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Chen C, Zhao LL, Lang Q, Xu Y. A Novel Detection and Classification Framework for Diagnosing of Cerebral Microbleeds Using Transformer and Language. Bioengineering (Basel) 2024; 11:993. [PMID: 39451369 PMCID: PMC11504022 DOI: 10.3390/bioengineering11100993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 09/24/2024] [Accepted: 09/27/2024] [Indexed: 10/26/2024] Open
Abstract
The detection of Cerebral Microbleeds (CMBs) is crucial for diagnosing cerebral small vessel disease. However, due to the small size and subtle appearance of CMBs in susceptibility-weighted imaging (SWI), manual detection is both time-consuming and labor-intensive. Meanwhile, the presence of similar-looking features in SWI images demands significant expertise from clinicians, further complicating this process. Recently, there has been a significant advancement in automated detection of CMBs using a Convolutional Neural Network (CNN) structure, aiming at enhancing diagnostic efficiency for neurologists. However, existing methods still show discrepancies when compared to the actual clinical diagnostic process. To bridge this gap, we introduce a novel multimodal detection and classification framework for CMBs' diagnosis, termed MM-UniCMBs. This framework includes a light-weight detection model and a multi-modal classification network. Specifically, we proposed a new CMBs detection network, CMBs-YOLO, designed to capture the salient features of CMBs in SWI images. Additionally, we design an innovative language-vision classification network, CMBsFormer (CF), which integrates patient textual descriptions-such as gender, age, and medical history-with image data. The MM-UniCMBs framework is designed to closely align with the diagnostic workflow of clinicians, offering greater interpretability and flexibility compared to existing methods. Extensive experimental results show that MM-UniCMBs achieves a sensitivity of 94% in CMBs' classification and can process a patient's data within 5 s.
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Affiliation(s)
- Cong Chen
- School of Clinical Medicine, College of Medicine, Nanjing Medical University, Nanjing 211166, China
- Department of Neurology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Lin-Lin Zhao
- Department of Computer Science and Technology, Shanghai University, 99 Shangda Road, Baoshan District, Shanghai 200444, China
| | - Qin Lang
- Department of Neurology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Yun Xu
- School of Clinical Medicine, College of Medicine, Nanjing Medical University, Nanjing 211166, China
- Department of Neurology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, 321 Zhongshan Road, Nanjing 210008, China
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Thorwald M, Godoy-Lugo JA, Garcia G, Silva J, Kim M, Christensen A, Mack WJ, Head E, O'Day PA, Benayoun BA, Morgan TE, Pike CJ, Higuchi-Sanabria R, Forman HJ, Finch CE. Iron associated lipid peroxidation in Alzheimers disease is increased in lipid rafts with decreased ferroptosis suppressors, tested by chelation in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.28.534324. [PMID: 37034750 PMCID: PMC10081222 DOI: 10.1101/2023.03.28.534324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Iron-mediated cell death (ferroptosis) is a proposed mechanism of Alzheimers disease (AD) pathology. While iron is essential for basic biological functions, its reactivity generates oxidants which contribute to cell damage and death. To further resolve mechanisms of iron-mediated toxicity in AD, we analyzed postmortem human brain and ApoEFAD mice. AD brains had decreased antioxidant enzymes, including those mediated by glutathione (GSH). Subcellular analyses of AD brains showed greater oxidative damage and lower antioxidant enzymes in lipid rafts, the site of amyloid processing, than in the non-raft membrane fraction. ApoE4 carriers had lower lipid raft yield with greater membrane oxidation. The hypothesized role of iron to AD pathology was tested in ApoEFAD mice by iron chelation with deferoxamine, which decreased fibrillar amyloid and lipid peroxidation, together with increased GSH-mediated antioxidants. These novel molecular pathways in iron mediated damage during AD.
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Ali Z, Naz S, Yasmin S, Bukhari M, Kim M. Deep learning-assisted IoMT framework for cerebral microbleed detection. Heliyon 2023; 9:e22879. [PMID: 38125517 PMCID: PMC10731074 DOI: 10.1016/j.heliyon.2023.e22879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/17/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023] Open
Abstract
The Internet of Things (IoT), big data, and artificial intelligence (AI) are all key technologies that influence the formation and implementation of digital medical services. Building Internet of Medical Things (IoMT) systems that combine advanced sensors with AI-powered insights is critical for intelligent medical systems. This paper presents an IoMT framework for brain magnetic resonance imaging (MRI) analysis to lessen the unavoidable diagnosis and therapy faults that occur in human clinical settings for the accurate detection of cerebral microbleeds (CMBs). The problems in accurate CMB detection include that CMBs are tiny dots 5-10 mm in diameter; they are similar to healthy tissues and are exceedingly difficult to identify, necessitating specialist guidance in remote and underdeveloped medical centers. Secondly, in the existing studies, computer-aided diagnostic (CAD) systems are designed for accurate CMB detection, however, their proposed approaches consist of two stages. Potential candidate CMBs from the complete MRI image are selected in the first stage and then passed to the phase of false-positive reduction. These pre-and post-processing steps make it difficult to build a completely automated CAD system for CMB that can produce results without human intervention. Hence, as a key goal of this work, an end-to-end enhanced UNet-based model for effective CMB detection and segmentation for IoMT devices is proposed. The proposed system requires no pre-processing or post-processing steps for CMB segmentation, and no existing research localizes each CMB pixel from the complete MRI image input. The findings indicate that the suggested method outperforms in detecting CMBs in the presence of contrast variations and similarities with other normal tissues and yields a good dice score of 0.70, an accuracy of 99 %, as well as a false-positive rate of 0.002 %. © 2017 Elsevier Inc. All rights reserved.
