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Qiao X, Sil A, Sangtarash S, Smith SM, Wu C, Robertson CM, Nichols RJ, Higgins SJ, Sadeghi H, Vezzoli A. Nuclear Magnetic Resonance Chemical Shift as a Probe for Single-Molecule Charge Transport. Angew Chem Int Ed Engl 2024; 63:e202402413. [PMID: 38478719 DOI: 10.1002/anie.202402413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Indexed: 04/05/2024]
Abstract
Existing modelling tools, developed to aid the design of efficient molecular wires and to better understand their charge-transport behaviour and mechanism, have limitations in accuracy and computational cost. Further research is required to develop faster and more precise methods that can yield information on how charge transport properties are impacted by changes in the chemical structure of a molecular wire. In this study, we report a clear semilogarithmic correlation between charge transport efficiency and nuclear magnetic resonance chemical shifts in multiple series of molecular wires, also accounting for the presence of chemical substituents. The NMR data was used to inform a simple tight-binding model that accurately captures the experimental single-molecule conductance values, especially useful in this case as more sophisticated density functional theory calculations fail due to inherent limitations. Our study demonstrates the potential of NMR spectroscopy as a valuable tool for characterising, rationalising, and gaining additional insights on the charge transport properties of single-molecule junctions.
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Affiliation(s)
- X Qiao
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, United Kingdom
| | - A Sil
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, United Kingdom
| | - S Sangtarash
- Device Modelling Group, School of Engineering, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - S M Smith
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, United Kingdom
| | - C Wu
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, United Kingdom
- Institute of Optoelectronic Materials and Devices, Faculty of Materials Metallurgy and Chemistry, Jiangxi University of Science and Technology, Ganzhou, 341000, China
| | - C M Robertson
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, United Kingdom
| | - R J Nichols
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, United Kingdom
| | - S J Higgins
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, United Kingdom
| | - H Sadeghi
- Device Modelling Group, School of Engineering, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - A Vezzoli
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, United Kingdom
- Stephenson Institute for Renewable Energy, University of Liverpool, Peach Street, Liverpool, L69 7ZF, United Kingdom
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Thompson AG, Taschler B, Smith SM, Turner MR. Premorbid brain structure influences risk of amyotrophic lateral sclerosis. J Neurol Neurosurg Psychiatry 2024; 95:360-365. [PMID: 38050140 PMCID: PMC10958375 DOI: 10.1136/jnnp-2023-332322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/25/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a disease of the motor network associated with brain structure and functional connectivity alterations that are implicated in disease progression. Whether such changes have a causal role in ALS, fitting with a postulated influence of premorbid cerebral architecture on the phenotypes associated with neurodegenerative disorders is not known. METHODS This study considered causal effects and shared genetic risk of 2240 structural and functional MRI brain scan imaging-derived phenotypes (IDPs) on ALS using two sample Mendelian randomisation, with putative associations further examined with extensive sensitivity analysis. Shared genetic predisposition between IDPs and ALS was explored using genetic correlation analysis. RESULTS Increased white matter volume in the cerebral hemispheres was causally associated with ALS. Weaker causal associations were observed for brain stem grey matter volume, parieto-occipital white matter surface and volume of the left thalamic ventral anterior nucleus. Genetic correlation was observed between ALS and intracellular volume fraction and isotropic free water volume fraction within the posterior limb of the internal capsule. CONCLUSIONS This study provides evidence that premorbid brain structure, in particular white matter volume, contributes to the risk of ALS.
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Affiliation(s)
| | - Bernd Taschler
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Stephen M Smith
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Martin R Turner
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
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Lou SSK, Ruff H, MacDonald S, Smith SM, Cheung CC. PD-L1 expression in fine-needle aspiration cell blocks of head and neck squamous-cell carcinoma and its cytohistological concordance. Diagn Cytopathol 2024; 52:163-170. [PMID: 38095142 DOI: 10.1002/dc.25264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 02/07/2024]
Abstract
BACKGROUND PD-L1 immunoexpression in head and neck squamous-cell carcinoma (HNSCC) determines immunotherapy eligibility. Patients are often diagnosed using fine-needle aspiration (FNA) of metastatic lymph nodes, however, the cytohistologic correlation of the combined positive score (CPS) is largely unknown. METHODS This study retrospectively identified 96 paired histologic (HS) and cytologic specimens (CyS), between 2016 and 2020, diagnosed with HNSCC. Cases with <100 tumor cells (n = 54) or missing block(s) (n = 8) were excluded. All 34 case pairs were scored with CPS using the PD-L1 22C3 pharmDx assay at clinically relevant cut-offs of <1%, 1%-19%, and ≥20% independently by three observers blinded to the case pairs (CyS with corresponding HS). RESULTS The CPS (<1/1-19/≥20) for CyS and HS were as follows: 10(29.4%)/10(29.4%)/14(41.2%) and 2(5.9%)/13(38.2%)/19(55.9%), respectively. There was fair overall cytohistologic agreement (OA) of 76.5% (k = 0.261) at the CPS cut-off of 1. The OA did not differ significantly between site-matched (n = 13) and -unmatched (n = 21) case pairs (p = .4653). CyS has a specificity and positive predictive value (PPV) of 100% but a negative predictive value (NPV) of only 20% as compared to its paired HS. CONCLUSIONS Our study demonstrates fair CPS cytohistologic correlation in HNSCC specimens using the PD-L1 IHC 22C3 pharmDx assay with high PPV but low NPV. This suggest that determining PD-L1 status in FNA specimens can play an important role in the clinical management of HNSCC patients.
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Affiliation(s)
- Sandy Si Kei Lou
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Division of Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Heather Ruff
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Division of Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
- Department of Pathology, Oregon Health Science University, Portland, Oregon, USA
| | - Scott MacDonald
- Division of Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Stephen M Smith
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Division of Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Carol C Cheung
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Division of Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
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de Almeida JR, Su JS, Kolarski MM, Truong T, Weinreb I, Perez-Ordonez B, Smith SM, Hosni A, Patel S, Valero C, Xu B, Ghossein R, Katabi N, Clark J, Low THH, Gupta R, Graboyes EM, Davies J, Richardson M, Pasham V, Jester R, Goldstein DP, Huang SH, Xu W, O'Sullivan B. Development and validation of a novel TNM staging N-classification of oral cavity squamous cell carcinoma. Cancer 2024; 130:410-420. [PMID: 37751180 DOI: 10.1002/cncr.35020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 09/27/2023]
Abstract
BACKGROUND For oral cavity squamous cell carcinoma (OSCC), extent of extranodal extension (ENE) (minor, ≤2 mm; major, >2 mm) is differentially prognostic, whereas limitations exist with the 8th edition of American Joint Committee on Cancer/International Union Against Cancer TNM N-classification (TNM-8-N). METHODS Resected OSCC patients at four centers were included and extent of ENE was recorded. Thresholds for optimal overall survival (OS) discrimination of lymph node (LN) features were established. After dividing into training and validation sets, two new N-classifications were created using 1) recursive partitioning analysis (RPA), and 2) adjusted hazard ratios (aHRs) and were ranked against TNM-8-N and two published proposals. RESULTS A total of 1460 patients were included (pN0: 696; pN+: 764). Of the pN+ cases, 135 (18%) had bilateral/contralateral LNs; 126 (17%) and 244 (32%) had minor and major ENE, and two (0.3%) had LN(s) >6 cm without ENE (N3a). LN number (1 and >1 vs. 0: aHRs, 1.92 [95% confidence interval (CI), 1.44-2.55] and 3.21 [95% CI, 2.44-4.22]), size (>3 vs. ≤3 cm: aHR, 1.88 [95% CI, 1.44-2.45]), and ENE extent (major vs. minor: aHR, 1.40 [95% CI, 1.05-1.87]) were associated with OS, whereas presence of contralateral LNs was not (aHR, 1.05 [95% CI, 0.81-1.36]). The aHR proposal provided optimal performance with these changes to TNM-8-N: 1) stratification of ENE extent, 2) elimination of N2c and 6-cm threshold, and 3) stratification of N2b by 3 cm threshold. CONCLUSION A new N-classification improved staging performance compared to TNM-8-N, by stratifying by ENE extent, eliminating the old N2c category and the 6 cm threshold, and by stratifying multiple nodes by size.
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Affiliation(s)
- John R de Almeida
- Department of Otolaryngology-Head and Neck Surgery, Princess Margaret Cancer Centre/University Health Network, University of Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management, and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Jie Susie Su
- Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Mirko Manojlovic Kolarski
- Department of Otolaryngology-Head and Neck Surgery, Princess Margaret Cancer Centre/University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Otolaryngology-Head and Neck Surgery, Health Sciences North, Sudbury, Ontario, Canada
| | - Tra Truong
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Ilan Weinreb
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | | | - Stephen M Smith
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Ali Hosni
- Department of Radiation Oncology, Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Snehal Patel
- Head and Neck Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Cristina Valero
- Head and Neck Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Bin Xu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ronald Ghossein
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nora Katabi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jonathan Clark
- Department of Head and Neck Surgery, Chris O'Brien Lifehouse, Sydney, New South Wales, Australia
- Sydney Medical School, Faculty of Medicine and Health Sciences, the University of Sydney, Sydney, New South Wales, Australia
| | - Tsu-Hui Hubert Low
- Department of Head and Neck Surgery, Chris O'Brien Lifehouse, Sydney, New South Wales, Australia
- Sydney Medical School, Faculty of Medicine and Health Sciences, the University of Sydney, Sydney, New South Wales, Australia
| | - Ruta Gupta
- Sydney Medical School, Faculty of Medicine and Health Sciences, the University of Sydney, Sydney, New South Wales, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, NSW Health Pathology, Sydney, New South Wales, Australia
| | - Evan M Graboyes
- Department of Otolaryngology-Head and Neck Surgery, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Joel Davies
- Department of Otolaryngology-Head and Neck Surgery, Medical University of South Carolina, Charleston, South Carolina, USA
- Department of Otolaryngology-Head and Neck Surgery, Sinai Health Systems, Toronto, Ontario, Canada
| | - Mary Richardson
- Department of Pathology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Vishu Pasham
- Department of Pathology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Rachel Jester
- Department of Pathology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - David P Goldstein
- Department of Otolaryngology-Head and Neck Surgery, Princess Margaret Cancer Centre/University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Shao Hui Huang
- Department of Otolaryngology-Head and Neck Surgery, Princess Margaret Cancer Centre/University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Radiation Oncology, Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Brian O'Sullivan
- Department of Otolaryngology-Head and Neck Surgery, Princess Margaret Cancer Centre/University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Radiation Oncology, Princess Margaret Cancer Center, Toronto, Ontario, Canada
- Department of Radiation Oncology, Centre Hospitalier de L'University de Montreal, Montreal, Quebec, Canada
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Yang C, Coalson TS, Smith SM, Elam JS, Van Essen DC, Glasser MF. Automating the Human Connectome Project's Temporal ICA Pipeline. bioRxiv 2024:2024.01.15.574667. [PMID: 38293188 PMCID: PMC10827070 DOI: 10.1101/2024.01.15.574667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Functional magnetic resonance imaging (fMRI) data are dominated by noise and artifacts, with only a small fraction of the variance relating to neural activity. Temporal independent component analysis (tICA) is a recently developed method that enables selective denoising of fMRI artifacts related to physiology such as respiration. However, an automated and easy to use pipeline for tICA has not previously been available; instead, two manual steps have been necessary: 1) setting the group spatial ICA dimensionality after MELODIC's Incremental Group-PCA (MIGP) and 2) labeling tICA components as artifacts versus signals. Moreover, guidance has been lacking as to how many subjects and timepoints are needed to adequately re-estimate the temporal ICA decomposition and what alternatives are available for smaller groups or even individual subjects. Here, we introduce a nine-step fully automated tICA pipeline which removes global artifacts from fMRI dense timeseries after sICA+FIX cleaning and MSMAll alignment driven by functionally relevant areal features. Additionally, we have developed an automated "reclean" Pipeline for improved spatial ICA (sICA) artifact removal. Two major automated components of the pipeline are 1) an automatic group spatial ICA (sICA) dimensionality selection for MIGP data enabled by fitting multiple Wishart distributions; 2) a hierarchical classifier to distinguish group tICA signal components from artifactual components, equipped with a combination of handcrafted features from domain expert knowledge and latent features obtained via self-supervised learning on spatial maps. We demonstrate that the dimensionality estimated for the MIGP data from HCP Young Adult 3T and 7T datasets is comparable to previous manual tICA estimates, and that the group sICA decomposition is highly reproducible. We also show that the tICA classifier achieved over 0.98 Precision-Recall Area Under Curve (PR-AUC) and that the correctly classified components account for over 95% of the tICA-represented variance on multiple held-out evaluation datasets including the HCP-Young Adult, HCP-Aging and HCP-Development datasets under various settings. Our automated tICA pipeline is now available as part of the HCP pipelines, providing a powerful and user-friendly tool for the neuroimaging community.
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Abrishami M, Smith SM, Slomovic AR, Altomare F, Krema H. Rhegmatogenous retinal detachment associated with an epibulbar tumour. Can J Ophthalmol 2023:S0008-4182(23)00380-0. [PMID: 38142713 DOI: 10.1016/j.jcjo.2023.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 12/26/2023]
Affiliation(s)
- Mojtaba Abrishami
- Ocular Oncology Service, Princess Margaret Cancer Center/University Health Network, Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON
| | - Stephen M Smith
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON
| | - Allan R Slomovic
- Department of Ophthalmology and Visual Sciences, University of Toronto, Toronto, ON
| | - Filiberto Altomare
- Ocular Oncology Service, Princess Margaret Cancer Center/University Health Network, Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON
| | - Hatem Krema
- Ocular Oncology Service, Princess Margaret Cancer Center/University Health Network, Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON.
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Cardwell K, Clyne B, Broderick N, Tyner B, Masukume G, Larkin L, McManus L, Carrigan M, Sharp M, Smith SM, Harrington P, Connolly M, Ryan M, O'Neill M. Lessons learnt from the COVID-19 pandemic in selected countries to inform strengthening of public health systems: a qualitative study. Public Health 2023; 225:343-352. [PMID: 37979311 DOI: 10.1016/j.puhe.2023.10.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/11/2023] [Accepted: 10/10/2023] [Indexed: 11/20/2023]
Abstract
INTRODUCTION The COVID-19 pandemic has prompted governments internationally to consider strengthening their public health systems. To support the work of Ireland's Public Health Reform Expert Advisory Group, the Health Information and Quality Authority, an independent governmental agency, was asked to describe the lessons learnt regarding the public health response to COVID-19 internationally and the applicability of this response for future pandemic preparedness. METHODS Semi-structured interviews with key public health representatives from nine countries were conducted. Interviews were conducted in March and April 2022 remotely via Zoom and were recorded. Notes were taken by two researchers, and a thematic analysis undertaken. RESULTS Lessons learnt from the COVID-19 pandemic related to three main themes: 1) setting policy; 2) delivering public health interventions; and 3) providing effective communication. Real-time surveillance, evidence synthesis, and cross-sectoral collaboration were reported as essential for policy setting; it was noted that having these functions established prior to the pandemic would lead to a more efficient implementation in a health emergency. Delivering public health interventions such as testing, contact tracing, and vaccination were key to limiting and or mitigating the spread of the SARS-CoV-2 virus. However, a number of challenges were highlighted such as staff capacity and burnout, delays in vaccination procurement, and reduced delivery of regular healthcare services. Clear, consistent, and regular communication of the scientific evidence was key to engaging citizens with mitigation strategies. However, these communication strategies had to compete with an infodemic of information being circulated, particularly through social media. CONCLUSIONS Overall, functions relating to policy setting, public health interventions, and communication are key to pandemic response. Ideally, these should be established in the preparedness phase so that they can be rapidly scaled-up during a pandemic.
