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Lin DF, Li HL, Liu T, Lv XF, Xie CM, Ou XM, Guan J, Zhang Y, Yan WB, He ML, Mao MY, Zhao X, Zhong LZ, Chen WH, Chen QY, Mai HQ, Peng RJ, Tian J, Tang LQ, Dong D. Radiomic signatures associated with tumor immune heterogeneity predict survival in locally recurrent nasopharyngeal carcinoma. J Natl Cancer Inst 2024:djae081. [PMID: 38637942 DOI: 10.1093/jnci/djae081] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 01/09/2024] [Accepted: 04/01/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND The prognostic value of traditional clinical indicators for locally recurrent nasopharyngeal carcinoma (lrNPC) is limited due to their inability to reflect intratumor heterogeneity. We aimed to develop a radiomic signature to reveal tumor immune heterogeneity and predict survival in lrNPC. METHODS This multicenter, retrospective study included 921 patients with lrNPC. A machine learning signature and nomogram based on pretreatment MRI features were developed for predicting overall survival (OS) in a training cohort and validated in two independent cohorts. A clinical nomogram and an integrated nomogram were constructed for comparison. Nomogram performance was evaluated by concordance index (C-index) and receiver operating characteristic curve analysis. Accordingly, patients were classified into risk groups. The biological characteristics and immune infiltration of the signature were explored by RNA sequencing (RNA-seq) analysis. RESULTS The machine learning signature and nomogram demonstrated comparable prognostic ability to a clinical nomogram, achieving C-indexes of 0.729, 0.718, and 0.731 in the training, internal, and external validation cohorts, respectively. Integration of the signature and clinical variables significantly improved the predictive performance. The proposed signature effectively distinguished patients between risk groups with significantly distinct OS rates. Subgroup analysis indicated the recommendation of local salvage treatments for low-risk patients. Exploratory RNA-seq analysis revealed differences in interferon response and lymphocyte infiltration between risk groups. CONCLUSIONS An MRI-based radiomic signature predicted OS more accurately. The proposed signature associated with tumor immune heterogeneity may serve as a valuable tool to facilitate prognostic stratification and guide individualized management for lrNPC patients.
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Affiliation(s)
- Da-Feng Lin
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology, in South China; Collaborative Innovation Center for Cancer Medicine, ; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy; Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Hai-Lin Li
- School of Engineering Medicine, Beihang University, Beijing, China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Ting Liu
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology, in South China; Collaborative Innovation Center for Cancer Medicine, ; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy; Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
- Breast Disease Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiao-Fei Lv
- Department of Radiology, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology, in South China; Collaborative Innovation Center for Cancer Medicine, ; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy; Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Chuan-Miao Xie
- Department of Radiology, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology, in South China; Collaborative Innovation Center for Cancer Medicine, ; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy; Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Xiao-Min Ou
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China and Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jian Guan
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ye Zhang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wen-Bin Yan
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China and Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Mei-Lin He
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Meng-Yuan Mao
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xun Zhao
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Lian-Zhen Zhong
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Hui Chen
- Department of Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Qiu-Yan Chen
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology, in South China; Collaborative Innovation Center for Cancer Medicine, ; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy; Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Hai-Qiang Mai
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology, in South China; Collaborative Innovation Center for Cancer Medicine, ; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy; Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Rou-Jun Peng
- Department of VIP Section, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology, in South China; Collaborative Innovation Center for Cancer Medicine, ; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy; Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Jie Tian
- School of Engineering Medicine, Beihang University, Beijing, China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
- National Key Laboratory of Kidney Diseases, Beijing, China
| | - Lin-Quan Tang
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology, in South China; Collaborative Innovation Center for Cancer Medicine, ; Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy; Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Di Dong
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
- National Key Laboratory of Kidney Diseases, Beijing, China
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Zhang P, Gao C, Huang Y, Chen X, Pan Z, Wang L, Dong D, Li S, Qi X. Artificial intelligence in liver imaging: methods and applications. Hepatol Int 2024; 18:422-434. [PMID: 38376649 DOI: 10.1007/s12072-023-10630-w] [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: 06/15/2023] [Accepted: 12/18/2023] [Indexed: 02/21/2024]
Abstract
Liver disease is regarded as one of the major health threats to humans. Radiographic assessments hold promise in terms of addressing the current demands for precisely diagnosing and treating liver diseases, and artificial intelligence (AI), which excels at automatically making quantitative assessments of complex medical image characteristics, has made great strides regarding the qualitative interpretation of medical imaging by clinicians. Here, we review the current state of medical-imaging-based AI methodologies and their applications concerning the management of liver diseases. We summarize the representative AI methodologies in liver imaging with focusing on deep learning, and illustrate their promising clinical applications across the spectrum of precise liver disease detection, diagnosis and treatment. We also address the current challenges and future perspectives of AI in liver imaging, with an emphasis on feature interpretability, multimodal data integration and multicenter study. Taken together, it is revealed that AI methodologies, together with the large volume of available medical image data, might impact the future of liver disease care.
