brain measures. Removing the influence of such scans requires identifying and excluding scans with noise and artefacts through a quality control (QC) procedure. While QC is critical for brain imaging analyses, it is not yet clear whether different QC approaches lead to the exclusion of the same participants. Further, the removal of poor-quality scans may unintentionally introduce a sampling bias by excluding the subset of participants who are younger and/or feature greater clinical impairment. This study had two aims: 1) examine whether different QC approaches applied to T1-weighted scans would exclude the same participants, and 2) examine how exclusion of poor-quality scans impacts specific demographic, clinical and brain measure characteristics between excluded and included participants in three large pediatric neuroimaging samples. METHODS We used T1-weighted, resting-state fMRI, demographic and clinical data from the Province of Ontario Neurodevelopmental Disorders network (Aim 1: n=553, Aim 2: n=465), the Healthy Brain Network (Aim 1: n=1051, Aim 2: n=558), and the Philadelphia Neurodevelopmental Cohort (Aim 1: n=1087; Aim 2: n=619). Four different QC approaches were applied to T1-weighted MRI (visual QC, metric QC, automated QC, fMRI-derived QC). We used tetrachoric correlation and inter-rater reliability analyses to examine whether different QC approaches excluded the same participants. We examined differences in age, mental health symptoms, everyday/adaptive functioning, IQ and structural MRI-derived brain indices between participants that were included versus excluded following each QC approach. RESULTS Dataset-specific findings revealed mixed results with respect to overlap of QC exclusion. However, in POND and HBN, we found a moderate level of overlap between visual and automated QC approaches (rtet=0.52-0.59). Implementation of QC excluded younger participants, and tended to exclude those with lower IQ, and lower everyday/adaptive functioning scores across several approaches in a dataset-specific manner. Across nearly all datasets and QC approaches examined, excluded participants had lower estimates of cortical thickness and subcortical volume, but this effect did not differ by QC approach. CONCLUSION The results of this study provide insight into the influence of QC decisions on structural pediatric imaging analyses. While different QC approaches exclude different subsets of participants, the variation of influence of different QC approaches on clinical and brain metrics is minimal in large datasets. Overall, implementation of QC tends to exclude participants who are younger, and those who have more cognitive and functional impairment. Given that automated QC is standardized and can reduce between-study differences, the results of this study support the potential to use automated QC for large pediatric neuroimaging datasets.
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Affiliation(s)
- Hajer Nakua
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Colin Hawco
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Natalie J Forde
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Michael Joseph
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Maud Grillet
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Delaney Johnson
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Grace R Jacobs
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Sean Hill
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Aristotle Voineskos
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Anne L Wheeler
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Meng-Chuan Lai
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada; Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Peter Szatmari
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada; Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Rob Nicolson
- Department of Psychiatry, University of Western Ontario, London, Ontario, Canada
| | - Russell Schachar
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada; Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jennifer Crosbie
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada; Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Evdokia Anagnostou
- Bloorview Research Institute, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada; Department of Pediatrics, University of Toronto, Toronto, Canada
| | - Jason P Lerch
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Canada; Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Paul D Arnold
- The Mathison Centre for Mental Health Research & Education, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Departments of Psychiatry and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Stephanie H Ameis
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada; Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada.