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Affiliation(s)
- K Cardwell
- Health Technology Assessment Directorate, Health Information and Quality Authority, Dublin, Ireland
| | - B Clyne
- Department of Public Health & Epidemiology, RCSI University of Medicine and Health Sciences, Dublin, Ireland.
| | - N Broderick
- Health Technology Assessment Directorate, Health Information and Quality Authority, Dublin, Ireland
| | - B Tyner
- Health Technology Assessment Directorate, Health Information and Quality Authority, Dublin, Ireland
| | - G Masukume
- Health Technology Assessment Directorate, Health Information and Quality Authority, Dublin, Ireland
| | - L Larkin
- Health Technology Assessment Directorate, Health Information and Quality Authority, Dublin, Ireland
| | - L McManus
- Health Technology Assessment Directorate, Health Information and Quality Authority, Dublin, Ireland
| | - M Carrigan
- Health Technology Assessment Directorate, Health Information and Quality Authority, Dublin, Ireland
| | - M Sharp
- Department of Public Health & Epidemiology, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - S M Smith
- Discipline of Public Health and Primary Care, Trinity College Dublin, Dublin, Ireland
| | - P Harrington
- Health Technology Assessment Directorate, Health Information and Quality Authority, Dublin, Ireland
| | - M Connolly
- School of Medicine, College of Medicine Nursing and Health Sciences, University of Galway, Galway, Ireland
| | - M Ryan
- Health Technology Assessment Directorate, Health Information and Quality Authority, Dublin, Ireland; Department of Pharmacology and Therapeutics, Trinity College Dublin, Dublin, Ireland
| | - M O'Neill
- Health Technology Assessment Directorate, Health Information and Quality Authority, Dublin, Ireland
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Scheele J, Smith SM, Wahab RJ, Bais B, Steegers-Theunissen RPM, Gaillard R, Harmsen van der Vliet-Torij HW. Current preconception care practice in the Netherlands - An evaluation study among birth care professionals. Midwifery 2023; 127:103855. [PMID: 37890235 DOI: 10.1016/j.midw.2023.103855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023]
Abstract
OBJECTIVE To evaluate the current practice of preconception care in the Netherlands and the perceptions of birth care professionals concerning preconception care. METHODS We have developed a digital questionnaire and conducted a cross-sectional study by distributing the questionnaire among 102 organisations: 90 primary care midwifery practices and obstetric departments of 12 hospitals in the Southwest region of the Netherlands between December 2020 and March 2021. One birth care professional per organization was asked to complete the questionnaire. Descriptive statistics were used to present the results. FINDINGS Respondents of eighty-three organisations (81.4 %) filled in the questionnaire, of whom 74 respondents were independent primary care midwives and 9 respondents were obstetricians. Preconception care mostly consisted of an individual consultation in which personalized health and lifestyle advice was given. Among the respondents, 44.4 % reported that the organization had a preconception care protocol. The way in which the consultation was carried out, as well as the health and lifestyle related questions asked, differed between respondents. More than 85 % of the respondents inquire about the following possible risk factors for complications: maternal illnesses, obstetric history, folic acid supplement intake, alcohol intake, smoking, substance abuse, hereditary disease, prescription medication, dietary habits, overweight, and birth defects in the family. The respondents acknowledged that preconception care should be offered to all couples who wish to become pregnant, as opposed to offering preconception care only to those with an increased risk of complications. Still, respondents do not receive many questions regarding the preconception period or requests for preconception care consultations. KEY CONCLUSION Birth care professionals acknowledge the need for preconception care for all couples. In the Netherlands, preconception care consists mostly of an individual consultation with recommendations for health and lifestyle advice. However, the identification of risk factors varies between birth care professionals and less than half of the respondents indicate that they have a protocol available in their practice. Furthermore, the demand of parents-to-be for preconception care is low. More research, that includes more obstetricians, is necessary to investigate if there is a difference between the care provided by primary care midwives and obstetricians. IMPLICATIONS FOR PRACTICE To increase the awareness and uptake of preconception care, it would be prudent to emphasize its importance to parents-to-be and professionals, and actively promote the use of widespread, standardized protocols for birth care professionals.
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Affiliation(s)
- J Scheele
- Research Center Innovations in Care, Rotterdam University of Applied Sciences, Rochussenstraat 198, 3015 EK Rotterdam, the Netherlands.
| | - S M Smith
- Department of Obstetrics and Gynaecology, Division of Obstetrics and Prenatal Medicine, Erasmus MC, Rotterdam the Netherlands
| | - R J Wahab
- The Generation R Study Group, Erasmus MC, University Medical Center, 3000 CA Rotterdam, the Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center, 3000 CA Rotterdam, the Netherlands
| | - B Bais
- Department of Obstetrics and Gynaecology, Division of Obstetrics and Prenatal Medicine, Erasmus MC, Rotterdam the Netherlands
| | - R P M Steegers-Theunissen
- Department of Obstetrics and Gynaecology, Division of Obstetrics and Prenatal Medicine, Erasmus MC, Rotterdam the Netherlands
| | - R Gaillard
- The Generation R Study Group, Erasmus MC, University Medical Center, 3000 CA Rotterdam, the Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center, 3000 CA Rotterdam, the Netherlands
| | - H W Harmsen van der Vliet-Torij
- Research Center Innovations in Care, Rotterdam University of Applied Sciences, Rochussenstraat 198, 3015 EK Rotterdam, the Netherlands; Department of Obstetrics and Gynaecology, Division of Obstetrics and Prenatal Medicine, Erasmus MC, Rotterdam the Netherlands
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Hahn E, Xu B, Katabi N, Dogan S, Smith SM, Perez-Ordonez B, Patel PB, MacMillan C, Lubin DJ, Gagan J, Weinreb I, Bishop JA. Comprehensive Molecular Characterization of Polymorphous Adenocarcinoma, Cribriform Subtype: Identifying Novel Fusions and Fusion Partners. Mod Pathol 2023; 36:100305. [PMID: 37595638 DOI: 10.1016/j.modpat.2023.100305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/12/2023] [Accepted: 08/07/2023] [Indexed: 08/20/2023]
Abstract
Polymorphous adenocarcinoma (PAC) is a common, usually low-grade salivary gland carcinoma. While conventional PACs are most associated with PRKD1 p.E710D hotspot mutations, the cribriform subtype is often associated with gene fusions in PRKD1, PRKD2, or PRKD3. These fusions have been primarily identified by fluorescence in situ hybridization (FISH) analysis, with a minority evaluated by next-generation sequencing (NGS). Many of the reported fusions were detected by break-apart FISH probes and therefore have unknown partners or were negative by FISH altogether. In this study, we aimed to further characterize the fusions associated with PAC with NGS. Fifty-four PACs (exclusively cribriform and mixed/intermediate types to enrich the study for fusion-positive cases) were identified and subjected to NGS. Fifty-one cases were successfully sequenced, 28 of which demonstrated gene fusions involving PRKD1, PRKD2, or PRKD3. There were 10 cases with the PRKD1 p.E710D mutation. We identified a diverse group of fusion partners, including 13 novel partners, 3 of which were recurrent. The most common partners for the PRKD genes were ARID1A and ARID1B. The wide variety of involved genes is unlike in other salivary gland malignancies and warrants a broader strategy of sequencing for molecular confirmation for particularly challenging cases, as our NGS study shows.
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Affiliation(s)
- Elan Hahn
- Department of Pathology and Laboratory Medicine, Sinai Health System, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada.
| | - Bin Xu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nora Katabi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Snjezana Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Stephen M Smith
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada; Laboratory Medicine Program, University Health Network, Toronto General Hospital, Toronto, Ontario, Canada
| | - Bayardo Perez-Ordonez
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada; Laboratory Medicine Program, University Health Network, Toronto General Hospital, Toronto, Ontario, Canada
| | | | - Christina MacMillan
- Department of Pathology and Laboratory Medicine, Sinai Health System, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada
| | - Daniel J Lubin
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, Georgia
| | - Jeffrey Gagan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ilan Weinreb
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada; Laboratory Medicine Program, University Health Network, Toronto General Hospital, Toronto, Ontario, Canada
| | - Justin A Bishop
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
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10
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Rajayer SR, Smith SM. Neurovirulent cytokines increase neuronal excitability in a model of coronavirus-induced neuroinflammation. Intensive Care Med Exp 2023; 11:71. [PMID: 37833408 PMCID: PMC10575822 DOI: 10.1186/s40635-023-00557-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Neurological manifestations of severe coronavirus infections, including SARS-CoV-2, are wide-ranging and may persist following virus clearance. Detailed understanding of the underlying changes in brain function may facilitate the identification of therapeutic targets. We directly tested how neocortical function is impacted by the specific panel of cytokines that occur in coronavirus brain infection. Using the whole-cell patch-clamp technique, we determined how the five cytokines (TNFα, IL-1β, IL-6, IL-12p40 and IL-15 for 22-28-h) at concentrations matched to those elicited by MHV-A59 coronavirus brain infection, affected neuronal function in cultured primary mouse neocortical neurons. RESULTS We evaluated how acute cytokine exposure affected neuronal excitability (propensity to fire action potentials), membrane properties, and action potential characteristics, as well as sensitivity to changes in extracellular calcium and magnesium (divalent) concentration. Neurovirulent cytokines increased spontaneous excitability and response to low divalent concentration by depolarizing the resting membrane potential and hyperpolarizing the action potential threshold. Evoked excitability was also enhanced by neurovirulent cytokines at physiological divalent concentrations. At low divalent concentrations, the change in evoked excitability was attenuated. One hour after cytokine removal, spontaneous excitability and hyperpolarization of the action potential threshold normalized but membrane depolarization and attenuated divalent-dependent excitability persisted. CONCLUSIONS Coronavirus-associated cytokine exposure increases spontaneous excitability in neocortical neurons, and some of the changes persist after cytokine removal.
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Affiliation(s)
- Salil R Rajayer
- Section of Pulmonary, Critical Care, Allergy, and Sleep Medicine, VA Portland Health Care System, 3710 SW U.S. Veterans Hospital Road, R&D 24, Portland, OR, 97239, USA
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Stephen M Smith
- Section of Pulmonary, Critical Care, Allergy, and Sleep Medicine, VA Portland Health Care System, 3710 SW U.S. Veterans Hospital Road, R&D 24, Portland, OR, 97239, USA.
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Oregon Health and Science University, Portland, OR, 97239, USA.
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11
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Smith SM, Parkash V. Normalized "medical inferiority bias" and cultural racism against international medical graduate physicians in academic medicine. Acad Pathol 2023; 10:100095. [PMID: 37767366 PMCID: PMC10520300 DOI: 10.1016/j.acpath.2023.100095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/28/2023] [Accepted: 08/05/2023] [Indexed: 09/29/2023] Open
Abstract
Socio-historical barriers remain a concern in Academic Medicine. Regrettably, despite the modern cultural era defined by increased recognition and response to such issues, widespread covert barriers and misperceptions continue to limit the advancement of many, in particular, international medical graduate physicians (IMGs) who represent a significant proportion of the US physician workforce. Adversity is experienced in the form of cultural racism, affinity bias, and underrepresentation in distinct specialties as well as in leadership roles. Often, these unnecessary hardships exacerbate pre-existing discrimination in Academic Medicine, further marginalizing IMGs. In this article, we discuss the prevalence of "medical inferiority bias" and the resulting impact on US healthcare, specifying considerations to be made from a policy perspective.
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Affiliation(s)
- Stephen M. Smith
- Department of Laboratory Medicine & Pathobiology at Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
- Laboratory Medicine and Pathobiology at the University of Toronto, Toronto, Ontario, Canada
| | - Vinita Parkash
- Yale University School of Medicine, New Haven, CT, USA
- Yale New Haven Hospital, New Haven, CT, USA
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12
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Bijsterbosch JD, Farahibozorg SR, Glasser MF, Essen DV, Snyder LH, Woolrich MW, Smith SM. Evaluating functional brain organization in individuals and identifying contributions to network overlap. bioRxiv 2023:2023.09.21.558809. [PMID: 37790508 PMCID: PMC10542549 DOI: 10.1101/2023.09.21.558809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Individual differences in the spatial organization of resting state networks have received increased attention in recent years. Measures of individual-specific spatial organization of brain networks and overlapping network organization have been linked to important behavioral and clinical traits and are therefore potential biomarker targets for personalized psychiatry approaches. To better understand individual-specific spatial brain organization, this paper addressed three key goals. First, we determined whether it is possible to reliably estimate weighted (non-binarized) resting state network maps using data from only a single individual, while also maintaining maximum spatial correspondence across individuals. Second, we determined the degree of spatial overlap between distinct networks, using test-retest and twin data. Third, we systematically tested multiple hypotheses (spatial mixing, temporal switching, and coupling) as candidate explanations for why networks overlap spatially. To estimate weighted network organization, we adopt the Probabilistic Functional Modes (PROFUMO) algorithm, which implements a Bayesian framework with hemodynamic and connectivity priors to supplement optimization for spatial sparsity/independence. Our findings showed that replicable individual-specific estimates of weighted resting state networks can be derived using high quality fMRI data within individual subjects. Network organization estimates using only data from each individual subject closely resembled group-informed network estimates (which was not explicitly modeled in our individual-specific analyses), suggesting that cross-subject correspondence was largely maintained. Furthermore, our results confirmed the presence of spatial overlap in network organization, which was replicable across sessions within individuals and in monozygotic twin pairs. Intriguingly, our findings provide evidence that network overlap is indicative of linear additive coupling. These results suggest that regions of network overlap concurrently process information from all contributing networks, potentially pointing to the role of overlapping network organization in the integration of information across multiple brain systems.
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Affiliation(s)
- Janine D Bijsterbosch
- Department of Radiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
| | | | - Matthew F Glasser
- Department of Radiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
- Department of Neuroscience, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
| | - David Van Essen
- Department of Neuroscience, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
| | - Lawrence H Snyder
- Department of Neuroscience, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
| | - Mark W Woolrich
- Oxford Centre for Human Brain Activity, Wellcome Centre for Integrative Neuroimaging, Department of Psychiatry, University of Oxford, Oxford, UK
| | - Stephen M Smith
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), Oxford University, Oxford, United Kingdom
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13
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Parkash V, Smith SM. Depression and Suicidality in Pathology and Laboratory Medicine: We Should Be Concerned. Arch Pathol Lab Med 2023; 147:987-988. [PMID: 37651391 DOI: 10.5858/arpa.2022-0272-le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2023] [Indexed: 09/02/2023]
Affiliation(s)
- Vinita Parkash
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Stephen M Smith
- Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada
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14
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Leonardsen EH, Vidal-Piñeiro D, Roe JM, Frei O, Shadrin AA, Iakunchykova O, de Lange AMG, Kaufmann T, Taschler B, Smith SM, Andreassen OA, Wolfers T, Westlye LT, Wang Y. Genetic architecture of brain age and its causal relations with brain and mental disorders. Mol Psychiatry 2023; 28:3111-3120. [PMID: 37165155 PMCID: PMC10615751 DOI: 10.1038/s41380-023-02087-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/12/2023]
Abstract
The difference between chronological age and the apparent age of the brain estimated from brain imaging data-the brain age gap (BAG)-is widely considered a general indicator of brain health. Converging evidence supports that BAG is sensitive to an array of genetic and nongenetic traits and diseases, yet few studies have examined the genetic architecture and its corresponding causal relationships with common brain disorders. Here, we estimate BAG using state-of-the-art neural networks trained on brain scans from 53,542 individuals (age range 3-95 years). A genome-wide association analysis across 28,104 individuals (40-84 years) from the UK Biobank revealed eight independent genomic regions significantly associated with BAG (p < 5 × 10-8) implicating neurological, metabolic, and immunological pathways - among which seven are novel. No significant genetic correlations or causal relationships with BAG were found for Parkinson's disease, major depressive disorder, or schizophrenia, but two-sample Mendelian randomization indicated a causal influence of AD (p = 7.9 × 10-4) and bipolar disorder (p = 1.35 × 10-2) on BAG. These results emphasize the polygenic architecture of brain age and provide insights into the causal relationship between selected neurological and neuropsychiatric disorders and BAG.