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Affiliation(s)
- Peng Zhang
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing, China
| | - Chaofei Gao
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing, China
| | - Yifei Huang
- Department of Gastroenterology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiangyi Chen
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing, China
| | - Zhuoshi Pan
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing, China
| | - Lan Wang
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing, China
| | - Di Dong
- CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
| | - Shao Li
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing, China.
| | - Xiaolong Qi
- Center of Portal Hypertension, Department of Radiology, Zhongda Hospital, Medical School, Nurturing Center of Jiangsu Province for State Laboratory of AI Imaging & Interventional Radiology, Southeast University, Nanjing, China.
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He B, Sun C, Li H, Wang Y, She Y, Zhao M, Fang M, Zhu Y, Wang K, Liu Z, Wei Z, Mu W, Wang S, Tang Z, Wei J, Shao L, Tong L, Huang F, Tang M, Guo Y, Zhang H, Dong D, Chen C, Ma J, Tian J. Breaking boundaries in radiology: redefining AI diagnostics via raw data ahead of reconstruction. Phys Med Biol 2024; 69:075015. [PMID: 38224617 DOI: 10.1088/1361-6560/ad1e7c] [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: 08/31/2023] [Accepted: 01/15/2024] [Indexed: 01/17/2024]
Abstract
Objective.In the realm of utilizing artificial intelligence (AI) for medical image analysis, the paradigm of 'signal-image-knowledge' has remained unchanged. However, the process of 'signal to image' inevitably introduces information distortion, ultimately leading to irrecoverable biases in the 'image to knowledge' process. Our goal is to skip reconstruction and build a diagnostic model directly from the raw data (signal).Approach. This study focuses on computed tomography (CT) and its raw data (sinogram) as the research subjects. We simulate the real-world process of 'human-signal-image' using the workflow 'CT-simulated data- reconstructed CT,' and we develop a novel AI predictive model directly targeting raw data (RCTM). This model comprises orientation, spatial, and global analysis modules, embodying the fusion of local to global information extraction from raw data. We selected 1994 patients with retrospective cases of solid lung nodules and modeled different types of data.Main results. We employed predefined radiomic features to assess the diagnostic feature differences caused by reconstruction. The results indicated that approximately 14% of the features had Spearman correlation coefficients below 0.8. These findings suggest that despite the increasing maturity of CT reconstruction algorithms, they still introduce perturbations to diagnostic features. Moreover, our proposed RCTM achieved an area under the curve (AUC) of 0.863 in the diagnosis task, showcasing a comprehensive superiority over models constructed from secondary reconstructed CTs (0.840, 0.822, and 0.825). Additionally, the performance of RCTM closely resembled that of models constructed from original CT scans (0.868, 0.878, and 0.866).Significance. The diagnostic and therapeutic approach directly based on CT raw data can enhance the precision of AI models and the concept of 'signal-to-image' can be extended to other types of imaging. AI diagnostic models tailored to raw data offer the potential to disrupt the traditional paradigm of 'signal-image-knowledge', opening up new avenues for more accurate medical diagnostics.