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Rai B, Naylor P, Sanchez MS, Wintermark M, Raman M, Jo B, Reiss A, Green T. Novel effects of Ras-MAPK pathogenic variants on the developing human brain and their link to gene expression and inhibition abilities. RESEARCH SQUARE 2023:rs.3.rs-2580911. [PMID: 36865206 PMCID: PMC9980214 DOI: 10.21203/rs.3.rs-2580911/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The RASopathies are genetic syndromes associated with pathogenic variants causing dysregulation of the Ras/mitogen-activated protein kinase (Ras-MAPK) pathway, essential for brain development, and increased risk for neurodevelopmental disorders. Yet, the effects of most pathogenic variants on the human brain are unknown. We examined: 1. How Ras-MAPK activating variants of PTPN11 / SOS1 protein-coding genes affect brain anatomy. 2. The relationship between PTPN11 gene expression levels and brain anatomy, and 3. The relevance of subcortical anatomy to attention and memory skills affected in the RASopathies. We collected structural brain MRI and cognitive-behavioral data from 40 pre-pubertal children with Noonan syndrome (NS), caused by PTPN11 ( n = 30) or SOS1 ( n = 10) variants (age 8.53 ± 2.15, 25 females), and compared them to 40 age- and sex-matched typically developing controls (9.24 ± 1.62, 27 females). We identified widespread effects of NS on cortical and subcortical volumes and on determinants of cortical gray matter volume, surface area (SA) and cortical thickness (CT). In NS, we observed smaller volumes of bilateral striatum, precentral gyri, and primary visual area ( d 's<-0.8), and extensive effects on SA ( d 's>|0.8|) and CT ( d 's>|0.5|) relative to controls. Further, SA effects were associated with increasing PTPN11 gene expression, most prominently in the temporal lobe. Lastly, PTPN11 variants disrupted normative relationships between the striatum and inhibition functioning. We provide evidence for effects of Ras-MAPK pathogenic variants on striatal and cortical anatomy as well as links between PTPN11 gene expression and cortical SA increases, and striatal volume and inhibition skills. These findings provide essential translational information on the Ras-MAPK pathway's effect on human brain development and function.
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42
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Voldsbekk I, Kjelkenes R, Wolfers T, Dahl A, Lund MJ, Kaufmann T, Fernandez-Cabello S, de Lange AMG, Tamnes CK, Andreassen OA, Westlye LT, Alnæs D. Shared pattern of impaired social communication and cognitive ability in the youth brain across diagnostic boundaries. Dev Cogn Neurosci 2023; 60:101219. [PMID: 36812678 PMCID: PMC9975702 DOI: 10.1016/j.dcn.2023.101219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/27/2023] [Accepted: 02/17/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND Abnormalities in brain structure are shared across diagnostic categories. Given the high rate of comorbidity, the interplay of relevant behavioural factors may also cross these classic boundaries. METHODS We aimed to detect brain-based dimensions of behavioural factors using canonical correlation and independent component analysis in a clinical youth sample (n = 1732, 64 % male, age: 5-21 years). RESULTS We identified two correlated patterns of brain structure and behavioural factors. The first mode reflected physical and cognitive maturation (r = 0.92, p = .005). The second mode reflected lower cognitive ability, poorer social skills, and psychological difficulties (r = 0.92, p = .006). Elevated scores on the second mode were a common feature across all diagnostic boundaries and linked to the number of comorbid diagnoses independently of age. Critically, this brain pattern predicted normative cognitive deviations in an independent population-based sample (n = 1253, 54 % female, age: 8-21 years), supporting the generalisability and external validity of the reported brain-behaviour relationships. CONCLUSIONS These results reveal dimensions of brain-behaviour associations across diagnostic boundaries, highlighting potent disorder-general patterns as the most prominent. In addition to providing biologically informed patterns of relevant behavioural factors for mental illness, this contributes to a growing body of evidence in favour of transdiagnostic approaches to prevention and intervention.
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Affiliation(s)
- Irene Voldsbekk
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine, University of Oslo, & Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Department of Psychology, University of Oslo, Oslo, Norway.
| | - Rikka Kjelkenes
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine, University of Oslo, & Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway,Department of Psychology, University of Oslo, Oslo, Norway
| | - Thomas Wolfers
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine, University of Oslo, & Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway,Department of Psychology, University of Oslo, Oslo, Norway
| | - Andreas Dahl
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine, University of Oslo, & Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway,Department of Psychology, University of Oslo, Oslo, Norway
| | - Martina J. Lund
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine, University of Oslo, & Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Tobias Kaufmann
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine, University of Oslo, & Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway,Department of Psychiatry and Psychotherapy, University of Tübingen, Germany
| | - Sara Fernandez-Cabello
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine, University of Oslo, & Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway,Department of Psychology, University of Oslo, Oslo, Norway
| | - Ann-Marie G. de Lange
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine, University of Oslo, & Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway,Department of Psychology, University of Oslo, Oslo, Norway,LREN, Centre for Research in Neurosciences, Department of Clinical Neurosciences, CHUV and University of Lausanne, Lausanne, Switzerland,Department of Psychiatry, University of Oxford, Oxford, UK
| | - Christian K. Tamnes
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine, University of Oslo, & Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway,Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway,PROMENTA Research Center, Department of Psychology, University of Oslo, Oslo, Norway
| | - Ole A. Andreassen
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine, University of Oslo, & Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway,KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - Lars T. Westlye
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine, University of Oslo, & Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway,Department of Psychology, University of Oslo, Oslo, Norway,KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - Dag Alnæs
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine, University of Oslo, & Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Kristiania University College, Oslo, Norway.