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Affiliation(s)
- Esten H Leonardsen
- Center for Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, 0317, Oslo, Norway
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, 0317, Oslo, Norway
| | - Didac Vidal-Piñeiro
- Center for Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, 0317, Oslo, Norway
| | - James M Roe
- Center for Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, 0317, Oslo, Norway
| | - Oleksandr Frei
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, 0317, Oslo, Norway
| | - Alexey A Shadrin
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, 0317, Oslo, Norway
- K.G. Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
| | - Olena Iakunchykova
- Center for Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, 0317, Oslo, Norway
| | - Ann-Marie G de Lange
- Department of Psychology, University of Oslo, 0317, Oslo, Norway
- LREN, Centre for Research in Neurosciences, Department of Clinical Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, 1015, Lausanne, Switzerland
- Department of Psychiatry, University of Oxford, OX1 2JD, Oxford, UK
| | - Tobias Kaufmann
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, 0317, Oslo, Norway
- Department of Psychiatry and Psychotherapy, Tübingen Center for Mental Health, University of Tübingen, 72074, Tübingen, Germany
| | - Bernd Taschler
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), University of Oxford, OX3 9DU, Oxford, United Kingdom
| | - Stephen M Smith
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), University of Oxford, OX3 9DU, Oxford, United Kingdom
| | - Ole A Andreassen
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, 0317, Oslo, Norway
- K.G. Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
| | - Thomas Wolfers
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, 0317, Oslo, Norway
- Department of Psychology, University of Oslo, 0317, Oslo, Norway
- Department of Psychiatry and Psychotherapy, Tübingen Center for Mental Health, University of Tübingen, 72074, Tübingen, Germany
| | - Lars T Westlye
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, 0317, Oslo, Norway
- K.G. Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
- Department of Psychology, University of Oslo, 0317, Oslo, Norway
| | - Yunpeng Wang
- Center for Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, 0317, Oslo, Norway.
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15
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Luettich A, Sievers C, Alfaro Almagro F, Allen M, Jbabdi S, Smith SM, Pattinson KTS. Functional connectivity between interoceptive brain regions is associated with distinct health-related domains: A population-based neuroimaging study. Hum Brain Mapp 2023; 44:3210-3221. [PMID: 36939141 PMCID: PMC10171512 DOI: 10.1002/hbm.26275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 02/08/2023] [Accepted: 02/27/2023] [Indexed: 03/21/2023] Open
Abstract
Interoception is the sensation, perception, and integration of signals from within the body. It has been associated with a broad range of physiological and psychological processes. Further, interoceptive variables are related to specific regions and networks in the human brain. However, it is not clear whether or how these networks relate empirically to different domains of physiological and psychological health at the population level. We analysed a data set of 19,020 individuals (10,055 females, 8965 males; mean age: 63 years, age range: 45-81 years), who have participated in the UK Biobank Study, a very large-scale prospective epidemiological health study. Using canonical correlation analysis (CCA), allowing for the examination of associations between two sets of variables, we related the functional connectome of brain regions implicated in interoception to a selection of nonimaging health and lifestyle related phenotypes, exploring their relationship within modes of population co-variation. In one integrated and data driven analysis, we obtained four statistically significant modes. Modes could be categorised into domains of arousal and affect and cardiovascular health, respiratory health, body mass, and subjective health (all p < .0001) and were meaningfully associated with distinct neural circuits. Circuits represent specific neural "fingerprints" of functional domains and set the scope for future studies on the neurobiology of interoceptive involvement in different lifestyle and health-related phenotypes. Therefore, our research contributes to the conceptualisation of interoception and may lead to a better understanding of co-morbid conditions in the light of shared interoceptive structures.
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Affiliation(s)
- Alexander Luettich
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
- Wellcome Centre for Integrative NeuroimagingUniversity of OxfordOxfordUK
| | - Carolin Sievers
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
- Wellcome Centre for Integrative NeuroimagingUniversity of OxfordOxfordUK
| | - Fidel Alfaro Almagro
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
- Wellcome Centre for Integrative NeuroimagingUniversity of OxfordOxfordUK
| | - Micah Allen
- Center of Functionally Integrative NeuroscienceAarhus UniversityAarhusDenmark
- Aarhus Institute of Advanced StudiesAarhus UniversityAarhusDenmark
- Cambridge PsychiatryUniversity of CambridgeCambridgeUK
| | - Saad Jbabdi
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
- Wellcome Centre for Integrative NeuroimagingUniversity of OxfordOxfordUK
| | - Stephen M. Smith
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
- Wellcome Centre for Integrative NeuroimagingUniversity of OxfordOxfordUK
| | - Kyle T. S. Pattinson
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
- Wellcome Centre for Integrative NeuroimagingUniversity of OxfordOxfordUK
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16
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Williams LZJ, Fitzgibbon SP, Bozek J, Winkler AM, Dimitrova R, Poppe T, Schuh A, Makropoulos A, Cupitt J, O'Muircheartaigh J, Duff EP, Cordero-Grande L, Price AN, Hajnal JV, Rueckert D, Smith SM, Edwards AD, Robinson EC. Structural and functional asymmetry of the neonatal cerebral cortex. Nat Hum Behav 2023; 7:942-955. [PMID: 36928781 DOI: 10.1038/s41562-023-01542-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/31/2023] [Indexed: 03/18/2023]
Abstract
Features of brain asymmetry have been implicated in a broad range of cognitive processes; however, their origins are still poorly understood. Here we investigated cortical asymmetries in 442 healthy term-born neonates using structural and functional magnetic resonance images from the Developing Human Connectome Project. Our results demonstrate that the neonatal cortex is markedly asymmetric in both structure and function. Cortical asymmetries observed in the term cohort were contextualized in two ways: by comparing them against cortical asymmetries observed in 103 preterm neonates scanned at term-equivalent age, and by comparing structural asymmetries against those observed in 1,110 healthy young adults from the Human Connectome Project. While associations with preterm birth and biological sex were minimal, significant differences exist between birth and adulthood.
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Affiliation(s)
- Logan Z J Williams
- Centre for the Developing Brain, Department of Perinatal Imaging and Health, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK.
- Department of Biomedical Engineering, School of Biomedical Engineering and Imaging Science, King's College London, London, UK.
| | - Sean P Fitzgibbon
- Centre for Functional MRI of the Brain (FMRIB), Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Jelena Bozek
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Anderson M Winkler
- Emotion and Development Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Ralica Dimitrova
- Centre for the Developing Brain, Department of Perinatal Imaging and Health, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Tanya Poppe
- Centre for the Developing Brain, Department of Perinatal Imaging and Health, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Andreas Schuh
- Department of Computing, Imperial College London, London, UK
| | - Antonios Makropoulos
- Centre for the Developing Brain, Department of Perinatal Imaging and Health, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - John Cupitt
- Department of Computing, Imperial College London, London, UK
| | - Jonathan O'Muircheartaigh
- Centre for the Developing Brain, Department of Perinatal Imaging and Health, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
- Department for Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Eugene P Duff
- Centre for Functional MRI of the Brain (FMRIB), Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
- UK Dementia Research Institute, Department of Brain Sciences, Imperial College London, London, UK
| | - Lucilio Cordero-Grande
- Centre for the Developing Brain, Department of Perinatal Imaging and Health, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
- Biomedical Image Technologies, ETSI Telecomunicación, Universidad Politécnica de Madrid and CIBER-BBN, ISCIII, Madrid, Spain
| | - Anthony N Price
- Centre for the Developing Brain, Department of Perinatal Imaging and Health, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
- Department of Biomedical Engineering, School of Biomedical Engineering and Imaging Science, King's College London, London, UK
| | - Joseph V Hajnal
- Centre for the Developing Brain, Department of Perinatal Imaging and Health, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
- Department of Biomedical Engineering, School of Biomedical Engineering and Imaging Science, King's College London, London, UK
| | - Daniel Rueckert
- Department of Computing, Imperial College London, London, UK
- Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Stephen M Smith
- Centre for Functional MRI of the Brain (FMRIB), Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - A David Edwards
- Centre for the Developing Brain, Department of Perinatal Imaging and Health, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
- Neonatal Intensive Care Unit, Evelina London Children's Hospital, London, UK
| | - Emma C Robinson
- Centre for the Developing Brain, Department of Perinatal Imaging and Health, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK.
- Department of Biomedical Engineering, School of Biomedical Engineering and Imaging Science, King's College London, London, UK.
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17
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Feldthouse MG, Vyleta NP, Smith SM. PLC regulates spontaneous glutamate release triggered by extracellular calcium and readily releasable pool size in neocortical neurons. Front Cell Neurosci 2023; 17:1193485. [PMID: 37260580 PMCID: PMC10228687 DOI: 10.3389/fncel.2023.1193485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/26/2023] [Indexed: 06/02/2023] Open
Abstract
Introduction Dynamic physiological changes in brain extracellular calcium ([Ca2+]o) occur when high levels of neuronal activity lead to substantial Ca2+ entry via ion channels reducing local [Ca2+]o. Perturbations of the extracellular microenvironment that increase [Ca2+]o are commonly used to study how [Ca2+] regulates neuronal activity. At excitatory synapses, the Ca2+-sensing receptor (CaSR) and other G-protein coupled receptors link [Ca2+]o and spontaneous glutamate release. Phospholipase C (PLC) is activated by G-proteins and is hypothesized to mediate this process. Methods Patch-clamping cultured neocortical neurons, we tested how spontaneous glutamate release was affected by [Ca2+]o and inhibition of PLC activity. We used hypertonic sucrose (HS) to evaluate the readily releasable pool (RRP) and test if it was affected by inhibition of PLC activity. Results Spontaneous glutamate release substantially increased with [Ca2+]o, and inhibition of PLC activity, with U73122, abolished this effect. PLC-β1 is an abundant isoform in the neocortex, however, [Ca2+]o-dependent spontaneous release was unchanged in PLC-β1 null mutants (PLC-β1-/-). U73122 completely suppressed this response in PLC-β1-/- neurons, indicating that this residual [Ca2+]o-sensitivity may be mediated by other PLC isoforms. The RRP size was substantially reduced after incubation in U73122, but not U73343. Phorbol esters increased RRP size after PLC inhibition. Discussion Together these data point to a strong role for PLC in mediating changes in spontaneous release elicited by [Ca2+]o and other extracellular cues, possibly by modifying the size of the RRP.
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Affiliation(s)
- Maya G. Feldthouse
- Section of Pulmonary and Critical Care Medicine and Research and Development, VA Portland Health Care System, Portland, OR, United States
| | - Nicholas P. Vyleta
- Division of Pulmonary and Critical Care Medicine, Oregon Health and Science University, Portland, OR, United States
| | - Stephen M. Smith
- Section of Pulmonary and Critical Care Medicine and Research and Development, VA Portland Health Care System, Portland, OR, United States
- Division of Pulmonary and Critical Care Medicine, Oregon Health and Science University, Portland, OR, United States
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18
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Weinreb I, Rooper LM, Dickson BC, Hahn E, Perez-Ordonez B, Smith SM, Lewis JS, Skalova A, Baněčková M, Wakely PE, Thompson LDR, Rupp NJ, Freiberger SN, Koduru P, Gagan J, Bishop JA. Adenoid Cystic Carcinoma With Striking Tubular Hypereosinophilia: A Unique Pattern Associated With Nonparotid Location and Both Canonical and Novel EWSR1::MYB and FUS::MYB Fusions. Am J Surg Pathol 2023; 47:497-503. [PMID: 36920022 DOI: 10.1097/pas.0000000000002023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
The classification of salivary gland tumors is ever-evolving with new variants of tumors being described every year. Next-generation sequencing panels have helped to prove and disprove prior assumptions about tumors' relationships to one another, and have helped refine this classification. Adenoid cystic carcinoma (AdCC) is one of the most common salivary gland malignancies and occurs at all major and minor salivary gland and seromucous gland sites. Most AdCC are predominantly myoepithelial and basaloid with variable cribriform, tubular, and solid growth. The luminal tubular elements are often less conspicuous. AdCC has largely been characterized by canonical MYB fusions, with MYB::NFIB and rarer MYBL1::NFIB. Anecdotal cases of AdCC, mostly in nonmajor salivary gland sites, have been noted to have unusual patterns, including squamous differentiation and macrocystic growth. Recently, this has led to the recognition of a subtype termed "metatypical adenoid cystic carcinoma." Another unusual histology that we have seen with a wide range of architecture, is striking tubular hypereosinophilia. The hypereosinophilia and luminal cell prominence is in stark contrast to the vast majority of AdCC that are basaloid and myoepithelial predominant. A total of 16 cases with tubular hypereosinophilia were collected, forming morular, solid, micropapillary, and glomeruloid growth, and occasionally having rhabdoid or Paneth-like cells. They were subjected to molecular profiling demonstrating canonical MYB::NFIB (5 cases) and MYBL1::NFIB (2 cases), as well as noncanonical EWSR1::MYB (2 cases) and FUS::MYB (1 case). The remaining 6 cases had either no fusion (3 cases) or failed sequencing (3 cases). All cases were present in nonmajor salivary gland sites, with seromucous glands being the most common. These include sinonasal tract (7 cases), laryngotracheal (2 cases), external auditory canal (2 cases), nasopharynx (1 case), base of tongue (2 cases), palate (1 case), and floor of mouth (1 case). A tissue microarray of 102 conventional AdCC, including many in major salivary gland sites was examined for EWSR1 and FUS by fluorescence in situ hybridization and showed that these novel fusions were isolated to this histology and nonmajor salivary gland location. In summary, complex and striking tubular hypereosinophilia and diverse architectures are present within the spectrum of AdCC, particularly in seromucous gland sites, and may show variant EWSR1/FUS::MYB fusions.
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Affiliation(s)
- Ilan Weinreb
- Laboratory Medicine Program, University Health Network, Toronto General Hospital
- Department of Pathobiology and Laboratory Medicine, University of Toronto
| | - Lisa M Rooper
- Department of Pathology, Johns Hopkins Medical Center, Baltimore, MD
| | - Brendan C Dickson
- Department of Pathobiology and Laboratory Medicine, University of Toronto
- Department of Pathology, Sinai Health System, Toronto, ON, Canada
| | - Elan Hahn
- Laboratory Medicine Program, University Health Network, Toronto General Hospital
- Department of Pathobiology and Laboratory Medicine, University of Toronto
| | - Bayardo Perez-Ordonez
- Laboratory Medicine Program, University Health Network, Toronto General Hospital
- Department of Pathobiology and Laboratory Medicine, University of Toronto
| | - Stephen M Smith
- Laboratory Medicine Program, University Health Network, Toronto General Hospital
- Department of Pathobiology and Laboratory Medicine, University of Toronto
| | - James S Lewis
- Department of Pathology, Vanderbilt University, Nashville, TN
| | - Alena Skalova
- Department of Pathology, Charles University, Plzen, Czech Republic
| | | | - Paul E Wakely
- Department of Pathology, The Ohio State University Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Columbus, OH
| | | | - Niels J Rupp
- Department of Pathology, and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Sandra N Freiberger
- Department of Pathology, and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Prasad Koduru
- University of Texas Southwestern Medical Center, Dallas, TX
| | - Jeffrey Gagan
- University of Texas Southwestern Medical Center, Dallas, TX
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19
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Bass C, Silva MD, Sudre C, Williams LZJ, Sousa HS, Tudosiu PD, Alfaro-Almagro F, Fitzgibbon SP, Glasser MF, Smith SM, Robinson EC. ICAM-Reg: Interpretable Classification and Regression With Feature Attribution for Mapping Neurological Phenotypes in Individual Scans. IEEE Trans Med Imaging 2023; 42:959-970. [PMID: 36374873 DOI: 10.1109/tmi.2022.3221890] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
An important goal of medical imaging is to be able to precisely detect patterns of disease specific to individual scans; however, this is challenged in brain imaging by the degree of heterogeneity of shape and appearance. Traditional methods, based on image registration, historically fail to detect variable features of disease, as they utilise population-based analyses, suited primarily to studying group-average effects. In this paper we therefore take advantage of recent developments in generative deep learning to develop a method for simultaneous classification, or regression, and feature attribution (FA). Specifically, we explore the use of a VAE-GAN (variational autoencoder - general adversarial network) for translation called ICAM, to explicitly disentangle class relevant features, from background confounds, for improved interpretability and regression of neurological phenotypes. We validate our method on the tasks of Mini-Mental State Examination (MMSE) cognitive test score prediction for the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort, as well as brain age prediction, for both neurodevelopment and neurodegeneration, using the developing Human Connectome Project (dHCP) and UK Biobank datasets. We show that the generated FA maps can be used to explain outlier predictions and demonstrate that the inclusion of a regression module improves the disentanglement of the latent space. Our code is freely available on GitHub https://github.com/CherBass/ICAM.