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Affiliation(s)
- Bingxi He
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, People's Republic of China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology, Beijing, People's Republic of China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Caixia Sun
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, People's Republic of China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology, Beijing, People's Republic of China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Hailin Li
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, People's Republic of China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology, Beijing, People's Republic of China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yongbo Wang
- School of Biomedical Engineering, Southern Medical University, Guangzhou, People's Republic of China
| | - Yunlang She
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Mengmeng Zhao
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Mengjie Fang
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, People's Republic of China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology, Beijing, People's Republic of China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yongbei Zhu
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, People's Republic of China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology, Beijing, People's Republic of China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Kun Wang
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Zhenyu Liu
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Ziqi Wei
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Wei Mu
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, People's Republic of China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology, Beijing, People's Republic of China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Shuo Wang
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, People's Republic of China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology, Beijing, People's Republic of China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Zhenchao Tang
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, People's Republic of China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology, Beijing, People's Republic of China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jingwei Wei
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Lizhi Shao
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Lixia Tong
- Neusoft Medical Systems Co. Ltd, Shenyang, People's Republic of China
| | - Feng Huang
- Neusoft Medical Systems Co. Ltd, Shenyang, People's Republic of China
| | - Mingze Tang
- School of Mechanical and Materials Engineering, North China University of Technology, Beijing, People's Republic of China
| | - Yu Guo
- Department of Radiology, The First Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Huimao Zhang
- Department of Radiology, The First Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Di Dong
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Jianhua Ma
- School of Biomedical Engineering, Southern Medical University, Guangzhou, People's Republic of China
| | - Jie Tian
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, People's Republic of China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology, Beijing, People's Republic of China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, People's Republic of China
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Chen S, Guo L, Xie Y, Dong D, Saber R, Alluhidan M, Alamri A, Alfaisal A, Alazemi N, Al-Farsi YM, Al Ohaly YA, Zhang Y, Rakic S, Hamza M, Herbst CH, Tang S. Government responses to the COVID-19 pandemic of the Gulf Cooperation Council countries: good practices and lessons for future preparedness. Glob Health Res Policy 2024; 9:10. [PMID: 38486301 PMCID: PMC10941437 DOI: 10.1186/s41256-024-00349-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] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 03/05/2024] [Indexed: 03/17/2024] Open
Abstract
The COVID-19 pandemic has dramatically threatened the Gulf Cooperation Council (GCC) countries which have a large proportion of foreign workers. The governments of GCC countries have proactively implemented a comprehensive set of policy measures, and up to our knowledge, a systematic analysis of qualitative and quantitative evidence on the government response is still lacking. We summarized the GCC countries' government response and quantitatively measured that response using four indexes-the Government Response Index, the Stringency Index, the Vaccine Index, and the Initial Response Index, to analyse their response for future pandemic preparedness. Overall, the government response of all the GCC countries to the COVID-19 pandemic has been comprehensive, stringent, and timely. Notably, the GCC countries have implemented comprehensive vaccine policies. In addition, they have worked actively to protect foreign workers to improve their access to health services and secure their essential living conditions, regardless of their immigrant status. All the GCC countries dynamically adjusted their response to the evolving COVID-19 epidemiological burden and started to relax the stringency of the control policies after the Omicron wave, though the governments had different response magnitudes as measured by the four indexes. These findings have provided several important lessons for future pandemic response and preparedness for countries with similar economic, demographic, and health contexts in (1) prompt actions of containment and closure policies with dynamic adjusting, (2) strengthening health system policies, (3) comprehensive vaccination policies with universal access, (4) equitable and free access to testing, diagnosis, and treatment for all, and (5) strengthening the resilience of health systems.
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Affiliation(s)
- Shu Chen
- Australian Research Council Centre of Excellence in Population Ageing Research (CEPAR), University of New South Wales, Sydney, NSW, Australia
- School of Risk and Actuarial Studies, University of New South Wales, Sydney, NSW, Australia
| | - Lei Guo
- Global Health Research Center, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Yewei Xie
- SingHealth Duke-NUS Global Health Institute, Duke-NUS, Singapore, Singapore
| | - Di Dong
- World Bank, Washington, D.C., USA
| | - Rana Saber
- General Directorate for National Health Economics and Policy, Saudi Health Council, Riyadh, Saudi Arabia
| | - Mohammed Alluhidan
- General Directorate for National Health Economics and Policy, Saudi Health Council, Riyadh, Saudi Arabia
| | - Adwa Alamri
- General Directorate for National Health Economics and Policy, Saudi Health Council, Riyadh, Saudi Arabia
| | - Abdulrahman Alfaisal
- General Directorate for National Health Economics and Policy, Saudi Health Council, Riyadh, Saudi Arabia
| | - Nahar Alazemi
- General Directorate for National Health Economics and Policy, Saudi Health Council, Riyadh, Saudi Arabia
| | | | | | - Yi Zhang
- World Bank, Washington, D.C., USA
| | | | | | | | - Shenglan Tang
- Global Health Research Center, Duke Kunshan University, Kunshan, Jiangsu, China.
