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Versace A, Hitchens TK, Wallace CT, Watkins SC, D’Aiuto L. 11.7T Diffusion Magnetic Resonance Imaging and Tractography to Probe Human Brain Organoid Microstructure. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2024; 4:100344. [PMID: 39099731 PMCID: PMC11295450 DOI: 10.1016/j.bpsgos.2024.100344] [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: 02/29/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 08/06/2024] Open
Abstract
Background Human brain organoids are 3-dimensional cellular models that mimic architectural features of a developing brain. Generated from human induced pluripotent stem cells, these organoids offer an unparalleled physiologically relevant in vitro system for disease modeling and drug screening. In the current study, we sought to establish a foundation for a magnetic resonance imaging (MRI)-based, label-free imaging system that offers high-resolution capabilities for deep tissue imaging of whole organoids. Methods An 11.7T Bruker/89 mm microimaging system was used to collect high-resolution multishell 3-dimensional diffusion images of 2 induced pluripotent stem cell-derived human hippocampal brain organoids. The MRI features identified in the study were interpreted on the basis of similarities with immunofluorescence microscopy. Results MRI microscopy at ≤40 μm isotropic resolution provided a 3-dimensional view of organoid microstructure. T2-weighted contrast showed a rosette-like internal structure and a protruding spherical structure that correlated with immunofluorescence staining for the choroid plexus. Diffusion tractography methods can be used to model tissue microstructural features and possibly map neuronal organization. This approach complements traditional immunohistochemistry imaging methods without the need for tissue clearing. Conclusions This proof-of-concept study shows, for the first time, the application of high-resolution diffusion MRI microscopy to image 2-mm diameter spherical human brain organoids. Application of ultrahigh-field MRI and diffusion tractography is a powerful modality for whole organoid imaging and has the potential to make a significant impact for probing microstructural changes in brain organoids used to model psychiatric disorders, neurodegenerative diseases, and viral infections of the human brain, as well as for assessing neurotoxicity in drug screening.
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Affiliation(s)
- Amelia Versace
- University of Pittsburgh Department of Psychiatry, Pittsburgh, Pennsylvania
- University of Pittsburgh Magnetic Resonance Research Center, Pittsburgh, Pennsylvania
| | - T. Kevin Hitchens
- University of Pittsburgh Department of Neurobiology, Pittsburgh, Pennsylvania
- Advanced Imaging Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Callen T. Wallace
- University of Pittsburgh Department of Cell Biology, Pittsburgh, Pennsylvania
| | - Simon C. Watkins
- University of Pittsburgh Department of Cell Biology, Pittsburgh, Pennsylvania
| | - Leonardo D’Aiuto
- University of Pittsburgh Department of Psychiatry, Pittsburgh, Pennsylvania
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Altham C, Zhang H, Pereira E. Machine learning for the detection and diagnosis of cognitive impairment in Parkinson's Disease: A systematic review. PLoS One 2024; 19:e0303644. [PMID: 38753740 PMCID: PMC11098383 DOI: 10.1371/journal.pone.0303644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Parkinson's Disease is the second most common neurological disease in over 60s. Cognitive impairment is a major clinical symptom, with risk of severe dysfunction up to 20 years post-diagnosis. Processes for detection and diagnosis of cognitive impairments are not sufficient to predict decline at an early stage for significant impact. Ageing populations, neurologist shortages and subjective interpretations reduce the effectiveness of decisions and diagnoses. Researchers are now utilising machine learning for detection and diagnosis of cognitive impairment based on symptom presentation and clinical investigation. This work aims to provide an overview of published studies applying machine learning to detecting and diagnosing cognitive impairment, evaluate the feasibility of implemented methods, their impacts, and provide suitable recommendations for methods, modalities and outcomes. METHODS To provide an overview of the machine learning techniques, data sources and modalities used for detection and diagnosis of cognitive impairment in Parkinson's Disease, we conducted a review of studies published on the PubMed, IEEE Xplore, Scopus and ScienceDirect databases. 70 studies were included in this review, with the most relevant information extracted from each. From each study, strategy, modalities, sources, methods and outcomes were extracted. RESULTS Literatures demonstrate that machine learning techniques have potential to provide considerable insight into investigation of cognitive impairment in Parkinson's Disease. Our review demonstrates the versatility of machine learning in analysing a wide range of different modalities for the detection and diagnosis of cognitive impairment in Parkinson's Disease, including imaging, EEG, speech and more, yielding notable diagnostic accuracy. CONCLUSIONS Machine learning based interventions have the potential to glean meaningful insight from data, and may offer non-invasive means of enhancing cognitive impairment assessment, providing clear and formidable potential for implementation of machine learning into clinical practice.