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20
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Topiwala A, Nichols TE, Williams LZJ, Robinson EC, Alfaro-Almagro F, Taschler B, Wang C, Nelson CP, Miller KL, Codd V, Samani NJ, Smith SM. Telomere length and brain imaging phenotypes in UK Biobank. PLoS One 2023; 18:e0282363. [PMID: 36947528 PMCID: PMC10032499 DOI: 10.1371/journal.pone.0282363] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/13/2023] [Indexed: 03/23/2023] Open
Abstract
Telomeres form protective caps at the ends of chromosomes, and their attrition is a marker of biological aging. Short telomeres are associated with an increased risk of neurological and psychiatric disorders including dementia. The mechanism underlying this risk is unclear, and may involve brain structure and function. However, the relationship between telomere length and neuroimaging markers is poorly characterized. Here we show that leucocyte telomere length (LTL) is associated with multi-modal MRI phenotypes in 31,661 UK Biobank participants. Longer LTL is associated with: i) larger global and subcortical grey matter volumes including the hippocampus, ii) lower T1-weighted grey-white tissue contrast in sensory cortices, iii) white-matter microstructure measures in corpus callosum and association fibres, iv) lower volume of white matter hyperintensities, and v) lower basal ganglia iron. Longer LTL was protective against certain related clinical manifestations, namely all-cause dementia (HR 0.93, 95% CI: 0.91-0.96), but not stroke or Parkinson's disease. LTL is associated with multiple MRI endophenotypes of neurodegenerative disease, suggesting a pathway by which longer LTL may confer protective against dementia.
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Affiliation(s)
- Anya Topiwala
- Nuffield Department Population Health, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Thomas E. Nichols
- Nuffield Department Population Health, Big Data Institute, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Clinical Neurosciences, Wellcome Centre for Integrative Neuroimaging, FMRIB, University of Oxford, Oxford, United Kingdom
| | - Logan Z. J. Williams
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Emma C. Robinson
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Fidel Alfaro-Almagro
- Nuffield Department of Clinical Neurosciences, Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), University of Oxford, Oxford, United Kingdom
| | - Bernd Taschler
- Nuffield Department of Clinical Neurosciences, Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), University of Oxford, Oxford, United Kingdom
| | - Chaoyue Wang
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), Oxford University, Oxford, United Kingdom
| | - Christopher P. Nelson
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Karla L. Miller
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), Oxford University, Oxford, United Kingdom
| | - Veryan Codd
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Nilesh J. Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Stephen M. Smith
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), Oxford University, Oxford, United Kingdom
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21
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Steiger LJ, Tsintsadze T, Mattheisen GB, Smith SM. Somatic and terminal CB1 receptors are differentially coupled to voltage-gated sodium channels in neocortical neurons. Cell Rep 2023; 42:112247. [PMID: 36933217 PMCID: PMC10106091 DOI: 10.1016/j.celrep.2023.112247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 01/13/2023] [Accepted: 02/24/2023] [Indexed: 03/19/2023] Open
Abstract
Endogenous cannabinoid signaling is vital for important brain functions, and the same pathways can be modified pharmacologically to treat pain, epilepsy, and posttraumatic stress disorder. Endocannabinoid-mediated changes to excitability are predominantly attributed to 2-arachidonoylglycerol (2-AG) acting presynaptically via the canonical cannabinoid receptor, CB1. Here, we identify a mechanism in the neocortex by which anandamide (AEA), another major endocannabinoid, but not 2-AG, powerfully inhibits somatically recorded voltage-gated sodium channel (VGSC) currents in the majority of neurons. This pathway involves intracellular CB1 that, when activated by anandamide, decreases the likelihood of recurrent action potential generation. WIN 55,212-2 similarly activates CB1 and inhibits VGSC currents, indicating that this pathway is also positioned to mediate the actions of exogenous cannabinoids on neuronal excitability. The coupling between CB1 and VGSCs is absent at nerve terminals, and 2-AG does not block somatic VGSC currents, indicating functional compartmentalization of the actions of two endocannabinoids.
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Affiliation(s)
- Luke J Steiger
- Section of Pulmonary and Critical Care Medicine, VA Portland Health Care System, Portland, OR, USA; Department of Medicine, Division of Pulmonary and Critical Care Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Timur Tsintsadze
- Section of Pulmonary and Critical Care Medicine, VA Portland Health Care System, Portland, OR, USA; Department of Medicine, Division of Pulmonary and Critical Care Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Glynis B Mattheisen
- Section of Pulmonary and Critical Care Medicine, VA Portland Health Care System, Portland, OR, USA; Department of Medicine, Division of Pulmonary and Critical Care Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Stephen M Smith
- Section of Pulmonary and Critical Care Medicine, VA Portland Health Care System, Portland, OR, USA; Department of Medicine, Division of Pulmonary and Critical Care Medicine, Oregon Health & Science University, Portland, OR 97239, USA; Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA.
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22
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Ritzau-Jost A, Nerlich J, Kaas T, Krueger M, Tsintsadze T, Eilers J, Barbour B, Smith SM, Hallermann S. Direct whole-cell patch-clamp recordings from small boutons in rodent primary neocortical neuron cultures. STAR Protoc 2023; 4:102168. [PMID: 36920913 PMCID: PMC10026040 DOI: 10.1016/j.xpro.2023.102168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/30/2023] [Accepted: 02/19/2023] [Indexed: 03/16/2023] Open
Abstract
Direct electrical recordings from conventional boutons in the mammalian central nervous system have proven challenging due to their small size. Here, we provide a protocol for direct whole-cell patch-clamp recordings from small presynaptic boutons of primary dissociated cultured neurons of the rodent neocortex. We describe steps to prepare primary neocortical cultures and recording pipettes, followed by identifying boutons and establishing a whole-cell bouton recording. We then provide details on precise pipette capacitance compensation required for high-resolution current-clamp recordings from boutons. For further details on the use and execution of this protocol, please refer to Ritzau-Jost et al.1.
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Affiliation(s)
- Andreas Ritzau-Jost
- Carl-Ludwig-Institute of Physiology, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany.
| | - Jana Nerlich
- Carl-Ludwig-Institute of Physiology, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany
| | - Thomas Kaas
- Carl-Ludwig-Institute of Physiology, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany
| | - Martin Krueger
- Institute of Anatomy, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany
| | - Timur Tsintsadze
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Oregon Health and Science University, Portland, OR 97239, USA; Section of Pulmonary and Critical Care Medicine, VA Portland Health Care System, Portland, OR 97239, USA
| | - Jens Eilers
- Carl-Ludwig-Institute of Physiology, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany
| | - Boris Barbour
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Stephen M Smith
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Oregon Health and Science University, Portland, OR 97239, USA; Section of Pulmonary and Critical Care Medicine, VA Portland Health Care System, Portland, OR 97239, USA
| | - Stefan Hallermann
- Carl-Ludwig-Institute of Physiology, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany.
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Abstract
Data-driven discovery of image-derived phenotypes (IDPs) from large-scale multimodal brain imaging data has enormous potential for neuroscientific and clinical research by linking IDPs to subjects' demographic, behavioural, clinical and cognitive measures (i.e., non-imaging derived phenotypes or nIDPs). However, current approaches are primarily based on unsupervised approaches, without the use of information in nIDPs. In this paper, we proposed a semi-supervised, multimodal, and multi-task fusion approach, termed SuperBigFLICA, for IDP discovery, which simultaneously integrates information from multiple imaging modalities as well as multiple nIDPs. SuperBigFLICA is computationally efficient and largely avoids the need for parameter tuning. Using the UK Biobank brain imaging dataset with around 40,000 subjects and 47 modalities, along with more than 17,000 nIDPs, we showed that SuperBigFLICA enhances the prediction power of nIDPs, benchmarked against IDPs derived by conventional expert-knowledge and unsupervised-learning approaches (with average nIDP prediction accuracy improvements of up to 46%). It also enables the learning of generic imaging features that can predict new nIDPs. Further empirical analysis of the SuperBigFLICA algorithm demonstrates its robustness in different prediction tasks and the ability to derive biologically meaningful IDPs in predicting health outcomes and cognitive nIDPs, such as fluid intelligence and hypertension.
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24
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Zack EH, Smith SM, Angielczyk KD. From Fairies to Giants: Untangling the Effect of Body Size, Phylogeny, and Ecology on Vertebral Bone Microstructure of Xenarthran Mammals. Integr Org Biol 2023; 5:obad002. [PMID: 36844392 PMCID: PMC9949600 DOI: 10.1093/iob/obad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/02/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Trabecular bone is a spongy bone tissue that serves as a scaffolding-like support inside many skeletal elements. Previous research found allometric variation in some aspects of trabecular bone architecture (TBA) and bone microstructure, whereas others scale isometrically. However, most of these studies examined very wide size and phylogenetic ranges or focused exclusively on primates or lab mice. We examined the impact of body size on TBA across a smaller size range in the mammalian clade Xenarthra (sloths, armadillos, and anteaters). We µCT-scanned the last six presacral vertebrae of 23 xenarthran specimens (body mass 120 g-35 kg). We collected ten gross-morphology measurements and seven TBA metrics and analyzed them using phylogenetic and nonphylogenetic methods. Most metrics had similar allometries to previous work. However, because ecology and phylogeny align closely in Xenarthra, the phylogenetic methods likely removed some covariance due to ecology; clarifying the impact of ecology on TBA in xenarthrans requires further work. Regressions for Folivora had high P-values and low R-squared values, indicating that the extant sloth sample either is too limited to determine patterns or that the unique way sloths load their vertebral columns causes unusually high TBA variation. The southern three-banded armadillo sits far below the regression lines, which may be related to its ability to roll into a ball. Body size, phylogeny, and ecology impact xenarthran TBA, but parsing these effects is highly complex.
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Affiliation(s)
| | - S M Smith
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
| | - K D Angielczyk
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
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25
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Lee S, Bijsterbosch JD, Almagro FA, Elliott L, McCarthy P, Taschler B, Sala-Llonch R, Beckmann CF, Duff EP, Smith SM, Douaud G. Amplitudes of resting-state functional networks - investigation into their correlates and biophysical properties. Neuroimage 2023; 265:119779. [PMID: 36462729 PMCID: PMC10933815 DOI: 10.1016/j.neuroimage.2022.119779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/31/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022] Open
Abstract
Resting-state fMRI studies have shown that multiple functional networks, which consist of distributed brain regions that share synchronised spontaneous activity, co-exist in the brain. As these resting-state networks (RSNs) have been thought to reflect the brain's intrinsic functional organization, intersubject variability in the networks' spontaneous fluctuations may be associated with individuals' clinical, physiological, cognitive, and genetic traits. Here, we investigated resting-state fMRI data along with extensive clinical, lifestyle, and genetic data collected from 37,842 UK Biobank participants, with the object of elucidating intersubject variability in the fluctuation amplitudes of RSNs. Functional properties of the RSN amplitudes were first examined by analyzing correlations with the well-established between-network functional connectivity. It was found that a network amplitude is highly correlated with the mean strength of the functional connectivity that the network has with the other networks. Intersubject clustering analysis showed the amplitudes are most strongly correlated with age, cardiovascular factors, body composition, blood cell counts, lung function, and sex, with some differences in the correlation strengths between sensory and cognitive RSNs. Genome-wide association studies (GWASs) of RSN amplitudes identified several significant genetic variants reported in previous GWASs for their implications in sleep duration. We provide insight into key factors determining RSN amplitudes and demonstrate that intersubject variability of the amplitudes primarily originates from differences in temporal synchrony between functionally linked brain regions, rather than differences in the magnitude of raw voxelwise BOLD signal changes. This finding additionally revealed intriguing differences between sensory and cognitive RSNs with respect to sex effects on temporal synchrony and provided evidence suggesting that synchronous coactivations of functionally linked brain regions, and magnitudes of BOLD signal changes, may be related to different genetic mechanisms. These results underscore that intersubject variability of the amplitudes in health and disease need to be interpreted largely as a measure of the sum of within-network temporal synchrony and amplitudes of BOLD signals, with a dominant contribution from the former.
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Affiliation(s)
- Soojin Lee
- Centre for Functional MRI of the Brain (FMRIB), Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, University of Oxford, UK; Pacific Parkinson's Research Institute, University of British Columbia, Canada.
| | - Janine D Bijsterbosch
- Centre for Functional MRI of the Brain (FMRIB), Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, University of Oxford, UK; Mallinckrodt Institute of Radiology, Washington University Medical School, Washington University in St Louis, USA
| | - Fidel Alfaro Almagro
- Centre for Functional MRI of the Brain (FMRIB), Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, University of Oxford, UK
| | - Lloyd Elliott
- Department of Statistics and Actuarial Science, Simon Fraser University (SFU), Canada
| | - Paul McCarthy
- Centre for Functional MRI of the Brain (FMRIB), Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, University of Oxford, UK
| | - Bernd Taschler
- Centre for Functional MRI of the Brain (FMRIB), Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, University of Oxford, UK
| | - Roser Sala-Llonch
- Department of Biomedicine, Institute of Neurosciences, University of Barcelona, Spain
| | - Christian F Beckmann
- Centre for Functional MRI of the Brain (FMRIB), Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, University of Oxford, UK; Department of Cognitive Neuroscience, Radboud University Medical Centre, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Eugene P Duff
- Centre for Functional MRI of the Brain (FMRIB), Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, University of Oxford, UK; Department of Brain Sciences, Imperial College London, UK Dementia Research Institute, London UK
| | - Stephen M Smith
- Centre for Functional MRI of the Brain (FMRIB), Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, University of Oxford, UK
| | - Gwenaëlle Douaud
- Centre for Functional MRI of the Brain (FMRIB), Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, University of Oxford, UK
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26
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Smith SM, Eadara A, Parkash V. Addressing quality and safety in anatomic pathology in low- and middle-income countries. Front Med (Lausanne) 2022; 9:1060179. [PMID: 36619634 PMCID: PMC9817141 DOI: 10.3389/fmed.2022.1060179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
The World Health Organization (WHO) has created a sustainable development goal of reducing preventable mortality from cancer in low- and middle-income countries (LMICs) by 30% by 2030. Central to achieving this goal is the creation and maintenance of quality anatomic pathology services (APS). Within the last decade, quality assurance programs and patient safety measures have become a major focus of research for upper middle- and high-income countries (UMHICs), which has led to marked documented improvement in the quality of services provided by laboratories, as well as a decrease in patient safety events. We propose that as APS are developed in LMICs, the lessons learned by UMHICs are necessary to incorporate to produce quality and safe services toward obtaining the aforementioned goal. Furthermore, data suggests that Quality Improvement work requires change at the macrosystems and microsystems levels to achieve these goals. Here, we propose five "microsystems" strategies for professional organizations, healthcare institutions in LMICs and UMHICs that would accelerate quality improvement programs/systems implementation in APS in LMICs.
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Affiliation(s)
- Stephen M. Smith
- Department of Laboratory Medicine & Pathobiology, University Health Network, Toronto, ON, Canada
| | | | - Vinita Parkash
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, United States,*Correspondence: Vinita Parkash,
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27
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Dinsdale NK, Bluemke E, Sundaresan V, Jenkinson M, Smith SM, Namburete AIL. Challenges for machine learning in clinical translation of big data imaging studies. Neuron 2022; 110:3866-3881. [PMID: 36220099 DOI: 10.1016/j.neuron.2022.09.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/27/2021] [Accepted: 09/08/2022] [Indexed: 12/15/2022]
Abstract
Combining deep learning image analysis methods and large-scale imaging datasets offers many opportunities to neuroscience imaging and epidemiology. However, despite these opportunities and the success of deep learning when applied to a range of neuroimaging tasks and domains, significant barriers continue to limit the impact of large-scale datasets and analysis tools. Here, we examine the main challenges and the approaches that have been explored to overcome them. We focus on issues relating to data availability, interpretability, evaluation, and logistical challenges and discuss the problems that still need to be tackled to enable the success of "big data" deep learning approaches beyond research.