- SingHealth Duke-NUS Global Health Institute, Duke-NUS, Singapore, Singapore.
- Duke Global Health Institute, Duke University, Durham, NC, USA.
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Fu J, Fang M, Lin Z, Qiu J, Yang M, Tian J, Dong D, Zou Y. CT-based radiomics: predicting early outcomes after percutaneous transluminal renal angioplasty in patients with severe atherosclerotic renal artery stenosis. Vis Comput Ind Biomed Art 2024; 7:1. [PMID: 38212451 PMCID: PMC10784441 DOI: 10.1186/s42492-023-00152-5] [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: 10/15/2023] [Accepted: 12/27/2023] [Indexed: 01/13/2024] Open
Abstract
This study aimed to comprehensively evaluate non-contrast computed tomography (CT)-based radiomics for predicting early outcomes in patients with severe atherosclerotic renal artery stenosis (ARAS) after percutaneous transluminal renal angioplasty (PTRA). A total of 52 patients were retrospectively recruited, and their clinical characteristics and pretreatment CT images were collected. During a median follow-up period of 3.7 mo, 18 patients were confirmed to have benefited from the treatment, defined as a 20% improvement from baseline in the estimated glomerular filtration rate. A deep learning network trained via self-supervised learning was used to enhance the imaging phenotype characteristics. Radiomics features, comprising 116 handcrafted features and 78 deep learning features, were extracted from the affected renal and perirenal adipose regions. More features from the latter were correlated with early outcomes, as determined by univariate analysis, and were visually represented in radiomics heatmaps and volcano plots. After using consensus clustering and the least absolute shrinkage and selection operator method for feature selection, five machine learning models were evaluated. Logistic regression yielded the highest leave-one-out cross-validation accuracy of 0.780 (95%CI: 0.660-0.880) for the renal signature, while the support vector machine achieved 0.865 (95%CI: 0.769-0.942) for the perirenal adipose signature. SHapley Additive exPlanations was used to visually interpret the prediction mechanism, and a histogram feature and a deep learning feature were identified as the most influential factors for the renal signature and perirenal adipose signature, respectively. Multivariate analysis revealed that both signatures served as independent predictive factors. When combined, they achieved an area under the receiver operating characteristic curve of 0.888 (95%CI: 0.784-0.992), indicating that the imaging phenotypes from both regions complemented each other. In conclusion, non-contrast CT-based radiomics can be leveraged to predict the early outcomes of PTRA, thereby assisting in identifying patients with ARAS suitable for this treatment, with perirenal adipose tissue providing added predictive value.
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Affiliation(s)
- Jia Fu
- Department of Interventional Radiology and Vascular Surgery, Peking University First Hospital, Beijing, 100043, China
- Department of Radiology, Peking University First Hospital, Beijing, 100043, China
| | - Mengjie Fang
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, 100191, China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
| | - Zhiyong Lin
- Department of Radiology, Peking University First Hospital, Beijing, 100043, China
| | - Jianxing Qiu
- Department of Radiology, Peking University First Hospital, Beijing, 100043, China
| | - Min Yang
- Department of Interventional Radiology and Vascular Surgery, Peking University First Hospital, Beijing, 100043, China
| | - Jie Tian
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, 100191, China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
| | - Di Dong
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China.
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yinghua Zou
- Department of Interventional Radiology and Vascular Surgery, Peking University First Hospital, Beijing, 100043, China.
