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Yang X, Zheng Y, Mei C, Jiang G, Tian B, Wang L. UGLS: an uncertainty guided deep learning strategy for accurate image segmentation. Front Physiol 2024; 15:1362386. [PMID: 38651048 PMCID: PMC11033460 DOI: 10.3389/fphys.2024.1362386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
Accurate image segmentation plays a crucial role in computer vision and medical image analysis. In this study, we developed a novel uncertainty guided deep learning strategy (UGLS) to enhance the performance of an existing neural network (i.e., U-Net) in segmenting multiple objects of interest from images with varying modalities. In the developed UGLS, a boundary uncertainty map was introduced for each object based on its coarse segmentation (obtained by the U-Net) and then combined with input images for the fine segmentation of the objects. We validated the developed method by segmenting optic cup (OC) regions from color fundus images and left and right lung regions from Xray images. Experiments on public fundus and Xray image datasets showed that the developed method achieved a average Dice Score (DS) of 0.8791 and a sensitivity (SEN) of 0.8858 for the OC segmentation, and 0.9605, 0.9607, 0.9621, and 0.9668 for the left and right lung segmentation, respectively. Our method significantly improved the segmentation performance of the U-Net, making it comparable or superior to five sophisticated networks (i.e., AU-Net, BiO-Net, AS-Net, Swin-Unet, and TransUNet).
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Affiliation(s)
- Xiaoguo Yang
- Wenzhou People’s Hospital, The Third Affiliated Hospital of Shanghai University, Wenzhou, China
| | - Yanyan Zheng
- Wenzhou People’s Hospital, The Third Affiliated Hospital of Shanghai University, Wenzhou, China
| | - Chenyang Mei
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Gaoqiang Jiang
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Bihan Tian
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Lei Wang
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
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Jin T, Zhang Y, Botchway BOA, Huang M, Lu Q, Liu X. Quercetin activates the Sestrin2/AMPK/SIRT1 axis to improve amyotrophic lateral sclerosis. Biomed Pharmacother 2023; 161:114515. [PMID: 36913894 DOI: 10.1016/j.biopha.2023.114515] [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: 01/04/2023] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a chronic neurodegenerative disease with poor prognosis. The intricacies surrounding its pathophysiology could partly account for the lack of effective treatment for ALS. Sestrin2 has been reported to improve metabolic, cardiovascular and neurodegenerative diseases, and is involved in the direct and indirect activation of the adenosine 5'-monophosphate (AMP)-activated protein kinase (AMPK)/silent information regulator 1 (SIRT1) axis. Quercetin, as a phytochemical, has considerable biological activities, such as anti-oxidation, anti-inflammation, anti-tumorigenicity, and neuroprotection. Interestingly, quercetin can activate the AMPK/SIRT1 signaling pathway to reduce endoplasmic reticulum stress, and alleviate apoptosis and inflammation. This report examines the molecular relationship between Sestrin2 and AMPK/SIRT1 axis, as well as the main biological functions and research progress of quercetin, together with the correlation between quercetin and Sestrin2/AMPK/SIRT1 axis in neurodegenerative diseases.
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Affiliation(s)
- Tian Jin
- Department of Histology and Embryology, Medical College, Shaoxing University, Zhejiang, China
| | - Yong Zhang
- Department of Histology and Embryology, Medical College, Shaoxing University, Zhejiang, China
| | - Benson O A Botchway
- Institute of Neuroscience, Zhejiang University School of Medicine, Hangzhou, China; Bupa Cromwell Hospital, London, UK
| | - Min Huang
- Department of Histology and Embryology, Medical College, Shaoxing University, Zhejiang, China
| | - Qicheng Lu
- Department of Histology and Embryology, Medical College, Shaoxing University, Zhejiang, China
| | - Xuehong Liu
- Department of Histology and Embryology, Medical College, Shaoxing University, Zhejiang, China.
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Delre P, Lavado GJ, Lamanna G, Saviano M, Roncaglioni A, Benfenati E, Mangiatordi GF, Gadaleta D. Ligand-based prediction of hERG-mediated cardiotoxicity based on the integration of different machine learning techniques. Front Pharmacol 2022; 13:951083. [PMID: 36133824 PMCID: PMC9483173 DOI: 10.3389/fphar.2022.951083] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Drug-induced cardiotoxicity is a common side effect of drugs in clinical use or under postmarket surveillance and is commonly due to off-target interactions with the cardiac human-ether-a-go-go-related (hERG) potassium channel. Therefore, prioritizing drug candidates based on their hERG blocking potential is a mandatory step in the early preclinical stage of a drug discovery program. Herein, we trained and properly validated 30 ligand-based classifiers of hERG-related cardiotoxicity based on 7,963 curated compounds extracted by the freely accessible repository ChEMBL (version 25). Different machine learning algorithms were tested, namely, random forest, K-nearest neighbors, gradient boosting, extreme gradient boosting, multilayer perceptron, and support vector machine. The application of 1) the best practices for data curation, 2) the feature selection method VSURF, and 3) the synthetic minority oversampling technique (SMOTE) to properly handle the unbalanced data, allowed for the development of highly predictive models (BAMAX = 0.91, AUCMAX = 0.95). Remarkably, the undertaken temporal validation approach not only supported the predictivity of the herein presented classifiers but also suggested their ability to outperform those models commonly used in the literature. From a more methodological point of view, the study put forward a new computational workflow, freely available in the GitHub repository (https://github.com/PDelre93/hERG-QSAR), as valuable for building highly predictive models of hERG-mediated cardiotoxicity.