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Affiliation(s)
- Nicola K Dinsdale
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Oxford Machine Learning in NeuroImaging Lab, OMNI, Department of Computer Science, University of Oxford, Oxford, UK.
| | - Emma Bluemke
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK
| | - Vaanathi Sundaresan
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Mark Jenkinson
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Australian Institute for Machine Learning (AIML), School of Computer Science, University of Adelaide, Adelaide, SA, Australia; South Australian Health and Medical Research Institute (SAHMRI), North Terrace, Adelaide, SA, Australia
| | - Stephen M Smith
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Ana I L Namburete
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Oxford Machine Learning in NeuroImaging Lab, OMNI, Department of Computer Science, University of Oxford, Oxford, UK
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Klein-Flügge MC, Jensen DEA, Takagi Y, Priestley L, Verhagen L, Smith SM, Rushworth MFS. Relationship between nuclei-specific amygdala connectivity and mental health dimensions in humans. Nat Hum Behav 2022; 6:1705-1722. [PMID: 36138220 PMCID: PMC7613949 DOI: 10.1038/s41562-022-01434-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/14/2022] [Indexed: 01/14/2023]
Abstract
There has been increasing interest in using neuroimaging measures to predict psychiatric disorders. However, predictions usually rely on large brain networks and large disorder heterogeneity. Thus, they lack both anatomical and behavioural specificity, preventing the advancement of targeted interventions. Here we address both challenges. First, using resting-state functional magnetic resonance imaging, we parcellated the amygdala, a region implicated in mood disorders, into seven nuclei. Next, a questionnaire factor analysis provided subclinical mental health dimensions frequently altered in anxious-depressive individuals, such as negative emotions and sleep problems. Finally, for each behavioural dimension, we identified the most predictive resting-state functional connectivity between individual amygdala nuclei and highly specific regions of interest, such as the dorsal raphe nucleus in the brainstem or medial frontal cortical regions. Connectivity in circumscribed amygdala networks predicted behaviours in an independent dataset. Our results reveal specific relations between mental health dimensions and connectivity in precise subcortical networks.
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Affiliation(s)
- Miriam C Klein-Flügge
- Wellcome Centre for Integrative Neuroimaging (WIN), Department of Experimental Psychology, University of Oxford, Oxford, UK.
- Wellcome Centre for Integrative Neuroimaging (WIN), Centre for Functional MRI of the Brain (FMRIB) and Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK.
- Department of Psychiatry, Warneford Hospital, University of Oxford, Oxford, UK.
| | - Daria E A Jensen
- Wellcome Centre for Integrative Neuroimaging (WIN), Department of Experimental Psychology, University of Oxford, Oxford, UK
- Department of Psychiatry, Warneford Hospital, University of Oxford, Oxford, UK
| | - Yu Takagi
- Wellcome Centre for Integrative Neuroimaging (WIN), Centre for Functional MRI of the Brain (FMRIB) and Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Department of Psychiatry, Warneford Hospital, University of Oxford, Oxford, UK
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Luke Priestley
- Wellcome Centre for Integrative Neuroimaging (WIN), Department of Experimental Psychology, University of Oxford, Oxford, UK
- Wellcome Centre for Integrative Neuroimaging (WIN), Centre for Functional MRI of the Brain (FMRIB) and Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Lennart Verhagen
- Wellcome Centre for Integrative Neuroimaging (WIN), Department of Experimental Psychology, University of Oxford, Oxford, UK
- Wellcome Centre for Integrative Neuroimaging (WIN), Centre for Functional MRI of the Brain (FMRIB) and Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Stephen M Smith
- Wellcome Centre for Integrative Neuroimaging (WIN), Centre for Functional MRI of the Brain (FMRIB) and Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Matthew F S Rushworth
- Wellcome Centre for Integrative Neuroimaging (WIN), Department of Experimental Psychology, University of Oxford, Oxford, UK
- Wellcome Centre for Integrative Neuroimaging (WIN), Centre for Functional MRI of the Brain (FMRIB) and Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
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29
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Murphy AW, Moran D, Smith SM, Wallace E, Glynn LG, Hanley K, Kelly ME. Supporting Medical Students Towards Future Careers in General Practice: A Quantitative Study of Irish Medical Schools. Ir Med J 2022; 115:10. [PMID: 36917466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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30
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Abstract
CONTEXT.— Despite widely prevalent burnout and attendant disengagement in medicine, the specific patterns and drivers within pathology and laboratory medicine are uncommonly studied. OBJECTIVE.— To assess the prevalence and drivers of burnout among pathology and laboratory medicine professionals, retrospectively, prior to the COVID-19 pandemic. DESIGN.— This was a cross-sectional, mixed-methods study engaging pathology and laboratory medicine professionals as subjects. RESULTS.— Of 2363 respondents, 438 identified as pathologists, 111 as pathology assistants, and 911 as pathology and laboratory professionals. The burnout rate was 58.4% (1380 of 2363) across all respondents in pathology and laboratory medicine. Burnout varied by job role (P < .01) and was highest among pathology and laboratory professionals. Disparities in burnout rate were observed by race. Fifty-six percent (1323 of 2363) of respondents felt that they had at least 1 symptom of burnout and were advancing toward a breaking point. Underlying factors ranked highly among all groups included control over workload and loss of meaning in work. CONCLUSIONS.— Data provided from this cohort may help departments create successful strategies to reduce disengagement and burnout in the laboratory, especially during periods of increased stress as experienced during the COVID-19 pandemic. Further, these data may serve as a baseline comparison for future studies.
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Affiliation(s)
- Stephen M Smith
- From the Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada (Smith)
| | - Daniel Liauw
- The Department of Internal Medicine, Brigham & Women's Hospital, Boston, Massachusetts (Liauw)
| | - David Dupee
- The Department of Psychiatry, Stanford University School of Medicine, Palo Alto, California (Dupee)
| | - Andrea L Barbieri
- The Department of Pathology (Barbieri, Parkash), Yale University School of Medicine, New Haven, Connecticut
| | - Kristine Olson
- The Department of Internal Medicine (Olson), Yale University School of Medicine, New Haven, Connecticut
| | - Vinita Parkash
- The Department of Pathology (Barbieri, Parkash), Yale University School of Medicine, New Haven, Connecticut
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Duff E, Zelaya F, Almagro FA, Miller KL, Martin N, Nichols TE, Taschler B, Griffanti L, Arthofer C, Douaud G, Wang C, Okell TW, Bethlehem RAI, Eickel K, Günther M, Menon DK, Williams G, Facer B, Lythgoe DJ, Dell’Acqua F, Wood GK, Williams SCR, Houston G, Keller SS, Holden C, Hartmann M, George L, Breen G, Michael BD, Jezzard P, Smith SM, Bullmore ET. Reliability of multi-site UK Biobank MRI brain phenotypes for the assessment of neuropsychiatric complications of SARS-CoV-2 infection: The COVID-CNS travelling heads study. PLoS One 2022; 17:e0273704. [PMID: 36173949 PMCID: PMC9522299 DOI: 10.1371/journal.pone.0273704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 08/11/2022] [Indexed: 12/29/2022] Open
Abstract
INTRODUCTION Magnetic resonance imaging (MRI) of the brain could be a key diagnostic and research tool for understanding the neuropsychiatric complications of COVID-19. For maximum impact, multi-modal MRI protocols will be needed to measure the effects of SARS-CoV-2 infection on the brain by diverse potentially pathogenic mechanisms, and with high reliability across multiple sites and scanner manufacturers. Here we describe the development of such a protocol, based upon the UK Biobank, and its validation with a travelling heads study. A multi-modal brain MRI protocol comprising sequences for T1-weighted MRI, T2-FLAIR, diffusion MRI (dMRI), resting-state functional MRI (fMRI), susceptibility-weighted imaging (swMRI), and arterial spin labelling (ASL), was defined in close approximation to prior UK Biobank (UKB) and C-MORE protocols for Siemens 3T systems. We iteratively defined a comparable set of sequences for General Electric (GE) 3T systems. To assess multi-site feasibility and between-site variability of this protocol, N = 8 healthy participants were each scanned at 4 UK sites: 3 using Siemens PRISMA scanners (Cambridge, Liverpool, Oxford) and 1 using a GE scanner (King's College London). Over 2,000 Imaging Derived Phenotypes (IDPs), measuring both data quality and regional image properties of interest, were automatically estimated by customised UKB image processing pipelines (S2 File). Components of variance and intra-class correlations (ICCs) were estimated for each IDP by linear mixed effects models and benchmarked by comparison to repeated measurements of the same IDPs from UKB participants. Intra-class correlations for many IDPs indicated good-to-excellent between-site reliability. Considering only data from the Siemens sites, between-site reliability generally matched the high levels of test-retest reliability of the same IDPs estimated in repeated, within-site, within-subject scans from UK Biobank. Inclusion of the GE site resulted in good-to-excellent reliability for many IDPs, although there were significant between-site differences in mean and scaling, and reduced ICCs, for some classes of IDP, especially T1 contrast and some dMRI-derived measures. We also identified high reliability of quantitative susceptibility mapping (QSM) IDPs derived from swMRI images, multi-network ICA-based IDPs from resting-state fMRI, and olfactory bulb structure IDPs from T1, T2-FLAIR and dMRI data. CONCLUSION These results give confidence that large, multi-site MRI datasets can be collected reliably at different sites across the diverse range of MRI modalities and IDPs that could be mechanistically informative in COVID brain research. We discuss limitations of the study and strategies for further harmonisation of data collected from sites using scanners supplied by different manufacturers. These acquisition and analysis protocols are now in use for MRI assessments of post-COVID patients (N = 700) as part of the ongoing COVID-CNS study.
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Affiliation(s)
- Eugene Duff
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), University of Oxford, Oxford, United Kingdom
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- Department of Brain Sciences, UK Dementia Research Institute, Imperial College London, London, United Kingdom
| | - Fernando Zelaya
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Fidel Alfaro Almagro
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), University of Oxford, Oxford, United Kingdom
| | - Karla L. Miller
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), University of Oxford, Oxford, United Kingdom
| | - Naomi Martin
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Thomas E. Nichols
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), University of Oxford, Oxford, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Bernd Taschler
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), University of Oxford, Oxford, United Kingdom
| | - Ludovica Griffanti
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Integrative Neuroimaging, Oxford Centre for Human Brain Activity, Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - Christoph Arthofer
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), University of Oxford, Oxford, United Kingdom
| | - Gwenaëlle Douaud
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), University of Oxford, Oxford, United Kingdom
| | - Chaoyue Wang
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), University of Oxford, Oxford, United Kingdom
| | - Thomas W. Okell
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), University of Oxford, Oxford, United Kingdom
| | | | | | - Matthias Günther
- mediri GmbH, Heidelberg, Germany
- University of Bremen, Bremen, Germany
- Fraunhofer MEVIS, Bremen, Germany
| | - David K. Menon
- Division of Anaesthesia, University of Cambridge, Cambridge, United Kingdom
| | - Guy Williams
- Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Bethany Facer
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - David J. Lythgoe
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Flavio Dell’Acqua
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- NatBrainLab, Department of Forensics and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- Sackler Institute for Translational Neurodevelopment, Institute of Psychiatry Psychology and Neuroscience, King’s College London, United Kingdom
| | - Greta K. Wood
- Clinical Infection Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, Liverpool, United Kingdom
| | - Steven C. R. Williams
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Gavin Houston
- GE Healthcare, Global Research Organisation, United Kingdom
| | - Simon S. Keller
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Catherine Holden
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Monika Hartmann
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Lily George
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Gerome Breen
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Benedict D. Michael
- Clinical Infection Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, Liverpool, United Kingdom
| | - Peter Jezzard
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), University of Oxford, Oxford, United Kingdom
| | - Stephen M. Smith
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), University of Oxford, Oxford, United Kingdom
| | - Edward T. Bullmore
- Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
- Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
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Taschler B, Smith SM, Nichols TE. Causal inference on neuroimaging data with Mendelian randomisation. Neuroimage 2022; 258:119385. [PMID: 35714886 PMCID: PMC10933777 DOI: 10.1016/j.neuroimage.2022.119385] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/30/2022] [Accepted: 06/12/2022] [Indexed: 10/18/2022] Open
Abstract
While population-scale neuroimaging studies offer the promise of discovery and characterisation of subtle risk factors, massive sample sizes increase the power for both meaningful associations and those attributable to confounds. This motivates the need for causal modelling of observational data that goes beyond statements of association and towards deeper understanding of complex relationships between individual traits and phenotypes, clinical biomarkers, genetic variation, and brain-related measures of health. Mendelian randomisation (MR) presents a way to obtain causal inference on the basis of genetic data and explicit assumptions about the relationship between genetic variables, exposure and outcome. In this work, we provide an introduction to and overview of causal inference methods based on Mendelian randomisation, with examples involving imaging-derived phenotypes from UK Biobank to make these methods accessible to neuroimaging researchers. We motivate the use of MR techniques, lay out the underlying assumptions, introduce common MR methods and focus on several scenarios in which modelling assumptions are potentially violated, resulting in biased effect estimates. Importantly, we give a detailed account of necessary steps to increase the reliability of MR results with rigorous sensitivity analyses.
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Affiliation(s)
- Bernd Taschler
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
| | - Stephen M Smith
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Thomas E Nichols
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, City Oxford, UK
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Smith SM, Lee A, Tong S, Leung S, Hongo H, Rivera J, Sweet-Cordero A, Michlitsch J, Stieglitz E. Detection of a GLIS3 fusion in an infant with AML refractory to chemotherapy. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006220. [PMID: 35927023 PMCID: PMC9528968 DOI: 10.1101/mcs.a006220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/21/2022] [Indexed: 11/25/2022] Open
Abstract
Infants diagnosed with acute myeloid leukemia (AML) frequently harbor cytogenetically cryptic fusions involving KMT2A, NUP98 or GLIS2. Those with AML driven specifically by CBFA2T3::GLIS2 fusions have a dismal prognosis and are currently risk-stratified to receive hematopoietic stem cell transplantation (HSCT) in first remission. Here we report an infant with AML who was refractory to multiple lines of chemotherapy but lacked an identifiable fusion despite cytogenetic, fluorescence in situ hybridization (FISH) and targeted next generation sequencing (NGS) testing. Research-grade RNASeq from a relapse sample revealed in-frame CBFA2T3::GLIS3 and GLIS3::CBFA2T3 fusions. A patient-derived xenograft (PDX) generated from this patient has a short latency period and represents a strategy to test novel agents that may be effective in this aggressive subtype of AML. This report describes the first case of AML with a CBFA2T3::GLIS3 fusion and highlights the need for unbiased NGS testing including RNASeq at diagnosis, as patients with CBFA2T3::GLIS3 fusions should be considered for HSCT in first remission.