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Wang Z, Fang M, Zhang J, Tang L, Zhong L, Li H, Cao R, Zhao X, Liu S, Zhang R, Xie X, Mai H, Qiu S, Tian J, Dong D. Radiomics and Deep Learning in Nasopharyngeal Carcinoma: A Review. IEEE Rev Biomed Eng 2024; 17:118-135. [PMID: 37097799 DOI: 10.1109/rbme.2023.3269776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Nasopharyngeal carcinoma is a common head and neck malignancy with distinct clinical management compared to other types of cancer. Precision risk stratification and tailored therapeutic interventions are crucial to improving the survival outcomes. Artificial intelligence, including radiomics and deep learning, has exhibited considerable efficacy in various clinical tasks for nasopharyngeal carcinoma. These techniques leverage medical images and other clinical data to optimize clinical workflow and ultimately benefit patients. In this review, we provide an overview of the technical aspects and basic workflow of radiomics and deep learning in medical image analysis. We then conduct a detailed review of their applications to seven typical tasks in the clinical diagnosis and treatment of nasopharyngeal carcinoma, covering various aspects of image synthesis, lesion segmentation, diagnosis, and prognosis. The innovation and application effects of cutting-edge research are summarized. Recognizing the heterogeneity of the research field and the existing gap between research and clinical translation, potential avenues for improvement are discussed. We propose that these issues can be gradually addressed by establishing standardized large datasets, exploring the biological characteristics of features, and technological upgrades.
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Liu S, Deng J, Dong D, Fang M, Ye Z, Hu Y, Li H, Zhong L, Cao R, Zhao X, Shang W, Li G, Liang H, Tian J. Deep learning-based radiomics model can predict extranodal soft tissue metastasis in gastric cancer. Med Phys 2024; 51:267-277. [PMID: 37573524 DOI: 10.1002/mp.16647] [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: 02/08/2023] [Revised: 05/24/2023] [Accepted: 06/23/2023] [Indexed: 08/15/2023] Open
Abstract
BACKGROUND The potential prognostic value of extranodal soft tissue metastasis (ESTM) has been confirmed by increasing studies about gastric cancer (GC). However, the gold standard of ESTM is determined by pathologic examination after surgery, and there are no preoperative methods for assessment of ESTM yet. PURPOSE This multicenter study aimed to develop a deep learning-based radiomics model to preoperatively identify ESTM and evaluate its prognostic value. METHODS A total of 959 GC patients were enrolled from two centers and split into a training cohort (N = 551) and a test cohort (N = 236) for ESTM evaluation. Additionally, an external survival cohort (N = 172) was included for prognostic analysis. Four models were established based on clinical characteristics and multiphase computed tomography (CT) images for preoperative identification of ESTM, including a deep learning model, a hand-crafted radiomic model, a clinical model, and a combined model. C-index, decision curve, and calibration curve were utilized to assess the model performances. Survival analysis was conducted to explore the ability of stratifying overall survival (OS). RESULTS The combined model showed good discrimination of the ESTM [C-indices (95% confidence interval, CI): 0.770 (0.729-0.812) and 0.761 (0.718-0.805) in training and test cohorts respectively], which outperformed deep learning model, radiomics model, and clinical model. The stratified analysis showed this model was not affected by patient's tumor size, the presence of lymphovascular invasion, and Lauren classification (p < 0.05). Moreover, the model score showed strong consistency with the OS [C-indices (95%CI): 0.723 (0.658-0.789, p < 0.0001) in the internal survival cohort and 0.715 (0.650-0.779, p < 0.0001) in the external survival cohort]. More interestingly, univariate analysis showed the model score was significantly associated with occult distant metastasis (p < 0.05) that was missed by preoperative diagnosis. CONCLUSIONS The model combining CT images and clinical characteristics had an impressive predictive ability of both ESTM and prognosis, which has the potential to serve as an effective complement to the preoperative TNM staging system.