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Affiliation(s)
- Pietro Delre
- CNR—Institute of Crystallography, Bari, Italy
- Chemistry Department, University of Bari “Aldo Moro”, Bari, Italy
| | - Giovanna J. Lavado
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Giuseppe Lamanna
- CNR—Institute of Crystallography, Bari, Italy
- Chemistry Department, University of Bari “Aldo Moro”, Bari, Italy
| | | | - Alessandra Roncaglioni
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Emilio Benfenati
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Giuseppe Felice Mangiatordi
- CNR—Institute of Crystallography, Bari, Italy
- *Correspondence: Giuseppe Felice Mangiatordi, ; Domenico Gadaleta,
| | - Domenico Gadaleta
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
- *Correspondence: Giuseppe Felice Mangiatordi, ; Domenico Gadaleta,
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Liu B, Li M, Zhang L, Chen Z, Lu P. Motor neuron replacement therapy for amyotrophic lateral sclerosis. Neural Regen Res 2022; 17:1633-1639. [PMID: 35017408 PMCID: PMC8820706 DOI: 10.4103/1673-5374.332123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Amyotrophic lateral sclerosis is a motor neuron degenerative disease that is also known as Lou Gehrig's disease in the United States, Charcot's disease in France, and motor neuron disease in the UK. The loss of motor neurons causes muscle wasting, paralysis, and eventually death, which is commonly related to respiratory failure, within 3-5 years after onset of the disease. Although there are a limited number of drugs approved for amyotrophic lateral sclerosis, they have had little success at treating the associated symptoms, and they cannot reverse the course of motor neuron degeneration. Thus, there is still a lack of effective treatment for this debilitating neurodegenerative disorder. Stem cell therapy for amyotrophic lateral sclerosis is a very attractive strategy for both basic and clinical researchers, particularly as transplanted stem cells and stem cell-derived neural progenitor/precursor cells can protect endogenous motor neurons and directly replace the lost or dying motor neurons. Stem cell therapies may also be able to re-establish the motor control of voluntary muscles. Here, we review the recent progress in the use of neural stem cells and neural progenitor cells for the treatment of amyotrophic lateral sclerosis. We focus on MN progenitor cells derived from fetal central nervous system tissue, embryonic stem cells, and induced pluripotent stem cells. In our recent studies, we found that transplanted human induced pluripotent stem cell-derived motor neuron progenitors survive well, differentiate into motor neurons, and extend axons into the host white matter, not only in the rostrocaudal direction, but also along motor axon tracts towards the ventral roots in the immunodeficient rat spinal cord. Furthermore, the significant motor axonal extension after neural progenitor cell transplantation in amyotrophic lateral sclerosis models demonstrates that motor neuron replacement therapy could be a promising therapeutic strategy for amyotrophic lateral sclerosis, particularly as a variety of stem cell derivatives, including induced pluripotent stem cells, are being considered for clinical trials for various diseases.
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Affiliation(s)
- Bochao Liu
- Cell Therapy Center, Beijing Institute of Geriatrics, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, and Key Laboratory of Neurodegenerative Diseases, Ministry of Education; Center of Neural Injury and Repair; Center of Parkinson's Disease, Beijing Institute for Brain Disorders, Beijing, China
| | - Mo Li
- Cell Therapy Center, Beijing Institute of Geriatrics, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, and Key Laboratory of Neurodegenerative Diseases, Ministry of Education; Center of Neural Injury and Repair; Center of Parkinson's Disease, Beijing Institute for Brain Disorders, Beijing, China
| | - Lingyan Zhang
- iXCells Biotechnologies USA, Inc., San Diego, CA, USA; Amogene Biotech, Xiamen, Fujian Province, China
| | - Zhiguo Chen
- Cell Therapy Center, Beijing Institute of Geriatrics, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, and Key Laboratory of Neurodegenerative Diseases, Ministry of Education; Center of Neural Injury and Repair; Center of Parkinson's Disease, Beijing Institute for Brain Disorders, Beijing, China
| | - Paul Lu
- Veterans Administration San Diego Healthcare System, San Diego; Department of Neurosciences, University of California - San Diego, La Jolla, CA, USA
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He Z, Ding Y, Mu Y, Xu X, Kong W, Chai R, Chen X. Stem Cell-Based Therapies in Hearing Loss. Front Cell Dev Biol 2021; 9:730042. [PMID: 34746126 PMCID: PMC8567027 DOI: 10.3389/fcell.2021.730042] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/04/2021] [Indexed: 12/19/2022] Open
Abstract
In recent years, neural stem cell transplantation has received widespread attention as a new treatment method for supplementing specific cells damaged by disease, such as neurodegenerative diseases. A number of studies have proved that the transplantation of neural stem cells in multiple organs has an important therapeutic effect on activation and regeneration of cells, and restore damaged neurons. This article describes the methods for inducing the differentiation of endogenous and exogenous stem cells, the implantation operation and regulation of exogenous stem cells after implanted into the inner ear, and it elaborates the relevant signal pathways of stem cells in the inner ear, as well as the clinical application of various new materials. At present, stem cell therapy still has limitations, but the role of this technology in the treatment of hearing diseases has been widely recognized. With the development of related research, stem cell therapy will play a greater role in the treatment of diseases related to the inner ear.
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Affiliation(s)
- Zuhong He
- Department of Otorhinolaryngology-Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yanyan Ding
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yurong Mu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoxiang Xu
- Department of Otorhinolaryngology-Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Weijia Kong
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Renjie Chai
- State Key Laboratory of Bioelectronics, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, School of Life Sciences and Technology, Southeast University, Nanjing, China.,Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing, China.,Beijing Key Laboratory of Neural Regeneration and Repair, Capital Medical University, Beijing, China
| | - Xiong Chen
- Department of Otorhinolaryngology-Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
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