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Affiliation(s)
- Zeeshan Ali
- Research and Development Setups, National University of Computer and Emerging Sciences, Islamabad, 44000, Pakistan
| | - Sheneela Naz
- Department of Computer Science, COMSATS University Islamabad, Islamabad, 45550, Pakistan
| | - Sadaf Yasmin
- Department of Computer Science, COMSATS University Islamabad, Attock Campus, Attock, 43600, Pakistan
| | - Maryam Bukhari
- Department of Computer Science, COMSATS University Islamabad, Attock Campus, Attock, 43600, Pakistan
| | - Mucheol Kim
- School of Computer Science and Engineering, Chung-Ang University, Seoul, 06974, South Korea
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Jensen PN, Rashid T, Ware JB, Cui Y, Sitlani CM, Austin TR, Longstreth W, Bertoni AG, Mamourian E, Bryan RN, Nasrallah IM, Habes M, Heckbert SR. Association of brain microbleeds with risk factors, cognition, and MRI markers in MESA. Alzheimers Dement 2023; 19:4139-4149. [PMID: 37289978 PMCID: PMC11163989 DOI: 10.1002/alz.13346] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 06/10/2023]
Abstract
INTRODUCTION Little is known about the epidemiology of brain microbleeds in racially/ethnically diverse populations. METHODS In the Multi-Ethnic Study of Atherosclerosis, brain microbleeds were identified from 3T magnetic resonance imaging susceptibility-weighted imaging sequences using deep learning models followed by radiologist review. RESULTS Among 1016 participants without prior stroke (25% Black, 15% Chinese, 19% Hispanic, 41% White, mean age 72), microbleed prevalence was 20% at age 60 to 64.9 and 45% at ≥85 years. Deep microbleeds were associated with older age, hypertension, higher body mass index, and atrial fibrillation, and lobar microbleeds with male sex and atrial fibrillation. Overall, microbleeds were associated with greater white matter hyperintensity volume and lower total white matter fractional anisotropy. DISCUSSION Results suggest differing associations for lobar versus deep locations. Sensitive microbleed quantification will facilitate future longitudinal studies of their potential role as an early indicator of vascular pathology.
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Affiliation(s)
- Paul N. Jensen
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington 98195, USA
- Department of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Tanweer Rashid
- Neuroimage Analytics Laboratory and Biggs Institute Neuroimaging Core, Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health Science Center San Antonio, San Antonio, Texas 78229, USA
| | - Jeffrey B. Ware
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19103, USA
| | - Yuhan Cui
- Center for AI and Data Science for Integrated Diagnostics and Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Colleen M. Sitlani
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington 98195, USA
- Department of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Thomas R. Austin
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington 98195, USA
- Department of Epidemiology, University of Washington, Seattle, Washington 98195, USA
| | - W.T. Longstreth
- Department of Epidemiology, University of Washington, Seattle, Washington 98195, USA
- Department of Neurology, University of Washington, Seattle, Washington 98195, USA
| | - Alain G. Bertoni
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, USA
| | - Elizabeth Mamourian
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19103, USA
- Center for AI and Data Science for Integrated Diagnostics and Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - R. Nick Bryan
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19103, USA
| | - Ilya M. Nasrallah
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19103, USA
- Center for AI and Data Science for Integrated Diagnostics and Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Mohamad Habes
- Neuroimage Analytics Laboratory and Biggs Institute Neuroimaging Core, Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health Science Center San Antonio, San Antonio, Texas 78229, USA
- Center for AI and Data Science for Integrated Diagnostics and Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Susan R. Heckbert
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington 98195, USA
- Department of Epidemiology, University of Washington, Seattle, Washington 98195, USA
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Sundaresan V, Arthofer C, Zamboni G, Murchison AG, Dineen RA, Rothwell PM, Auer DP, Wang C, Miller KL, Tendler BC, Alfaro-Almagro F, Sotiropoulos SN, Sprigg N, Griffanti L, Jenkinson M. Automated detection of cerebral microbleeds on MR images using knowledge distillation framework. Front Neuroinform 2023; 17:1204186. [PMID: 37492242 PMCID: PMC10363739 DOI: 10.3389/fninf.2023.1204186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/19/2023] [Indexed: 07/27/2023] Open
Abstract