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Affiliation(s)
- Callum Altham
- Department of Computer Science, Edge Hill University, Ormskirk, Lancashire, United Kingdom
| | - Huaizhong Zhang
- Department of Computer Science, Edge Hill University, Ormskirk, Lancashire, United Kingdom
| | - Ella Pereira
- Department of Computer Science, Edge Hill University, Ormskirk, Lancashire, United Kingdom
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Huang ML, Huang ZB. An ensemble-acute lymphoblastic leukemia model for acute lymphoblastic leukemia image classification. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2024; 21:1959-1978. [PMID: 38454670 DOI: 10.3934/mbe.2024087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
The timely diagnosis of acute lymphoblastic leukemia (ALL) is of paramount importance for enhancing the treatment efficacy and the survival rates of patients. In this study, we seek to introduce an ensemble-ALL model for the image classification of ALL, with the goal of enhancing early diagnostic capabilities and streamlining the diagnostic and treatment processes for medical practitioners. In this study, a publicly available dataset is partitioned into training, validation, and test sets. A diverse set of convolutional neural networks, including InceptionV3, EfficientNetB4, ResNet50, CONV_POOL-CNN, ALL-CNN, Network in Network, and AlexNet, are employed for training. The top-performing four individual models are meticulously chosen and integrated with the squeeze-and-excitation (SE) module. Furthermore, the two most effective SE-embedded models are harmoniously combined to create the proposed ensemble-ALL model. This model leverages the Bayesian optimization algorithm to enhance its performance. The proposed ensemble-ALL model attains remarkable accuracy, precision, recall, F1-score, and kappa scores, registering at 96.26, 96.26, 96.26, 96.25, and 91.36%, respectively. These results surpass the benchmarks set by state-of-the-art studies in the realm of ALL image classification. This model represents a valuable contribution to the field of medical image recognition, particularly in the diagnosis of acute lymphoblastic leukemia, and it offers the potential to enhance the efficiency and accuracy of medical professionals in the diagnostic and treatment processes.
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Affiliation(s)
- Mei-Ling Huang
- Department of Industrial Engineering & Management, National Chin-Yi University of Technology, Taichung, Taiwan
| | - Zong-Bin Huang
- Department of Industrial Engineering & Management, National Chin-Yi University of Technology, Taichung, Taiwan
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Jellinger KA. Pathobiology of Cognitive Impairment in Parkinson Disease: Challenges and Outlooks. Int J Mol Sci 2023; 25:498. [PMID: 38203667 PMCID: PMC10778722 DOI: 10.3390/ijms25010498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/11/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Cognitive impairment (CI) is a characteristic non-motor feature of Parkinson disease (PD) that poses a severe burden on the patients and caregivers, yet relatively little is known about its pathobiology. Cognitive deficits are evident throughout the course of PD, with around 25% of subtle cognitive decline and mild CI (MCI) at the time of diagnosis and up to 83% of patients developing dementia after 20 years. The heterogeneity of cognitive phenotypes suggests that a common neuropathological process, characterized by progressive degeneration of the dopaminergic striatonigral system and of many other neuronal systems, results not only in structural deficits but also extensive changes of functional neuronal network activities and neurotransmitter dysfunctions. Modern neuroimaging studies revealed multilocular cortical and subcortical atrophies and alterations in intrinsic neuronal connectivities. The decreased functional connectivity (FC) of the default mode network (DMN) in the bilateral prefrontal cortex is affected already before the development of clinical CI and in the absence of structural changes. Longitudinal cognitive decline is associated with frontostriatal and limbic affections, white matter microlesions and changes between multiple functional neuronal networks, including thalamo-insular, frontoparietal and attention networks, the cholinergic forebrain and the noradrenergic system. Superimposed Alzheimer-related (and other concomitant) pathologies due to interactions between α-synuclein, tau-protein and β-amyloid contribute to dementia pathogenesis in both PD and dementia with Lewy bodies (DLB). To further elucidate the interaction of the pathomechanisms responsible for CI in PD, well-designed longitudinal clinico-pathological studies are warranted that are supported by fluid and sophisticated imaging biomarkers as a basis for better early diagnosis and future disease-modifying therapies.