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Affiliation(s)
- Shengyuan Liu
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Jingyu Deng
- Department of Gastrointestinal Surgery, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Di Dong
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Mengjie Fang
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, China
| | - Zhaoxiang Ye
- Department of Gastrointestinal Surgery, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Yanfeng Hu
- Nanfang Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Hailin Li
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, China
| | - Lianzhen Zhong
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Runnan Cao
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Xun Zhao
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Wenting Shang
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Guoxin Li
- Nanfang Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Han Liang
- Department of Gastrointestinal Surgery, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Jie Tian
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, China
- Beijing Key Lab of Molecular Imaging, Beijing, China
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8
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Li H, Huang W, Wang S, Balasubramanian PS, Wu G, Fang M, Xie X, Zhang J, Dong D, Tian J, Chen F. Comprehensive integrated analysis of MR and DCE-MR radiomics models for prognostic prediction in nasopharyngeal carcinoma. Vis Comput Ind Biomed Art 2023; 6:23. [PMID: 38036750 PMCID: PMC10689317 DOI: 10.1186/s42492-023-00149-0] [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: 06/29/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Although prognostic prediction of nasopharyngeal carcinoma (NPC) remains a pivotal research area, the role of dynamic contrast-enhanced magnetic resonance (DCE-MR) has been less explored. This study aimed to investigate the role of DCR-MR in predicting progression-free survival (PFS) in patients with NPC using magnetic resonance (MR)- and DCE-MR-based radiomic models. A total of 434 patients with two MR scanning sequences were included. The MR- and DCE-MR-based radiomics models were developed based on 289 patients with only MR scanning sequences and 145 patients with four additional pharmacokinetic parameters (volume fraction of extravascular extracellular space (ve), volume fraction of plasma space (vp), volume transfer constant (Ktrans), and reverse reflux rate constant (kep) of DCE-MR. A combined model integrating MR and DCE-MR was constructed. Utilizing methods such as correlation analysis, least absolute shrinkage and selection operator regression, and multivariate Cox proportional hazards regression, we built the radiomics models. Finally, we calculated the net reclassification index and C-index to evaluate and compare the prognostic performance of the radiomics models. Kaplan-Meier survival curve analysis was performed to investigate the model's ability to stratify risk in patients with NPC. The integration of MR and DCE-MR radiomic features significantly enhanced prognostic prediction performance compared to MR- and DCE-MR-based models, evidenced by a test set C-index of 0.808 vs 0.729 and 0.731, respectively. The combined radiomics model improved net reclassification by 22.9%-52.6% and could significantly stratify the risk levels of patients with NPC (p = 0.036). Furthermore, the MR-based radiomic feature maps achieved similar results to the DCE-MR pharmacokinetic parameters in terms of reflecting the underlying angiogenesis information in NPC. Compared to conventional MR-based radiomics models, the combined radiomics model integrating MR and DCE-MR showed promising results in delivering more accurate prognostic predictions and provided more clinical benefits in quantifying and monitoring phenotypic changes associated with NPC prognosis.
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Affiliation(s)
- Hailin Li
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, 100191, China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
| | - Weiyuan Huang
- Department of Radiology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, 570311, China
| | - Siwen Wang
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Gang Wu
- Department of Radiotherapy, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, 570311, China
| | - Mengjie Fang
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, 100191, China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
| | - Xuebin Xie
- Department of Radiology, Kiang Wu Hospital, Santo António, Macao, 999078, China
| | - Jie Zhang
- Department of Radiology, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, Guangdong, 519000, China
| | - Di Dong
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China.
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jie Tian
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, 100191, China.
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China.
- Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China.
- Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai, Guangdong, 519000, China.
| | - Feng Chen
- Department of Radiology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, 570311, China.
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9
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Liu T, Dong D, Zhao X, Ou XM, Yi JL, Guan J, Zhang Y, Xiao-Fei L, Xie CM, Luo DH, Sun R, Chen QY, Xing L, Guo SS, Liu LT, Lin DF, Chen YZ, Lin JY, Luo MJ, Yan WB, He ML, Mao MY, Zhu MY, Chen WH, Shen BW, Wang SQ, Li HL, Zhong LZ, Hu CS, Wu DH, Mai HQ, Tian J, Tang LQ. Radiomic signatures reveal multiscale intratumor heterogeneity associated with tissue tolerance and survival in re-irradiated nasopharyngeal carcinoma: a multicenter study. BMC Med 2023; 21:464. [PMID: 38012705 PMCID: PMC10683300 DOI: 10.1186/s12916-023-03164-3] [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: 12/13/2022] [Accepted: 11/08/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Post-radiation nasopharyngeal necrosis (PRNN) is a severe adverse event following re-radiotherapy for patients with locally recurrent nasopharyngeal carcinoma (LRNPC) and associated with decreased survival. Biological heterogeneity in recurrent tumors contributes to the different risks of PRNN. Radiomics can be used to mine high-throughput non-invasive image features to predict clinical outcomes and capture underlying biological functions. We aimed to develop a radiogenomic signature for the pre-treatment prediction of PRNN to guide re-radiotherapy in patients with LRNPC. METHODS This multicenter study included 761 re-irradiated patients with LRNPC at four centers in NPC endemic area and divided them into training, internal validation, and external validation cohorts. We built a machine learning (random forest) radiomic signature based on the pre-treatment multiparametric magnetic resonance images for predicting PRNN following re-radiotherapy. We comprehensively assessed