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Hong J, Hwang J, Lee JH. General psychopathology factor (p-factor) prediction using resting-state functional connectivity and a scanner-generalization neural network. J Psychiatr Res 2023; 158:114-125. [PMID: 36580867 DOI: 10.1016/j.jpsychires.2022.12.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/09/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
The general psychopathology factor (p-factor) represents shared variance across mental disorders based on psychopathologic symptoms. The Adolescent Brain Cognitive Development (ABCD) Study offers an unprecedented opportunity to investigate functional networks (FNs) from functional magnetic resonance imaging (fMRI) associated with the psychopathology of an adolescent cohort (n > 10,000). However, the heterogeneities associated with the use of multiple sites and multiple scanners in the ABCD Study need to be overcome to improve the prediction of the p-factor using fMRI. We proposed a scanner-generalization neural network (SGNN) to predict the individual p-factor by systematically reducing the scanner effect for resting-state functional connectivity (RSFC). We included 6905 adolescents from 18 sites whose fMRI data were collected using either Siemens or GE scanners. The p-factor was estimated based on the Child Behavior Checklist (CBCL) scores available in the ABCD study using exploratory factor analysis. We evaluated the Pearson's correlation coefficients (CCs) for p-factor prediction via leave-one/two-site-out cross-validation (LOSOCV/LTSOCV) and identified important FNs from the weight features (WFs) of the SGNN. The CCs were higher for the SGNN than for alternative models when using both LOSOCV (0.1631 ± 0.0673 for the SGNN vs. 0.1497 ± 0.0710 for kernel ridge regression [KRR]; p < 0.05 from a two-tailed paired t-test) and LTSOCV (0.1469 ± 0.0381 for the SGNN vs. 0.1394 ± 0.0359 for KRR; p = 0.01). It was found that (a) the default-mode and dorsal attention FNs were important for p-factor prediction, and (b) the intra-visual FN was important for scanner generalization. We demonstrated the efficacy of our novel SGNN model for p-factor prediction while simultaneously eliminating scanner-related confounding effects for RSFC.
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Affiliation(s)
- Jinwoo Hong
- Department of Brain and Cognitive Engineering, Korea University, Seoul, Republic of Korea
| | - Jundong Hwang
- Department of Brain and Cognitive Engineering, Korea University, Seoul, Republic of Korea
| | - Jong-Hwan Lee
- Department of Brain and Cognitive Engineering, Korea University, Seoul, Republic of Korea.
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Mehta K, Pines A, Adebimpe A, Larsen B, Bassett DS, Calkins ME, Baller E, Gell M, Patrick LM, Gur RE, Gur RC, Roalf DR, Romer D, Wolf DH, Kable JW, Satterthwaite TD. Individual Differences in Delay Discounting are Associated with Dorsal Prefrontal Cortex Connectivity in Youth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525577. [PMID: 36747838 PMCID: PMC9900814 DOI: 10.1101/2023.01.25.525577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Delay discounting is a measure of impulsive choice relevant in adolescence as it predicts many real-life outcomes, including substance use disorders, obesity, and academic achievement. However, the functional networks underlying individual differences in delay discounting during youth remain incompletely described. Here we investigate the association between multivariate patterns of functional connectivity and individual differences in impulsive choice in a large sample of youth. A total of 293 youth (9-23 years) completed a delay discounting task and underwent resting-state fMRI at 3T. A connectome-wide analysis using multivariate distance-based matrix regression was used to examine whole-brain relationships between delay discounting and functional connectivity was then performed. These analyses revealed that individual differences in delay discounting were associated with patterns of connectivity emanating from the left dorsal prefrontal cortex, a hub of the default mode network. Delay discounting was associated with greater functional connectivity between the dorsal prefrontal cortex and other parts of the default mode network, and reduced connectivity with regions in the dorsal and ventral attention networks. These results suggest that delay discounting in youth is associated with individual differences in relationships both within the default mode network and between the default mode and networks involved in attentional and cognitive control.