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Affiliation(s)
| | - Alex Lee
- UCSF Benioff Children's Hospital San Francisco
| | | | | | - Henry Hongo
- UCSF Benioff Children's Hospital San Francisco
| | - Jose Rivera
- UCSF Benioff Children's Hospital San Francisco
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Leonardsen EH, Peng H, Kaufmann T, Agartz I, Andreassen OA, Celius EG, Espeseth T, Harbo HF, Høgestøl EA, Lange AMD, Marquand AF, Vidal-Piñeiro D, Roe JM, Selbæk G, Sørensen Ø, Smith SM, Westlye LT, Wolfers T, Wang Y. Deep neural networks learn general and clinically relevant representations of the ageing brain. Neuroimage 2022; 256:119210. [PMID: 35462035 PMCID: PMC7614754 DOI: 10.1016/j.neuroimage.2022.119210] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/16/2022] [Accepted: 04/11/2022] [Indexed: 12/17/2022] Open
Abstract
The discrepancy between chronological age and the apparent age of the brain based on neuroimaging data - the brain age delta - has emerged as a reliable marker of brain health. With an increasing wealth of data, approaches to tackle heterogeneity in data acquisition are vital. To this end, we compiled raw structural magnetic resonance images into one of the largest and most diverse datasets assembled (n=53542), and trained convolutional neural networks (CNNs) to predict age. We achieved state-of-the-art performance on unseen data from unknown scanners (n=2553), and showed that higher brain age delta is associated with diabetes, alcohol intake and smoking. Using transfer learning, the intermediate representations learned by our model complemented and partly outperformed brain age delta in predicting common brain disorders. Our work shows we can achieve generalizable and biologically plausible brain age predictions using CNNs trained on heterogeneous datasets, and transfer them to clinical use cases.
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Affiliation(s)
- Esten H Leonardsen
- Department of Psychology, University of Oslo, Oslo, Norway; Norwegian Centre for Mental Disorders Research (NORMENT), Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Han Peng
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), University of Oxford, Oxford, OX3 9DU, United Kingdom
| | - Tobias Kaufmann
- Norwegian Centre for Mental Disorders Research (NORMENT), Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Psychiatry and Psychotherapy, Tübingen Center for Mental Health, University of Tübingen, Germany
| | - Ingrid Agartz
- Norwegian Centre for Mental Disorders Research (NORMENT), Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway; Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet & Stockholm Health Care Services, Stockholm County Council, Stockholm, Sweden
| | - Ole A Andreassen
- Norwegian Centre for Mental Disorders Research (NORMENT), Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Elisabeth Gulowsen Celius
- Department of Neurology, Oslo University Hospital, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Thomas Espeseth
- Department of Psychology, University of Oslo, Oslo, Norway; Department of Psychology, Bjørknes University College, Oslo, Norway
| | - Hanne F Harbo
- Department of Neurology, Oslo University Hospital, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Einar A Høgestøl
- Department of Psychology, University of Oslo, Oslo, Norway; Norwegian Centre for Mental Disorders Research (NORMENT), Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Neurology, Oslo University Hospital, Norway
| | - Ann-Marie de Lange
- 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
| | - Andre F Marquand
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, Netherlands
| | | | - James M Roe
- Department of Psychology, University of Oslo, Oslo, Norway
| | - Geir Selbæk
- Norwegian National Advisory Unit on Aging and Health, Vestfold Hospital Trust, Tønsberg, Norway; Department of Geriatric Medicine, Oslo University Hospital, Oslo, Norway
| | | | - Stephen M Smith
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), University of Oxford, Oxford, OX3 9DU, United Kingdom
| | - Lars T Westlye
- Department of Psychology, University of Oslo, Oslo, Norway; Norwegian Centre for Mental Disorders Research (NORMENT), Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway; KG Jebsen Center for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - Thomas Wolfers
- Department of Psychology, University of Oslo, Oslo, Norway; Norwegian Centre for Mental Disorders Research (NORMENT), Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Yunpeng Wang
- Department of Psychology, University of Oslo, Oslo, Norway
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Wang X, Lundblad J, Smith SM. Reduced affinity of calcium sensing-receptor heterodimers and reduced mutant homodimer trafficking combine to impair function in a model of familial hypocalciuric hypercalcemia type 1. PLoS One 2022; 17:e0266993. [PMID: 35857775 PMCID: PMC9299317 DOI: 10.1371/journal.pone.0266993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/30/2022] [Indexed: 11/18/2022] Open
Abstract
Heterozygous loss-of-function mutation of the calcium sensing-receptor (CaSR), causes familial hypocalciuric hypercalcemia type 1 (FHH1), a typically benign condition characterized by mild hypercalcemia. In contrast, homozygous mutation of this dimer-forming G-protein coupled receptor manifests as the lethal neonatal severe hyperparathyroidism (NSHPT). To investigate the mechanisms by which CaSR mutations lead to these distinct disease states, we engineered wild-type (WT) and an exon 5-deficient disease-causing mutation, and transfected expression constructs into human embryonic kidney (HEK) cells. WT protein was mainly membrane-expressed whereas the mutant CaSR protein (mCaSR) was confined to the cytoplasm. Co-expression of WT CaSR directed mCaSR to the cell membrane. In assays of CaSR function, increases in extracellular [Ca2+] ([Ca2+]o) increased intracellular [Ca2+] ([Ca2+]i) in cells expressing WT CaSR while the response was reduced in cells co-expressing mutant and WT receptor. Untransfected cells or those expressing mCaSR alone, showed minimal, equivalent responses to increased [Ca2+]o. Immunoprecipitation experiments confirmed an association between mutant and wild-type CaSR. The affinity of the WT CaSR for calcium was three times greater than that of the heterodimer. The maximal functional response to [Ca]o was dependent on localization of CaSR to the membrane level and independent of homo- or heterodimerizations. In summary, these results suggest that heterodimerization of WT and mCaSR receptors, rescues the trafficking defect of the mutant receptors and also reduces the affinity of the WT-mutant heterodimer for [Ca]o. In contrast, the homozygous mutants do not produce functional receptors on cell membrane. These data indicate how substantial differences between signaling of hetero- and homodimeric mutants may lead to profound differences in the severity of disease in heterozygous and homozygous carriers of these mutations.
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Affiliation(s)
- Xiaohua Wang
- Division of Pulmonary and Critical Care Medicine, Oregon Health and Science University, Portland, Oregon, United States of America
| | - James Lundblad
- Division of Endocrinology and Diabetes, Oregon Health and Science University, Portland, Oregon, United States of America
- Section of Endocrinology and Diabetes, VA Portland Health Care System, Portland, Oregon, United States of America
| | - Stephen M. Smith
- Division of Pulmonary and Critical Care Medicine, Oregon Health and Science University, Portland, Oregon, United States of America
- Sections of Pulmonary and Critical Care Medicine and Research & Development, VA Portland Health Care System, Portland, Oregon, United States of America
- * E-mail:
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Topiwala A, Wang C, Ebmeier KP, Burgess S, Bell S, Levey DF, Zhou H, McCracken C, Roca-Fernández A, Petersen SE, Raman B, Husain M, Gelernter J, Miller KL, Smith SM, Nichols TE. Associations between moderate alcohol consumption, brain iron, and cognition in UK Biobank participants: Observational and mendelian randomization analyses. PLoS Med 2022; 19:e1004039. [PMID: 35834561 PMCID: PMC9282660 DOI: 10.1371/journal.pmed.1004039] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/01/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Brain iron deposition has been linked to several neurodegenerative conditions and reported in alcohol dependence. Whether iron accumulation occurs in moderate drinkers is unknown. Our objectives were to investigate evidence in support of causal relationships between alcohol consumption and brain iron levels and to examine whether higher brain iron represents a potential pathway to alcohol-related cognitive deficits. METHODS AND FINDINGS Observational associations between brain iron markers and alcohol consumption (n = 20,729 UK Biobank participants) were compared with associations with genetically predicted alcohol intake and alcohol use disorder from 2-sample mendelian randomization (MR). Alcohol intake was self-reported via a touchscreen questionnaire at baseline (2006 to 2010). Participants with complete data were included. Multiorgan susceptibility-weighted magnetic resonance imaging (9.60 ± 1.10 years after baseline) was used to ascertain iron content of each brain region (quantitative susceptibility mapping (QSM) and T2*) and liver tissues (T2*), a marker of systemic iron. Main outcomes were susceptibility (χ) and T2*, measures used as indices of iron deposition. Brain regions of interest included putamen, caudate, hippocampi, thalami, and substantia nigra. Potential pathways to alcohol-related iron brain accumulation through elevated systemic iron stores (liver) were explored in causal mediation analysis. Cognition was assessed at the scan and in online follow-up (5.82 ± 0.86 years after baseline). Executive function was assessed with the trail-making test, fluid intelligence with puzzle tasks, and reaction time by a task based on the "Snap" card game. Mean age was 54.8 ± 7.4 years and 48.6% were female. Weekly alcohol consumption was 17.7 ± 15.9 units and never drinkers comprised 2.7% of the sample. Alcohol consumption was associated with markers of higher iron (χ) in putamen (β = 0.08 standard deviation (SD) [95% confidence interval (CI) 0.06 to 0.09], p < 0.001), caudate (β = 0.05 [0.04 to 0.07], p < 0.001), and substantia nigra (β = 0.03 [0.02 to 0.05], p < 0.001) and lower iron in the thalami (β = -0.06 [-0.07 to -0.04], p < 0.001). Quintile-based analyses found these associations in those consuming >7 units (56 g) alcohol weekly. MR analyses provided weak evidence these relationships are causal. Genetically predicted alcoholic drinks weekly positively associated with putamen and hippocampus susceptibility; however, these associations did not survive multiple testing corrections. Weak evidence for a causal relationship between genetically predicted alcohol use disorder and higher putamen susceptibility was observed; however, this was not robust to multiple comparisons correction. Genetically predicted alcohol use disorder was associated with serum iron and transferrin saturation. Elevated liver iron was observed at just >11 units (88 g) alcohol weekly c.f. <7 units (56 g). Systemic iron levels partially mediated associations of alcohol intake with brain iron. Markers of higher basal ganglia iron associated with slower executive function, lower fluid intelligence, and slower reaction times. The main limitations of the study include that χ and T2* can reflect changes in myelin as well as iron, alcohol use was self-reported, and MR estimates can be influenced by genetic pleiotropy. CONCLUSIONS To the best of our knowledge, this study represents the largest investigation of moderate alcohol consumption and iron homeostasis to date. Alcohol consumption above 7 units weekly associated with higher brain iron. Iron accumulation represents a potential mechanism for alcohol-related cognitive decline.
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Affiliation(s)
- Anya Topiwala
- Nuffield Department Population Health, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Chaoyue Wang
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), Oxford University, Oxford, United Kingdom
| | - Klaus P. Ebmeier
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, United Kingdom
| | - Stephen Burgess
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Steven Bell
- Department of Clinical Neurosciences, University of Cambridge, United Kingdom
| | - Daniel F. Levey
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Psychiatry, Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, United States of America
| | - Hang Zhou
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Psychiatry, Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, United States of America
| | - Celeste McCracken
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | | | - Steffen E. Petersen
- William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London, Charterhouse Square, London, United Kingdom
- Barts Heart Centre, St Bartholomew’s Hospital, Barts Health NHS Trust, West Smithfield, London, United Kingdom
- Health Data Research UK, London, United Kingdom
- Alan Turing Institute, London, United Kingdom
| | - Betty Raman
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Masud Husain
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), Oxford University, Oxford, United Kingdom
- Department of Experimental Psychology, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, United Kingdom
- Division of Clinical Neurology, John Radcliffe Hospital, Oxford University Hospitals Trust, Oxford, United Kingdom
| | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Psychiatry, Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, United States of America
| | - Karla L. Miller
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), Oxford University, Oxford, United Kingdom
| | - Stephen M. Smith
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), Oxford University, Oxford, United Kingdom
| | - Thomas E. Nichols
- Nuffield Department Population Health, Big Data Institute, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), Oxford University, Oxford, United Kingdom
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Liu Z, Whitaker KJ, Smith SM, Nichols TE. Improved Interpretability of Brain-Behavior CCA With Domain-Driven Dimension Reduction. Front Neurosci 2022; 16:851827. [PMID: 35812221 PMCID: PMC9262103 DOI: 10.3389/fnins.2022.851827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Canonical Correlation Analysis (CCA) has been widely applied to study correlations between neuroimaging data and behavioral data. Practical use of CCA typically requires dimensionality reduction with, for example, Principal Components Analysis (PCA), however, this can result in CCA components that are difficult to interpret. In this paper, we introduce a Domain-driven Dimension Reduction (DDR) method, reducing the dimensionality of the original datasets and combining human knowledge of the structure of the variables studied. We apply the method to the Human Connectome Project S1200 release and compare standard PCA across all variables with DDR applied to individual classes of variables, finding that DDR-CCA results are more stable and interpretable, allowing the contribution of each class of variable to be better understood. By carefully designing the analysis pipeline and cross-validating the results, we offer more insights into the interpretation of CCA applied to brain-behavior data.
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Affiliation(s)
- Zhangdaihong Liu
- Mathematics for Real-World Systems Centre for Doctor Training, University of Warwick, Coventry, United Kingdom
| | | | - Stephen M. Smith
- Wellcome Centre for Integrative Neuroimaging, Functional MRI of the Brain, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Thomas E. Nichols
- Wellcome Centre for Integrative Neuroimaging, Functional MRI of the Brain, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Population Health, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
- *Correspondence: Thomas E. Nichols
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Blasco MA, Noel CW, Truong T, Huang SH, Goldstein DP, Irish JC, Gilbert R, Hosni A, Hope A, O'Sullivan B, Waldron J, Perez-Ordonez B, Weinreb I, Smith SM, Bartlett E, Yu E, de Almeida JR. Radiologic-pathologic correlation of major versus minor extranodal extension in oral cavity cancer. Head Neck 2022; 44:1422-1429. [PMID: 35315548 DOI: 10.1002/hed.27036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 02/12/2022] [Accepted: 03/09/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND To evaluate the diagnostic performance of radiologic extranodal extension (rENE) in predicting major (>2 mm) and minor (≤2 mm) pathologic ENE (pENE). METHODS All oral cavity squamous cell carcinoma patients who underwent neck dissection with pathological nodal disease (pN+) between 2010 and 2015 were reviewed. Preoperative computed tomography and/or magnetic resonance imaging were reviewed by two head and neck neuroradiologists. RESULTS Three hundred and thirty-four patients were included. The sensitivity and specificity of rENE were 37% [95% CI 29-44] and 98% [95% CI 96-100], respectively. Sensitivity for pENE improved in the subset of patients with major ENE (48% [95% CI 38-57]). The presence of rENE was associated with inferior 3-year overall survival: 26% [95% CI 17-41] versus 60% [95% CI 54-67]. CONCLUSIONS This large cohort study demonstrates high specificity, but low sensitivity for preoperative imaging in the detection of pENE in OCSCC. Patients with rENE demonstrated poor OS. pENE in the absence of rENE is still an adverse risk factor.
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Affiliation(s)
- Michael A Blasco
- Department of Otolaryngology-Head and Neck Surgery/Surgical Oncology, Princess Margaret Cancer Centre-University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Christopher W Noel
- Department of Otolaryngology-Head and Neck Surgery/Surgical Oncology, Princess Margaret Cancer Centre-University Health Network, University of Toronto, Toronto, Ontario, Canada.,Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Tra Truong
- Department of Pathology, Princess Margaret Cancer Centre-University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Shao Hui Huang
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada.,Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - David P Goldstein
- Department of Otolaryngology-Head and Neck Surgery/Surgical Oncology, Princess Margaret Cancer Centre-University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan C Irish
- Department of Otolaryngology-Head and Neck Surgery/Surgical Oncology, Princess Margaret Cancer Centre-University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Ralph Gilbert
- Department of Otolaryngology-Head and Neck Surgery/Surgical Oncology, Princess Margaret Cancer Centre-University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Ali Hosni
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada.,Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Andrew Hope
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada.,Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Brian O'Sullivan
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada.,Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - John Waldron
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada.,Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Bayardo Perez-Ordonez
- Department of Pathology, Princess Margaret Cancer Centre-University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Ilan Weinreb
- Department of Pathology, Princess Margaret Cancer Centre-University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Stephen M Smith
- Department of Pathology, Princess Margaret Cancer Centre-University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Eric Bartlett
- Department of Neuroradiology and Head and Neck Imaging, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Eugene Yu
- Department of Neuroradiology and Head and Neck Imaging, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - John R de Almeida
- Department of Otolaryngology-Head and Neck Surgery/Surgical Oncology, Princess Margaret Cancer Centre-University Health Network, University of Toronto, Toronto, Ontario, Canada.,Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
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Wang C, Martins-Bach AB, Alfaro-Almagro F, Douaud G, Klein JC, Llera A, Fiscone C, Bowtell R, Elliott LT, Smith SM, Tendler BC, Miller KL. Phenotypic and genetic associations of quantitative magnetic susceptibility in UK Biobank brain imaging. Nat Neurosci 2022; 25:818-831. [PMID: 35606419 PMCID: PMC9174052 DOI: 10.1038/s41593-022-01074-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 04/11/2022] [Indexed: 12/17/2022]
Abstract
A key aim in epidemiological neuroscience is identification of markers to assess brain health and monitor therapeutic interventions. Quantitative susceptibility mapping (QSM) is an emerging magnetic resonance imaging technique that measures tissue magnetic susceptibility and has been shown to detect pathological changes in tissue iron, myelin and calcification. We present an open resource of QSM-based imaging measures of multiple brain structures in 35,273 individuals from the UK Biobank prospective epidemiological study. We identify statistically significant associations of 251 phenotypes with magnetic susceptibility that include body iron, disease, diet and alcohol consumption. Genome-wide associations relate magnetic susceptibility to 76 replicating clusters of genetic variants with biological functions involving iron, calcium, myelin and extracellular matrix. These patterns of associations include relationships that are unique to QSM, in particular being complementary to T2* signal decay time measures. These new imaging phenotypes are being integrated into the core UK Biobank measures provided to researchers worldwide, creating the potential to discover new, non-invasive markers of brain health.