the performance of the radiomic signature. Transcriptomic sequencing and gene set enrichment analyses were conducted to identify the associated biological processes. RESULTS The radiomic signature showed discrimination of 1-year PRNN in the training, internal validation, and external validation cohorts (area under the curve (AUC) 0.713-0.756). Stratified by a cutoff score of 0.735, patients with high-risk signature had higher incidences of PRNN than patients with low-risk signature (1-year PRNN rates 42.2-62.5% vs. 16.3-18.8%, P < 0.001). The signature significantly outperformed the clinical model (P < 0.05) and was generalizable across different centers, imaging parameters, and patient subgroups. The radiomic signature had prognostic value concerning its correlation with PRNN-related deaths (hazard ratio (HR) 3.07-6.75, P < 0.001) and all causes of deaths (HR 1.53-2.30, P < 0.01). Radiogenomics analyses revealed associations between the radiomic signature and signaling pathways involved in tissue fibrosis and vascularity. CONCLUSIONS We present a radiomic signature for the individualized risk assessment of PRNN following re-radiotherapy, which may serve as a noninvasive radio-biomarker of radiation injury-associated processes and a useful clinical tool to personalize treatment recommendations for patients with LANPC.
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Affiliation(s)
- Ting Liu
- Sun Yat-Sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
- Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China
- Breast Disease Center, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Di Dong
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Xun Zhao
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Min Ou
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jun-Lin Yi
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jian Guan
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ye Zhang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lv Xiao-Fei
- Sun Yat-Sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
- Department of Radiology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Chuan-Miao Xie
- Sun Yat-Sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
- Department of Radiology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Dong-Hua Luo
- Sun Yat-Sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
- Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China
| | - Rui Sun
- Sun Yat-Sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
- Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China
| | - Qiu-Yan Chen
- Sun Yat-Sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
- Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China
| | - Lv Xing
- Sun Yat-Sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
- Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China
| | - Shan-Shan Guo
- Sun Yat-Sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
- Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China
| | - Li-Ting Liu
- Sun Yat-Sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
- Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China
| | - Da-Feng Lin
- Sun Yat-Sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
- Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China
| | - Yan-Zhou Chen
- Sun Yat-Sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
- Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China
| | - Jie-Yi Lin
- Sun Yat-Sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
- Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China
| | - Mei-Juan Luo
- Sun Yat-Sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
- Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China
| | - Wen-Bin Yan
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Mei-Lin He
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Meng-Yuan Mao
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Man-Yi Zhu
- Sun Yat-Sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
- Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China
| | - Wen-Hui Chen
- Department of Oncology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Bo-Wen Shen
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Shi-Qian Wang
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Hai-Lin Li
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Lian-Zhen Zhong
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
| | - Chao-Su Hu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - De-Hua Wu
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hai-Qiang Mai
- Sun Yat-Sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China.
- Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China.
| | - Jie Tian
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China.
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, China.
| | - Lin-Quan Tang
- Sun Yat-Sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China.
- Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China.
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10
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Wang HZ, Zheng X, Sun J, Zhu X, Dong D, Du Y, Feng Z, Gong J, Wu H, Geng J, Li S, Song M, Zhang Y, Liu Z, Cai Y, Li Y, Wang W. 4D-MRI Guided Stereotactic Body Radiation Therapy for Unresectable Colorectal Liver Metastases. Int J Radiat Oncol Biol Phys 2023; 117:e359. [PMID: 37785235 DOI: 10.1016/j.ijrobp.2023.06.2445] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) This study evaluated the feasibilities and outcomes following four-dimensional magnetic resonance imaging (4D-MRI) guided stereotactic body radiation therapy (SBRT) for unresectable colorectal liver metastases (CRLM). MATERIALS/METHODS From March 2018 to January 2022, we identified 76 unresectable CRLM patients with 123 lesions who received 4D-MRI guided SBRT in our institution. 4D-MRI simulation with or without abdominal compression was conducted for all patients. The prescription dose was 50-65 Gy in 5-12 fractions. The image quality of computed tomography (CT) and MRI were compared using the Clarity Score. Clinical outcomes and toxicity profiles were evaluated. RESULTS The 4D-MRI significantly improved the image quality compared with CT images (mean Clarity Score: 1.67 vs 2.88, P < 0.001). The abdominal compression significantly reduced motions in cranial-caudal direction (P = 0.03) with 2 phase T2 weighted images assessing tumor motion. The median follow-up time was 12.5 months. For 98 lesions assessed for best response, the complete response, partial response and stable disease rate were 57.1 %, 30.6 % and 12.2 %, respectively. The local control (LC) rate at 2 year was 97.3%. 46.1% of patients experienced grade 1-2 toxicities and only 2.6% patients experienced grade 3 hematologic toxicities. CONCLUSION The 4D-MRI technique allowed precise target delineation and motion tracking in unresectable CRLM patients. High LC rate and mild toxicities were achieved. This study provided evidence for using 4D-MRI guided SBRT as an alternative treatment in unresectable CRLM.