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Affiliation(s)
- Kurt A Jellinger
- Institute of Clinical Neurobiology, Alberichgasse 5/13, A-1150 Vienna, Austria
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Huang X, He Q, Ruan X, Li Y, Kuang Z, Wang M, Guo R, Bu S, Wang Z, Yu S, Chen A, Wei X. Structural connectivity from DTI to predict mild cognitive impairment in de novo Parkinson's disease. Neuroimage Clin 2023; 41:103548. [PMID: 38061176 PMCID: PMC10755095 DOI: 10.1016/j.nicl.2023.103548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 01/01/2024]
Abstract
BACKGROUND Early detection of Parkinson's disease (PD) patients at high risk for mild cognitive impairment (MCI) can help with timely intervention. White matter structural connectivity is considered an early and sensitive indicator of neurodegenerative disease. OBJECTIVES To investigate whether baseline white matter structural connectivity features from diffusion tensor imaging (DTI) of de novo PD patients can help predict PD-MCI conversion at an individual level using machine learning methods. METHODS We included 90 de novo PD patients who underwent DTI and 3D T1-weighted imaging. Elastic net-based feature consensus ranking (ENFCR) was used with 1000 random training sets to select clinical and structural connectivity features. Linear discrimination analysis (LDA), support vector machine (SVM), K-nearest neighbor (KNN) and naïve Bayes (NB) classifiers were trained based on features selected more than 500 times. The area under the ROC curve (AUC), accuracy (ACC), sensitivity (SEN) and specificity (SPE) were used to evaluate model performance. RESULTS A total of 57 PD patients were classified as PD-MCI nonconverters, and 33 PD patients were classified as PD-MCI converters. The models trained with clinical data showed moderate performance (AUC range: 0.62-0.68; ACC range: 0.63-0.77; SEN range: 0.45-0.66; SPE range: 0.64-0.84). Models trained with structural connectivity (AUC range, 0.81-0.84; ACC range, 0.75-0.86; SEN range, 0.77-0.91; SPE range, 0.71-0.88) performed similar to models that were trained with both clinical and structural connectivity data (AUC range, 0.81-0.85; ACC range, 0.74-0.85; SEN range, 0.79-0.91; SPE range, 0.70-0.89). CONCLUSIONS Baseline white matter structural connectivity from DTI is helpful in predicting future MCI conversion in de novo PD patients.
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Affiliation(s)
- Xiaofei Huang
- Department of Radiology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangdong, China
| | - Qing He
- Department of Radiology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangdong, China
| | - Xiuhang Ruan
- Department of Radiology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangdong, China
| | - Yuting Li
- Department of Radiology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangdong, China; Affiliated Dongguan Hospital, Southern Medical University (Dongguan People's Hospital), Guangdong, China
| | - Zhanyu Kuang
- Department of Radiology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangdong, China
| | - Mengfan Wang
- Department of Radiology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangdong, China
| | - Riyu Guo
- Department of Radiology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangdong, China
| | - Shuwen Bu
- Department of Radiology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangdong, China
| | - Zhaoxiu Wang
- Department of Radiology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangdong, China
| | - Shaode Yu
- School of Information and Communication Engineering, Communication University of China, Beijing, China.
| | - Amei Chen
- Department of Radiology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangdong, China.
| | - Xinhua Wei
- Department of Radiology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangdong, China.
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