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Affiliation(s)
- Chaoyue Wang
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
| | - Aurea B Martins-Bach
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Fidel Alfaro-Almagro
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Gwenaëlle Douaud
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Johannes C Klein
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK
| | - Alberto Llera
- Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Nijmegen, the Netherlands
| | - Cristiana Fiscone
- Sir Peter Mansfield Imaging Centre, School of Physics and Astronomy, University of Nottingham, Nottingham, UK
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Richard Bowtell
- Sir Peter Mansfield Imaging Centre, School of Physics and Astronomy, University of Nottingham, Nottingham, UK
| | - Lloyd T Elliott
- Department of Statistics and Actuarial Science, Simon Fraser University, Vancouver, British Columbia, Canada
| | - Stephen M Smith
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Benjamin C Tendler
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Karla L Miller
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
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40
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Edwards AD, Rueckert D, Smith SM, Abo Seada S, Alansary A, Almalbis J, Allsop J, Andersson J, Arichi T, Arulkumaran S, Bastiani M, Batalle D, Baxter L, Bozek J, Braithwaite E, Brandon J, Carney O, Chew A, Christiaens D, Chung R, Colford K, Cordero-Grande L, Counsell SJ, Cullen H, Cupitt J, Curtis C, Davidson A, Deprez M, Dillon L, Dimitrakopoulou K, Dimitrova R, Duff E, Falconer S, Farahibozorg SR, Fitzgibbon SP, Gao J, Gaspar A, Harper N, Harrison SJ, Hughes EJ, Hutter J, Jenkinson M, Jbabdi S, Jones E, Karolis V, Kyriakopoulou V, Lenz G, Makropoulos A, Malik S, Mason L, Mortari F, Nosarti C, Nunes RG, O’Keeffe C, O’Muircheartaigh J, Patel H, Passerat-Palmbach J, Pietsch M, Price AN, Robinson EC, Rutherford MA, Schuh A, Sotiropoulos S, Steinweg J, Teixeira RPAG, Tenev T, Tournier JD, Tusor N, Uus A, Vecchiato K, Williams LZJ, Wright R, Wurie J, Hajnal JV. The Developing Human Connectome Project Neonatal Data Release. Front Neurosci 2022; 16:886772. [PMID: 35677357 PMCID: PMC9169090 DOI: 10.3389/fnins.2022.886772] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/19/2022] [Indexed: 11/24/2022] Open
Abstract
The Developing Human Connectome Project has created a large open science resource which provides researchers with data for investigating typical and atypical brain development across the perinatal period. It has collected 1228 multimodal magnetic resonance imaging (MRI) brain datasets from 1173 fetal and/or neonatal participants, together with collateral demographic, clinical, family, neurocognitive and genomic data from 1173 participants, together with collateral demographic, clinical, family, neurocognitive and genomic data. All subjects were studied in utero and/or soon after birth on a single MRI scanner using specially developed scanning sequences which included novel motion-tolerant imaging methods. Imaging data are complemented by rich demographic, clinical, neurodevelopmental, and genomic information. The project is now releasing a large set of neonatal data; fetal data will be described and released separately. This release includes scans from 783 infants of whom: 583 were healthy infants born at term; as well as preterm infants; and infants at high risk of atypical neurocognitive development. Many infants were imaged more than once to provide longitudinal data, and the total number of datasets being released is 887. We now describe the dHCP image acquisition and processing protocols, summarize the available imaging and collateral data, and provide information on how the data can be accessed.
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Affiliation(s)
- A. David Edwards
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King’s College London, London, United Kingdom
| | - Daniel Rueckert
- Biomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom
- Institute for AI and Informatics in Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Stephen M. Smith
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Samy Abo Seada
- Biomedical Engineering Department, School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
| | - Amir Alansary
- Biomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom
| | - Jennifer Almalbis
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Joanna Allsop
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Jesper Andersson
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Tomoki Arichi
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King’s College London, London, United Kingdom
| | - Sophie Arulkumaran
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Matteo Bastiani
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Sir Peter Mansfield Imaging Centre, Mental Health and Clinical Neurosciences, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Dafnis Batalle
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Luke Baxter
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Jelena Bozek
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Eleanor Braithwaite
- Centre for Brain and Cognitive Development, Department of Psychological Sciences, Birkbeck, University of London, London, United Kingdom
| | - Jacqueline Brandon
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Olivia Carney
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Andrew Chew
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Daan Christiaens
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Raymond Chung
- BioResource Centre, NIHR Biomedical Research Centre, South London and Maudsley NHS Trust, London, United Kingdom
| | - Kathleen Colford
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Lucilio Cordero-Grande
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Biomedical Image Technologies, ETSI Telecomunicación, Universidad Politécnica de Madrid and CIBER-BBN, Madrid, Spain
| | - Serena J. Counsell
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Harriet Cullen
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King’s College London, London, United Kingdom
| | - John Cupitt
- Biomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom
| | - Charles Curtis
- BioResource Centre, NIHR Biomedical Research Centre, South London and Maudsley NHS Trust, London, United Kingdom
| | - Alice Davidson
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Maria Deprez
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Biomedical Engineering Department, School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
| | - Louise Dillon
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Konstantina Dimitrakopoulou
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Translational Bioinformatics Platform, NIHR Biomedical Research Centre, Guy’s and St. Thomas’ NHS Foundation Trust and King’s College London, London, United Kingdom
| | - Ralica Dimitrova
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Eugene Duff
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Shona Falconer
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Seyedeh-Rezvan Farahibozorg
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Sean P. Fitzgibbon
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Jianliang Gao
- Biomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom
| | - Andreia Gaspar
- Institute for Systems and Robotics (ISR-Lisboa)/LaRSyS, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Nicholas Harper
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Sam J. Harrison
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Emer J. Hughes
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Jana Hutter
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Biomedical Engineering Department, School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
| | - Mark Jenkinson
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Saad Jbabdi
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Emily Jones
- Centre for Brain and Cognitive Development, Department of Psychological Sciences, Birkbeck, University of London, London, United Kingdom
| | - Vyacheslav Karolis
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Vanessa Kyriakopoulou
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Gregor Lenz
- Biomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom
| | - Antonios Makropoulos
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Biomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom
| | - Shaihan Malik
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Biomedical Engineering Department, School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
| | - Luke Mason
- Centre for Brain and Cognitive Development, Department of Psychological Sciences, Birkbeck, University of London, London, United Kingdom
| | - Filippo Mortari
- Biomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom
| | - Chiara Nosarti
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Rita G. Nunes
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Institute for Systems and Robotics (ISR-Lisboa)/LaRSyS, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Camilla O’Keeffe
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Jonathan O’Muircheartaigh
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King’s College London, London, United Kingdom
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Hamel Patel
- BioResource Centre, NIHR Biomedical Research Centre, South London and Maudsley NHS Trust, London, United Kingdom
| | - Jonathan Passerat-Palmbach
- Biomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom
| | - Maximillian Pietsch
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Anthony N. Price
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Biomedical Engineering Department, School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
| | - Emma C. Robinson
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Biomedical Engineering Department, School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
| | - Mary A. Rutherford
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Andreas Schuh
- Biomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom
| | - Stamatios Sotiropoulos
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Sir Peter Mansfield Imaging Centre, Mental Health and Clinical Neurosciences, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Johannes Steinweg
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Rui Pedro Azeredo Gomes Teixeira
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Biomedical Engineering Department, School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
| | - Tencho Tenev
- Biomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom
| | - Jacques-Donald Tournier
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Biomedical Engineering Department, School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
| | - Nora Tusor
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Alena Uus
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Biomedical Engineering Department, School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
| | - Katy Vecchiato
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Logan Z. J. Williams
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Robert Wright
- Biomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom
| | - Julia Wurie
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
| | - Joseph V. Hajnal
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King’s College London, London, United Kingdom
- Biomedical Engineering Department, School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
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Smith SM, Parkash V. Impeded Delivery of Pathology and Laboratory Medicine Services by Corruption Is Not Unique to Resource-Limited Settings. Am J Clin Pathol 2022; 158:443. [PMID: 35599544 DOI: 10.1093/ajcp/aqac057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Stephen M Smith
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Canada
| | - Vinita Parkash
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
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42
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Douaud G, Lee S, Alfaro-Almagro F, Arthofer C, Wang C, McCarthy P, Lange F, Andersson JLR, Griffanti L, Duff E, Jbabdi S, Taschler B, Keating P, Winkler AM, Collins R, Matthews PM, Allen N, Miller KL, Nichols TE, Smith SM. SARS-CoV-2 is associated with changes in brain structure in UK Biobank. Nature 2022. [DOI: 10.1038/s41586-022-04569-5 3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
AbstractThere is strong evidence of brain-related abnormalities in COVID-191–13. However, it remains unknown whether the impact of SARS-CoV-2 infection can be detected in milder cases, and whether this can reveal possible mechanisms contributing to brain pathology. Here we investigated brain changes in 785 participants of UK Biobank (aged 51–81 years) who were imaged twice using magnetic resonance imaging, including 401 cases who tested positive for infection with SARS-CoV-2 between their two scans—with 141 days on average separating their diagnosis and the second scan—as well as 384 controls. The availability of pre-infection imaging data reduces the likelihood of pre-existing risk factors being misinterpreted as disease effects. We identified significant longitudinal effects when comparing the two groups, including (1) a greater reduction in grey matter thickness and tissue contrast in the orbitofrontal cortex and parahippocampal gyrus; (2) greater changes in markers of tissue damage in regions that are functionally connected to the primary olfactory cortex; and (3) a greater reduction in global brain size in the SARS-CoV-2 cases. The participants who were infected with SARS-CoV-2 also showed on average a greater cognitive decline between the two time points. Importantly, these imaging and cognitive longitudinal effects were still observed after excluding the 15 patients who had been hospitalised. These mainly limbic brain imaging results may be the in vivo hallmarks of a degenerative spread of the disease through olfactory pathways, of neuroinflammatory events, or of the loss of sensory input due to anosmia. Whether this deleterious effect can be partially reversed, or whether these effects will persist in the long term, remains to be investigated with additional follow-up.
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43
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Zhao B, Li T, Smith SM, Xiong D, Wang X, Yang Y, Luo T, Zhu Z, Shan Y, Matoba N, Sun Q, Yang Y, Hauberg ME, Bendl J, Fullard JF, Roussos P, Lin W, Li Y, Stein JL, Zhu H. Common variants contribute to intrinsic human brain functional networks. Nat Genet 2022; 54:508-517. [PMID: 35393594 DOI: 10.1038/s41588-022-01039-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/28/2022] [Indexed: 01/01/2023]
Abstract
The human brain forms functional networks of correlated activity, which have been linked with both cognitive and clinical outcomes. However, the genetic variants affecting brain function are largely unknown. Here, we used resting-state functional magnetic resonance images from 47,276 individuals to discover and validate common genetic variants influencing intrinsic brain activity. We identified 45 new genetic regions associated with brain functional signatures (P < 2.8 × 10-11), including associations to the central executive, default mode, and salience networks involved in the triple-network model of psychopathology. A number of brain activity-associated loci colocalized with brain disorders (e.g., the APOE ε4 locus with Alzheimer's disease). Variation in brain function was genetically correlated with brain disorders, such as major depressive disorder and schizophrenia. Together, our study provides a step forward in understanding the genetic architecture of brain functional networks and their genetic links to brain-related complex traits and disorders.
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Affiliation(s)
- Bingxin Zhao
- Department of Statistics, Purdue University, West Lafayette, IN, USA
| | - Tengfei Li
- Department of Radiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Biomedical Research Imaging Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stephen M Smith
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Di Xiong
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xifeng Wang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yue Yang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tianyou Luo
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ziliang Zhu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yue Shan
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nana Matoba
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yuchen Yang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mads E Hauberg
- Department of Psychiatry, 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.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark
| | - Jaroslav Bendl
- Department of Psychiatry, 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 and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John F Fullard
- Department of Psychiatry, 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 and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Panagiotis Roussos
- Department of Psychiatry, 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.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Department of Genetics and Genomic Science and Institute for Multiscale Biology, 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, Bronx, NY, USA
| | - Weili Lin
- Biomedical Research Imaging Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hongtu Zhu
- Biomedical Research Imaging Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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44
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Douaud G, Lee S, Alfaro-Almagro F, Arthofer C, Wang C, McCarthy P, Lange F, Andersson JLR, Griffanti L, Duff E, Jbabdi S, Taschler B, Keating P, Winkler AM, Collins R, Matthews PM, Allen N, Miller KL, Nichols TE, Smith SM. SARS-CoV-2 is associated with changes in brain structure in UK Biobank. Nature 2022; 604:697-707. [PMID: 35255491 PMCID: PMC9046077 DOI: 10.1038/s41586-022-04569-5] [Citation(s) in RCA: 661] [Impact Index Per Article: 330.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/21/2022] [Indexed: 01/01/2023]
Abstract
There is strong evidence of brain-related abnormalities in COVID-191-13. However, it remains unknown whether the impact of SARS-CoV-2 infection can be detected in milder cases, and whether this can reveal possible mechanisms contributing to brain pathology. Here we investigated brain changes in 785 participants of UK Biobank (aged 51-81 years) who were imaged twice using magnetic resonance imaging, including 401 cases who tested positive for infection with SARS-CoV-2 between their two scans-with 141 days on average separating their diagnosis and the second scan-as well as 384 controls. The availability of pre-infection imaging data reduces the likelihood of pre-existing risk factors being misinterpreted as disease effects. We identified significant longitudinal effects when comparing the two groups, including (1) a greater reduction in grey matter thickness and tissue contrast in the orbitofrontal cortex and parahippocampal gyrus; (2) greater changes in markers of tissue damage in regions that are functionally connected to the primary olfactory cortex; and (3) a greater reduction in global brain size in the SARS-CoV-2 cases. The participants who were infected with SARS-CoV-2 also showed on average a greater cognitive decline between the two time points. Importantly, these imaging and cognitive longitudinal effects were still observed after excluding the 15 patients who had been hospitalised. These mainly limbic brain imaging results may be the in vivo hallmarks of a degenerative spread of the disease through olfactory pathways, of neuroinflammatory events, or of the loss of sensory input due to anosmia. Whether this deleterious effect can be partially reversed, or whether these effects will persist in the long term, remains to be investigated with additional follow-up.