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Affiliation(s)
- Kahini Mehta
- Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Adam Pines
- Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Azeez Adebimpe
- Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Bart Larsen
- Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dani 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
| | - Monica E. Calkins
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Erica Baller
- Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Martin Gell
- Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Psychiatry, Psychotherapy and Psychosomatics, Medical Faculty, RWTH Aachen University, Aachen, Germany,Institute of Neuroscience and Medicine (INM-7: Brain & Behaviour), Research Centre Jülich, Jülich, Germany
| | - Lauren M. Patrick
- Department of Psychology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Raquel E. Gur
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA,Penn/CHOP Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Neurology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ruben C. Gur
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA,Penn/CHOP Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Neurology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - David R. Roalf
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Daniel Romer
- Annenberg Public Policy Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel H. Wolf
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Joseph W. Kable
- Department of Psychology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Theodore D. Satterthwaite
- Lifespan Informatics and Neuroimaging Center (PennLINC), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA,Penn/CHOP Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
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Huang W, Tan K, Zhang Z, Hu J, Dong S. A Review of Fusion Methods for Omics and Imaging Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:74-93. [PMID: 35044920 DOI: 10.1109/tcbb.2022.3143900] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The development of omics data and biomedical images has greatly advanced the progress of precision medicine in diagnosis, treatment, and prognosis. The fusion of omics and imaging data, i.e., omics-imaging fusion, offers a new strategy for understanding complex diseases. However, due to a variety of issues such as the limited number of samples, high dimensionality of features, and heterogeneity of different data types, efficiently learning complementary or associated discriminative fusion information from omics and imaging data remains a challenge. Recently, numerous machine learning methods have been proposed to alleviate these problems. In this review, from the perspective of fusion levels and fusion methods, we first provide an overview of preprocessing and feature extraction methods for omics and imaging data, and comprehensively analyze and summarize the basic forms and variations of commonly used and newly emerging fusion methods, along with their advantages, disadvantages and the applicable scope. We then describe public datasets and compare experimental results of various fusion methods on the ADNI and TCGA datasets. Finally, we discuss future prospects and highlight remaining challenges in the field.
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Imperiale MN, Lieb R, Calkins ME, Meinlschmidt G. Transdiagnostic symptom networks in relation to mental health service use in community youth. Clin Psychol Psychother 2023; 30:119-130. [PMID: 36059253 PMCID: PMC10087894 DOI: 10.1002/cpp.2782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 07/28/2022] [Accepted: 07/31/2022] [Indexed: 02/03/2023]
Abstract
OBJECTIVE The objective of this study is to scrutinize whether psychopathology symptom networks differ between those with and without lifetime: treatment seeking, treatment and treatment of longer duration. METHODS We created non-exclusive groups of subjects with versus without lifetime treatment seeking, treatment and treatment of mid-long-term duration. We estimated Ising models and carried out network comparison tests (NCTs) to compare (a) overall connectivity and (b) network structure. Furthermore, we examined node strength. We used propensity score matching (PSM) to minimize potential confounding by indication for service use. RESULTS Based on data from 9,172 participants, there were no statistically significant differences in overall connectivity and network structure in those with versus without lifetime: treatment seeking (p = .75 and p = .82, respectively), treatment (p = .63 and p = .49, respectively) and treatment of mid-longterm duration (p = .15 and p = .62, respectively). Notably, comparing networks with versus without service use consistently revealed higher node strength in 'obsessions' and 'aggression' and lower node strength in 'elevated mood' in all networks with service use. CONCLUSIONS Findings suggest that after adjusting for potential confounding by indication for service use, there was no indication of an association in overall connectivity or network structure for lifetime treatment seeking, treatment and treatment of longer duration. However, selected structurally important symptoms differed consistently in all three comparisons. Our findings highlight the potential of network analysis methods to examine treatment mechanisms and outcomes. Specifically, more granular network characteristics on the node level may complement and enrich traditional outcomes in clinical research.