Introduction Cerebral microbleeds (CMBs) are associated with white matter damage, and various neurodegenerative and cerebrovascular diseases. CMBs occur as small, circular hypointense lesions on T2*-weighted gradient recalled echo (GRE) and susceptibility-weighted imaging (SWI) images, and hyperintense on quantitative susceptibility mapping (QSM) images due to their paramagnetic nature. Accurate automated detection of CMBs would help to determine quantitative imaging biomarkers (e.g., CMB count) on large datasets. In this work, we propose a fully automated, deep learning-based, 3-step algorithm, using structural and anatomical properties of CMBs from any single input image modality (e.g., GRE/SWI/QSM) for their accurate detections. Methods In our method, the first step consists of an initial candidate detection step that detects CMBs with high sensitivity. In the second step, candidate discrimination step is performed using a knowledge distillation framework, with a multi-tasking teacher network that guides the student network to classify CMB and non-CMB instances in an offline manner. Finally, a morphological clean-up step further reduces false positives using anatomical constraints. We used four datasets consisting of different modalities specified above, acquired using various protocols and with a variety of pathological and demographic characteristics. Results On cross-validation within datasets, our method achieved a cluster-wise true positive rate (TPR) of over 90% with an average of <2 false positives per subject. The knowledge distillation framework improves the cluster-wise TPR of the student model by 15%. Our method is flexible in terms of the input modality and provides comparable cluster-wise TPR and better cluster-wise precision compared to existing state-of-the-art methods. When evaluating across different datasets, our method showed good generalizability with a cluster-wise TPR >80 % with different modalities. The python implementation of the proposed method is openly available.
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Affiliation(s)
- Vaanathi Sundaresan
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, Karnataka, India
- Wellcome Centre for Integrative Neuroimaging, Oxford Centre for Functional MRI of the Brain, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Christoph Arthofer
- Wellcome Centre for Integrative Neuroimaging, Oxford Centre for Functional MRI of the Brain, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research (NIHR) Nottingham Biomedical Research Centre, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
- Sir Peter Mansfield Imaging Centre, University of Nottingham, Nottingham, United Kingdom
| | - Giovanna Zamboni
- Wellcome Centre for Integrative Neuroimaging, Oxford Centre for Functional MRI of the Brain, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Centre for Prevention of Stroke and Dementia, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Dipartimento di Scienze Biomediche, Metaboliche e Neuroscienze, Universitá di Modena e Reggio Emilia, Modena, Italy
| | - Andrew G. Murchison
- Department of Neuroradiology, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Robert A. Dineen
- National Institute for Health and Care Research (NIHR) Nottingham Biomedical Research Centre, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
- Sir Peter Mansfield Imaging Centre, University of Nottingham, Nottingham, United Kingdom
- Radiological Sciences, Mental Health and Clinical Neurosciences, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Peter M. Rothwell
- Centre for Prevention of Stroke and Dementia, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Dorothee P. Auer
- National Institute for Health and Care Research (NIHR) Nottingham Biomedical Research Centre, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
- Sir Peter Mansfield Imaging Centre, University of Nottingham, Nottingham, United Kingdom
- Radiological Sciences, Mental Health and Clinical Neurosciences, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Chaoyue Wang
- Wellcome Centre for Integrative Neuroimaging, Oxford Centre for Functional MRI of the Brain, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Karla L. Miller
- Wellcome Centre for Integrative Neuroimaging, Oxford Centre for Functional MRI of the Brain, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Benjamin C. Tendler
- Wellcome Centre for Integrative Neuroimaging, Oxford Centre for Functional MRI of the Brain, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Fidel Alfaro-Almagro
- Wellcome Centre for Integrative Neuroimaging, Oxford Centre for Functional MRI of the Brain, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Stamatios N. Sotiropoulos
- Wellcome Centre for Integrative Neuroimaging, Oxford Centre for Functional MRI of the Brain, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research (NIHR) Nottingham Biomedical Research Centre, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
- Sir Peter Mansfield Imaging Centre, University of Nottingham, Nottingham, United Kingdom
| | - Nikola Sprigg
- Stroke Trials Unit, Mental Health and Clinical Neuroscience, University of Nottingham, Nottingham, United Kingdom
| | - Ludovica Griffanti
- Wellcome Centre for Integrative Neuroimaging, Oxford Centre for Functional MRI of the Brain, Nuffield Department of Clinical Neurosciences, 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
| | - Mark Jenkinson
- Wellcome Centre for Integrative Neuroimaging, Oxford Centre for Functional MRI of the Brain, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Australian Institute for Machine Learning, School of Computer Science, The University of Adelaide, Adelaide, SA, Australia
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