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Affiliation(s)
- Gwenaëlle Douaud
- FMRIB Centre, Wellcome Centre for Integrative Neuroimaging (WIN), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
| | - Soojin Lee
- FMRIB Centre, Wellcome Centre for Integrative Neuroimaging (WIN), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Fidel Alfaro-Almagro
- FMRIB Centre, Wellcome Centre for Integrative Neuroimaging (WIN), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Christoph Arthofer
- FMRIB Centre, Wellcome Centre for Integrative Neuroimaging (WIN), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Chaoyue Wang
- FMRIB Centre, Wellcome Centre for Integrative Neuroimaging (WIN), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Paul McCarthy
- FMRIB Centre, Wellcome Centre for Integrative Neuroimaging (WIN), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Frederik Lange
- FMRIB Centre, Wellcome Centre for Integrative Neuroimaging (WIN), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Jesper L R Andersson
- FMRIB Centre, Wellcome Centre for Integrative Neuroimaging (WIN), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Ludovica Griffanti
- FMRIB Centre, Wellcome Centre for Integrative Neuroimaging (WIN), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- OHBA, Wellcome Centre for Integrative Neuroimaging (WIN), Department of Psychiatry, University of Oxford, Oxford, UK
| | - Eugene Duff
- FMRIB Centre, Wellcome Centre for Integrative Neuroimaging (WIN), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Saad Jbabdi
- FMRIB Centre, Wellcome Centre for Integrative Neuroimaging (WIN), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Bernd Taschler
- FMRIB Centre, Wellcome Centre for Integrative Neuroimaging (WIN), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Peter Keating
- Ear Institute, University College London, London, UK
| | - Anderson M Winkler
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Rory Collins
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Paul M Matthews
- UK Dementia Research Institute and Department of Brain Sciences, Imperial College, London, UK
| | - Naomi Allen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Karla L Miller
- FMRIB Centre, Wellcome Centre for Integrative Neuroimaging (WIN), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | | | - Stephen M Smith
- FMRIB Centre, Wellcome Centre for Integrative Neuroimaging (WIN), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
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45
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Douaud G, Lee S, Alfaro-Almagro F, Arthofer C, Wang C, McCarthy P, Lange F, Andersson JLR, Griffanti L, Duff E, Jbabdi S, Taschler B, Keating P, Winkler AM, Collins R, Matthews PM, Allen N, Miller KL, Nichols TE, Smith SM. SARS-CoV-2 is associated with changes in brain structure in UK Biobank. medRxiv 2022:2021.06.11.21258690. [PMID: 34189535 PMCID: PMC8240690 DOI: 10.1101/2021.06.11.21258690] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
There is strong evidence for brain-related abnormalities in COVID-19 1-13 . It remains unknown however whether the impact of SARS-CoV-2 infection can be detected in milder cases, and whether this can reveal possible mechanisms contributing to brain pathology. Here, we investigated brain changes in 785 UK Biobank participants (aged 51-81) imaged twice, including 401 cases who tested positive for infection with SARS-CoV-2 between their two scans, with 141 days on average separating their diagnosis and second scan, and 384 controls. The availability of pre-infection imaging data reduces the likelihood of pre-existing risk factors being misinterpreted as disease effects. We identified significant longitudinal effects when comparing the two groups, including: (i) greater reduction in grey matter thickness and tissue-contrast in the orbitofrontal cortex and parahippocampal gyrus, (ii) greater changes in markers of tissue damage in regions functionally-connected to the primary olfactory cortex, and (iii) greater reduction in global brain size. The infected participants also showed on average larger cognitive decline between the two timepoints. Importantly, these imaging and cognitive longitudinal effects were still seen after excluding the 15 cases who had been hospitalised. These mainly limbic brain imaging results may be the in vivo hallmarks of a degenerative spread of the disease via olfactory pathways, of neuroinflammatory events, or of the loss of sensory input due to anosmia. Whether this deleterious impact can be partially reversed, or whether these effects will persist in the long term, remains to be investigated with additional follow up.
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46
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Allen MR, Peters GP, Shine KP, Azar C, Balcombe P, Boucher O, Cain M, Ciais P, Collins W, Forster PM, Frame DJ, Friedlingstein P, Fyson C, Gasser T, Hare B, Jenkins S, Hamburg SP, Johansson DJA, Lynch J, Macey A, Morfeldt J, Nauels A, Ocko I, Oppenheimer M, Pacala SW, Pierrehumbert R, Rogelj J, Schaeffer M, Schleussner CF, Shindell D, Skeie RB, Smith SM, Tanaka K. Indicate separate contributions of long-lived and short-lived greenhouse gases in emission targets. NPJ Clim Atmos Sci 2022; 5:5. [PMID: 35295182 PMCID: PMC7612487 DOI: 10.1038/s41612-021-00226-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Myles R. Allen
- School of Geography and the Environment and Department of Physics, University of Oxford, Oxford, UK
| | - Glen P. Peters
- CICERO Centre for International Climate Research, Oslo, Norway
| | - Keith P. Shine
- Department of Meteorology, University of Reading, Reading, UK
| | | | | | | | | | - Philippe Ciais
- Laboratoire des Sciences du Climat et de l’Environnement, Gif-sur-Yvette, France
| | | | | | - Dave J. Frame
- Victoria University of Wellington, Wellington, New Zealand
| | | | | | - Thomas Gasser
- International Institute for Applied Systems Analysis (IIASA), Vienna, Austria
| | | | | | | | | | | | - Adrian Macey
- Victoria University of Wellington, Wellington, New Zealand
| | | | | | - Ilissa Ocko
- Environmental Defence Fund, New York, NY, USA
| | | | | | | | | | | | | | | | | | | | - Katsumasa Tanaka
- Laboratoire des Sciences du Climat et de l’Environnement, Gif-sur-Yvette, France
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47
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Feusner JD, Farrell NR, Kreyling J, McGrath PB, Rhode A, Faneuff T, Lonsway S, Mohideen R, Jurich JE, Trusky L, Smith SM. Online Video Teletherapy Treatment of Obsessive-Compulsive Disorder Using Exposure and Response Prevention: Clinical Outcomes from a Retrospective Longitudinal Observational Study (Preprint). J Med Internet Res 2022; 24:e36431. [PMID: 35587365 PMCID: PMC9164091 DOI: 10.2196/36431] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/07/2022] [Accepted: 04/25/2022] [Indexed: 12/22/2022] Open
Abstract
Background Exposure and response prevention, a type of cognitive-behavioral therapy, is an effective first-line treatment for obsessive-compulsive disorder (OCD). Despite extensive evidence of the efficacy of exposure and response prevention (ERP) from clinical studies and in real-world samples, it is still underused as a treatment. This is likely due to the limits to access to care that include the availability of adequately trained therapists, as well as geographical location, time, and cost barriers. To address these, NOCD created a digital behavioral health treatment for OCD using ERP delivered via video teletherapy and with technology-assisted elements including app-based therapy tools and between-session therapist messaging. Objective We examined treatment outcomes in a large naturalistic sample of 3552 adults with a primary OCD diagnosis who received NOCD treatment. Methods The treatment model consisted of twice-weekly, live, face-to-face video teletherapy ERP for 3 weeks, followed by 6 weeks of once-weekly brief video teletherapy check-ins for 30 minutes. Assessments were conducted at baseline, at midpoint after completion of 3 weeks of twice-weekly sessions, and at the end of 6 weeks of brief check-ins (endpoint). Longitudinal assessments were also obtained at 3, 6, 9, and 12 months after endpoint. Results Treatment resulted in clinically and statistically significant improvements, with a 43.4% mean reduction in obsessive-compulsive symptoms (g=1.0; 95% CI 0.93 to 1.03) and a 62.9% response rate. Treatment also resulted in a 44.2% mean reduction in depression, a 47.8% mean reduction in anxiety, and a 37.3% mean reduction in stress symptoms. Quality of life improved by a mean of 22.7%. Reduction in OCD symptoms and response rates were similar for those with mild, moderate, or severe symptoms. The mean duration of treatment was 11.5 (SD 4.0) weeks, and the mean total therapist time was 10.6 (SD 1.1) hours. Improvements were maintained at 3, 6, 9, and 12 months. Conclusions In this sample, representing the largest reported treated cohort of patients with OCD to date, video teletherapy treatment demonstrated effectiveness in reducing obsessive-compulsive and comorbid symptoms and improved quality of life. Further, it achieved meaningful results in less than half the total therapist time compared with standard once-weekly outpatient treatment, an efficiency that represents substantial monetary and time savings. The effect size was large and similar to studies of in-person ERP. This technology-assisted remote treatment is readily accessible for patients, offering an advancement in the field in the dissemination of effective evidence-based care for OCD.
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Affiliation(s)
- Jamie D Feusner
- NOCD Inc, Chicago, IL, United States
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- General Adult Psychiatry & Health Systems Division, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
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48
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Lindner JS, Rajayer SR, Martiszus BJ, Smith SM. Cinacalcet inhibition of neuronal action potentials preferentially targets the fast inactivated state of voltage-gated sodium channels. Front Physiol 2022; 13:1066467. [PMID: 36601343 PMCID: PMC9806421 DOI: 10.3389/fphys.2022.1066467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Voltage-gated sodium channel (VGSC) activation is essential for action potential generation in the brain. Allosteric calcium-sensing receptor (CaSR) agonist, cinacalcet, strongly and ubiquitously inhibits VGSC currents in neocortical neurons via an unidentified, G-protein-dependent inhibitory molecule. Here, using whole-cell patch VGSC clamp methods, we investigated the voltage-dependence of cinacalcet-mediated inhibition of VGSCs and the channel state preference of cinacalcet. The rate of inhibition of VGSC currents was accelerated at more depolarized holding potentials. Cinacalcet shifted the voltage-dependence of both fast and slow inactivation of VGSC currents in the hyperpolarizing direction. Utilizing a simple model, the voltage-dependence of VGSC current inhibition may be explained if the affinity of the inhibitory molecule to the channel states follows the sequence: fast-inactivated > slow-inactivated > resting. The state dependence of VGSC current inhibition contributes to the non-linearity of action potential block by cinacalcet. This dynamic and abundant signaling pathway by which cinacalcet regulates VGSC currents provides an important voltage-dependent mechanism for modulating central neuronal excitability.
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Affiliation(s)
- Jamie S Lindner
- Section of Pulmonary and Critical Care Medicine, VA Portland Health Care System, Portland, OR, United States.,Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Salil R Rajayer
- Section of Pulmonary and Critical Care Medicine, VA Portland Health Care System, Portland, OR, United States.,Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Briana J Martiszus
- Section of Pulmonary and Critical Care Medicine, VA Portland Health Care System, Portland, OR, United States.,Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Stephen M Smith
- Section of Pulmonary and Critical Care Medicine, VA Portland Health Care System, Portland, OR, United States.,Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Oregon Health & Science University, Portland, OR, United States
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49
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Griffanti L, Gillis G, O'Donoghue MC, Blane J, Pretorius PM, Mitchell R, Aikin N, Lindsay K, Campbell J, Semple J, Alfaro-Almagro F, Smith SM, Miller KL, Martos L, Raymont V, Mackay CE. Adapting UK Biobank imaging for use in a routine memory clinic setting: The Oxford Brain Health Clinic. Neuroimage Clin 2022; 36:103273. [PMID: 36451375 PMCID: PMC9723313 DOI: 10.1016/j.nicl.2022.103273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/24/2022] [Accepted: 11/20/2022] [Indexed: 11/23/2022]
Abstract
The Oxford Brain Health Clinic (BHC) is a joint clinical-research service that provides memory clinic patients and clinicians access to high-quality assessments not routinely available, including brain MRI aligned with the UK Biobank imaging study (UKB). In this work we present how we 1) adapted the UKB MRI acquisition protocol to be suitable for memory clinic patients, 2) modified the imaging analysis pipeline to extract measures that are in line with radiology reports and 3) explored the alignment of measures from BHC patients to the largest brain MRI study in the world (ultimately 100,000 participants). Adaptations of the UKB acquisition protocol for BHC patients include dividing the scan into core and optional sequences (i.e., additional imaging modalities) to improve patients' tolerance for the MRI assessment. We adapted the UKB structural MRI analysis pipeline to take into account the characteristics of a memory clinic population (e.g., high amount of white matter hyperintensities and hippocampal atrophy). We then compared the imaging derived phenotypes (IDPs) extracted from the structural scans to visual ratings from radiology reports, non-imaging factors (age, cognition) and to reference distributions derived from UKB data. Of the first 108 BHC attendees (August 2020-November 2021), 92.5 % completed the clinical scans, 88.0 % consented to use of data for research, and 43.5 % completed the additional research sequences, demonstrating that the protocol is well tolerated. The high rates of consent to research makes this a valuable real-world quality research dataset routinely captured in a clinical service. Modified tissue-type segmentation with lesion masking greatly improved grey matter volume estimation. CSF-masking marginally improved hippocampal segmentation. The IDPs were in line with radiology reports and showed significant associations with age and cognitive performance, in line with the literature. Due to the age difference between memory clinic patients of the BHC (age range 65-101 years, average 78.3 years) and UKB participants (44-82 years, average 64 years), additional scans on elderly healthy controls are needed to improve reference distributions. Current and future work aims to integrate automated quantitative measures in the radiology reports and evaluate their clinical utility.
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Affiliation(s)
- Ludovica Griffanti
- Department of Psychiatry, University of Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom; Nuffield Department of Clinical Neurosciences, University of Oxford, United Kingdom; Wellcome Centre for Integrative Neuroimaging, University of Oxford, United Kingdom.
| | - Grace Gillis
- Department of Psychiatry, University of Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom; Wellcome Centre for Integrative Neuroimaging, University of Oxford, United Kingdom
| | - M Clare O'Donoghue
- Department of Psychiatry, University of Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom; Wellcome Centre for Integrative Neuroimaging, University of Oxford, United Kingdom
| | - Jasmine Blane
- Department of Psychiatry, University of Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom
| | - Pieter M Pretorius
- Nuffield Department of Clinical Neurosciences, University of Oxford, United Kingdom; Oxford University Hospitals NHS Trust, Oxford, United Kingdom
| | | | - Nicola Aikin
- Department of Psychiatry, University of Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom; Wellcome Centre for Integrative Neuroimaging, University of Oxford, United Kingdom
| | - Karen Lindsay
- Department of Psychiatry, University of Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom
| | - Jon Campbell
- Department of Psychiatry, University of Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom; Wellcome Centre for Integrative Neuroimaging, University of Oxford, United Kingdom
| | - Juliet Semple
- Department of Psychiatry, University of Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom; Wellcome Centre for Integrative Neuroimaging, University of Oxford, United Kingdom
| | - Fidel Alfaro-Almagro
- Nuffield Department of Clinical Neurosciences, University of Oxford, United Kingdom; Wellcome Centre for Integrative Neuroimaging, University of Oxford, United Kingdom
| | - Stephen M Smith
- Nuffield Department of Clinical Neurosciences, University of Oxford, United Kingdom; Wellcome Centre for Integrative Neuroimaging, University of Oxford, United Kingdom
| | - Karla L Miller
- Nuffield Department of Clinical Neurosciences, University of Oxford, United Kingdom; Wellcome Centre for Integrative Neuroimaging, University of Oxford, United Kingdom
| | - Lola Martos
- Department of Psychiatry, University of Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom
| | - Vanessa Raymont
- Department of Psychiatry, University of Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom
| | - Clare E Mackay
- Department of Psychiatry, University of Oxford, United Kingdom; Wellcome Centre for Integrative Neuroimaging, University of Oxford, United Kingdom
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50
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Vidal-Pineiro D, Wang Y, Krogsrud SK, Amlien IK, Baaré WFC, Bartres-Faz D, Bertram L, Brandmaier AM, Drevon CA, Düzel S, Ebmeier K, Henson RN, Junqué C, Kievit RA, Kühn S, Leonardsen E, Lindenberger U, Madsen KS, Magnussen F, Mowinckel AM, Nyberg L, Roe JM, Segura B, Smith SM, Sørensen Ø, Suri S, Westerhausen R, Zalesky A, Zsoldos E, Walhovd KB, Fjell A. Correction: Individual variations in 'Brain Age' relate to early-life factors more than to longitudinal brain change. eLife 2022; 11:79475. [PMID: 35470797 PMCID: PMC9042230 DOI: 10.7554/elife.79475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
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