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Affiliation(s)
- Marina N Imperiale
- Division of Clinical Psychology and Epidemiology, Department of Psychology, University of Basel, Basel, Switzerland.,Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Roselind Lieb
- Division of Clinical Psychology and Epidemiology, Department of Psychology, University of Basel, Basel, Switzerland
| | - Monica E Calkins
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gunther Meinlschmidt
- Division of Clinical Psychology and Epidemiology, Department of Psychology, University of Basel, Basel, Switzerland.,Department of Clinical Psychology and Cognitive Behavioral Therapy, International Psychoanalytic University, Berlin, Germany.,Department of Psychosomatic Medicine, University Hospital Basel and University of Basel, Basel, Switzerland
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Parkes L, Kim JZ, Stiso J, Calkins ME, Cieslak M, Gur RE, Gur RC, Moore TM, Ouellet M, Roalf DR, Shinohara RT, Wolf DH, Satterthwaite TD, Bassett DS. Asymmetric signaling across the hierarchy of cytoarchitecture within the human connectome. SCIENCE ADVANCES 2022; 8:eadd2185. [PMID: 36516263 PMCID: PMC9750154 DOI: 10.1126/sciadv.add2185] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/10/2022] [Indexed: 05/30/2023]
Abstract
Cortical variations in cytoarchitecture form a sensory-fugal axis that shapes regional profiles of extrinsic connectivity and is thought to guide signal propagation and integration across the cortical hierarchy. While neuroimaging work has shown that this axis constrains local properties of the human connectome, it remains unclear whether it also shapes the asymmetric signaling that arises from higher-order topology. Here, we used network control theory to examine the amount of energy required to propagate dynamics across the sensory-fugal axis. Our results revealed an asymmetry in this energy, indicating that bottom-up transitions were easier to complete compared to top-down. Supporting analyses demonstrated that asymmetries were underpinned by a connectome topology that is wired to support efficient bottom-up signaling. Lastly, we found that asymmetries correlated with differences in communicability and intrinsic neuronal time scales and lessened throughout youth. Our results show that cortical variation in cytoarchitecture may guide the formation of macroscopic connectome topology.
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Affiliation(s)
- Linden Parkes
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jason Z. Kim
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer Stiso
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Monica E. Calkins
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute, University of Pennsylvania and Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Matthew Cieslak
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute, University of Pennsylvania and Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Raquel E. Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute, University of Pennsylvania and Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Neurology, Perelman School of Medicine, Philadelphia, PA 19104, USA
- Department of Radiology, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ruben C. Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute, University of Pennsylvania and Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Neurology, Perelman School of Medicine, Philadelphia, PA 19104, USA
- Department of Radiology, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Tyler M. Moore
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute, University of Pennsylvania and Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mathieu Ouellet
- Department of Electrical and Systems Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David R. Roalf
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute, University of Pennsylvania and Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Russell T. Shinohara
- Center for Biomedical Image Computing and Analytics, 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 19104, USA
| | - Daniel H. Wolf
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Theodore D. Satterthwaite
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute, University of Pennsylvania and Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dani S. Bassett
- 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
- Department of Neurology, Perelman School of Medicine, Philadelphia, PA 19104, USA
- Department of Electrical and Systems Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Physics and Astronomy, College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
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48
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Kia SM, Huijsdens H, Rutherford S, de Boer A, Dinga R, Wolfers T, Berthet P, Mennes M, Andreassen OA, Westlye LT, Beckmann CF, Marquand AF. Closing the life-cycle of normative modeling using federated hierarchical Bayesian regression. PLoS One 2022; 17:e0278776. [PMID: 36480551 PMCID: PMC9731431 DOI: 10.1371/journal.pone.0278776] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
Clinical neuroimaging data availability has grown substantially in the last decade, providing the potential for studying heterogeneity in clinical cohorts on a previously unprecedented scale. Normative modeling is an emerging statistical tool for dissecting heterogeneity in complex brain disorders. However, its application remains technically challenging due to medical data privacy issues and difficulties in dealing with nuisance variation, such as the variability in the image acquisition process. Here, we approach the problem of estimating a reference normative model across a massive population using a massive multi-center neuroimaging dataset. To this end, we introduce a federated probabilistic framework using hierarchical Bayesian regression (HBR) to complete the life-cycle of normative modeling. The proposed model provides the possibilities to learn, update, and adapt the model parameters on decentralized neuroimaging data. Our experimental results confirm the superiority of HBR in deriving more accurate normative ranges on large multi-site neuroimaging datasets compared to the current standard methods. In addition, our approach provides the possibility to recalibrate and reuse the learned model on local datasets and even on datasets with very small sample sizes. The proposed method will facilitate applications of normative modeling as a medical tool for screening the biological deviations in individuals affected by complex illnesses such as mental disorders.
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Affiliation(s)
- Seyed Mostafa Kia
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
- Department for Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hester Huijsdens
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Saige Rutherford
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
- Department for Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Augustijn de Boer
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Richard Dinga
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
- Department for Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Thomas Wolfers
- Department of Psychology, University of Oslo, Oslo, Norway
- Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Pierre Berthet
- Department of Psychology, University of Oslo, Oslo, Norway
- Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Maarten Mennes
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Ole A. Andreassen
- Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Lars T. Westlye
- Department of Psychology, University of Oslo, Oslo, Norway
- Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Christian F. Beckmann
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
- Department for Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
- Centre for Functional MRI of the Brain, University of Oxford, Oxford, United Kingdom
| | - Andre F. Marquand
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
- Department for Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Neuroimaging, Institute of Psychiatry, King’s College London, London, United Kingdom
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49
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Moujaes F, Preller KH, Ji JL, Murray JD, Berkovitch L, Vollenweider FX, Anticevic A. Towards mapping neuro-behavioral heterogeneity of psychedelic neurobiology in humans. Biol Psychiatry 2022:S0006-3223(22)01805-4. [PMID: 36715317 DOI: 10.1016/j.biopsych.2022.10.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/10/2022] [Accepted: 10/31/2022] [Indexed: 12/12/2022]
Abstract
Precision psychiatry aims to identify markers of inter-individual variability that allow predicting the right treatment for each patient. However, bridging the gap between molecular-level manipulations and neural systems-level functional alterations remains an unsolved problem in psychiatry. After decades of low success rates in pharmaceutical R&D for psychiatric drugs, multiple studies now point to the potential of psychedelics as a promising fast-acting and long-lasting treatment for some psychiatric symptoms. Yet, given the highly psychoactive nature of these substances, a precision medicine approach is essential to map the neural signals related to clinical efficacy in order to identify patients who can maximally benefit from this treatment. Recent studies have shown that bridging the gap between pharmacology, systems-level neural response in humans and individual experience is possible for psychedelic substances, therefore paving the way for a precision neuropsychiatric therapeutic development. Specifically, it has been shown that the integration of brain-wide PET or transcriptomic data, i.e. receptor distribution for the serotonin 2A receptor, with computational neuroimaging methods can simulate the effect of psychedelics on the human brain. These novel 'computational psychiatry' approaches allow for modeling inter-individual differences in neural as well as subjective effects of psychedelic substances. Collectively, this review provides a deep dive into psychedelic pharmaco-neuroimaging studies with a core focus on how recent computational psychiatry advances in biophysically based circuit modeling can be leveraged to predict individual responses. Finally, we emphasize the importance of human pharmacological neuroimaging for the continued precision therapeutic development of psychedelics.
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Affiliation(s)
- Flora Moujaes
- Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital for Psychiatry Zurich, Lenggstr. 31, 8032 Zurich, Switzerland; Department of Psychiatry, Yale University School of Medicine, 40 Temple Street, New Haven, CT, 06511, United States
| | - Katrin H Preller
- Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital for Psychiatry Zurich, Lenggstr. 31, 8032 Zurich, Switzerland; Department of Psychiatry, Yale University School of Medicine, 40 Temple Street, New Haven, CT, 06511, United States
| | - Jie Lisa Ji
- Department of Psychiatry, Yale University School of Medicine, 40 Temple Street, New Haven, CT, 06511, United States
| | - John D Murray
- Department of Psychiatry, Yale University School of Medicine, 40 Temple Street, New Haven, CT, 06511, United States; Department of Physics, Yale University, New Haven, CT, 06511, United States; Interdepartmental Neuroscience Program, Yale University, New Haven, CT, 06511, United States
| | - Lucie Berkovitch
- Department of Psychiatry, Yale University School of Medicine, 40 Temple Street, New Haven, CT, 06511, United States; Université de Paris, 15 Rue de l'École de Médecine, F-75006 Paris, France; Department of Psychiatry, Service Hospitalo-Universitaire, GHU Paris Psychiatrie & Neurosciences, 1 rue Cabanis, F-75014, Paris, France
| | - Franz X Vollenweider
- Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital for Psychiatry Zurich, Lenggstr. 31, 8032 Zurich, Switzerland
| | - Alan Anticevic
- Department of Psychiatry, Yale University School of Medicine, 40 Temple Street, New Haven, CT, 06511, United States; Interdepartmental Neuroscience Program, Yale University, New Haven, CT, 06511, United States.
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50
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Rodriguez RX, Noble S, Tejavibulya L, Scheinost D. Leveraging edge-centric networks complements existing network-level inference for functional connectomes. Neuroimage 2022; 264:119742. [PMID: 36368501 PMCID: PMC9838718 DOI: 10.1016/j.neuroimage.2022.119742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022] Open
Abstract
The human connectome is modular with distinct brain regions clustering together to form large-scale communities, or networks. This concept has recently been leveraged in novel inferencing procedures by averaging the edge-level statistics within networks to induce more powerful inferencing at the network level. However, these networks are constructed based on the similarity between pairs of nodes. Emerging work has described novel edge-centric networks, which instead use the similarity between pairs of edges to construct networks. In this work, we use these edge-centric networks in a network-level inferencing procedure and compare this novel method to traditional inferential procedures and the network-level procedure using node-centric networks. We use data from the Human Connectome Project, the Healthy Brain Network, and the Philadelphia Neurodevelopmental Cohort and use a resampling technique with various sample sizes (n=40, 80, 120) to probe the power and specificity of each method. Across datasets and sample sizes, using the edge-centric networks outperforms using node-centric networks for inference as well as edge-level FDR correction and NBS. Additionally, the edge-centric networks were found to be more consistent in clustering effect sizes of similar values as compared to node-centric networks, although node-centric networks often had a lower average within-network effect size variability. Together, these findings suggest that using edge-centric networks for network-level inference can procure relatively powerful results while remaining similarly accurate to the underlying edge-level effects across networks, complementing previous inferential methods.
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Affiliation(s)
- Raimundo X. Rodriguez
- Interdepartmental Neuroscience Program, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA,Corresponding author. (R.X. Rodriguez)
| | - Stephanie Noble
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, 330 Cedar Street, New Haven, CT 06520, USA
| | - Link Tejavibulya
- Interdepartmental Neuroscience Program, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Dustin Scheinost
- Interdepartmental Neuroscience Program, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA,Department of Radiology and Biomedical Imaging, Yale School of Medicine, 330 Cedar Street, New Haven, CT 06520, USA,Department of Biomedical Engineering, Yale School of Engineering and Applied Science, 17 Hillhouse Avenue, New Haven, CT 06511, USA,Department of Statistics and Data Science, Yale University, 24 Hillhouse Avenue, New Haven, CT 06511, USA,Child Study Center, Yale School of Medicine, 230 South Frontage Road, New Haven, CT 06519, USA,Wu Tsai Institute, Yale University, 100 College Street, New Haven, CT 06510, USA
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