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Affiliation(s)
- H Z Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - X Zheng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, Beijing, China
| | - J Sun
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, Beijing, China
| | - X Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - D Dong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, Beijing, China
| | - Y Du
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, Beijing, China
| | - Z Feng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, Beijing, China
| | - J Gong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, Beijing, China
| | - H Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, Beijing, China
| | - J Geng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - S Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - M Song
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Y Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Z Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Y Cai
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Y Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - W Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital and Institute, Beijing, China
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11
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Zhu Y, Li H, Huang Y, Fu W, Wang S, Sun N, Dong D, Tian J, Peng Y. CT-based identification of pediatric non-Wilms tumors using convolutional neural networks at a single center. Pediatr Res 2023; 94:1104-1110. [PMID: 36959318 DOI: 10.1038/s41390-023-02553-x] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/21/2022] [Accepted: 01/05/2023] [Indexed: 03/25/2023]
Abstract
BACKGROUND Deep learning (DL) is more and more widely used in children's medical treatment. In this study, we have developed a computed tomography (CT)-based DL model for identifying undiagnosed non-Wilms tumors (nWTs) from pediatric renal tumors. METHODS This study collected and analyzed the preoperative clinical data and CT images of pediatric renal tumor patients diagnosed by our center from 2008 to 2020, and established a DL model to identify nWTs noninvasively. RESULTS A total of 364 children who had been confirmed by histopathology with renal tumors from our center were enrolled, including 269 Wilms tumors (WTs) and 95 nWTs. For DL model development, all cases were randomly allocated to training set (218 cases), validation set (73 cases), and test set (73 cases). In the test set, the DL model achieved area under the curve of 0.831 (95% CI: 0.712-0.951) in discriminating WTs from nWTs, with the accuracy, sensitivity, and specificity of 0.781, 0.563, and 0.842, respectively. The sensitivity of our model was higher than a radiologist with 15 years of experience. CONCLUSIONS We presented a DL model for identifying undiagnosed nWTs from pediatric renal tumors, with the potential to improve the image-based diagnosis. IMPACT Deep learning model was used for the first time to identify pediatric renal tumors in this study. Deep learning model can identify non-Wilms tumors from pediatric renal tumors. Deep learning model based on computed tomography images can improve tumor diagnosis rate.
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Affiliation(s)
- Yupeng Zhu
- Department of Radiology, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
- Department of Radiology, Peking University Third Hospital, Beijing, 100191, China
| | - Hailin Li
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, 100191, China
- CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yangyue Huang
- Department of Pediatric Urology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Wangxing Fu
- Department of Radiology, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Siwen Wang
- CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ning Sun
- Department of Pediatric Urology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
| | - Di Dong
- CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China.
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jie Tian
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, 100191, China.
- CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China.
- Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China.
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (affiliated with Jinan University), Zhuhai, 519000, China.
| | - Yun Peng
- Department of Radiology, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
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12
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Xiao H, Song Q, Wang YT, Dong D. [Massive ascites and gastrointestinal bleeding caused by idiopathic inferior mesenteric arteriovenous fistula: a case report]. Zhonghua Nei Ke Za Zhi 2023; 62:852-854. [PMID: 37394856 DOI: 10.3760/cma.j.cn112138-20220718-00528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Affiliation(s)
- H Xiao
- Department of Radiology, the First Hospital of Jilin University, Changchun 130012, China
| | - Q Song
- Department of Radiology, the First Hospital of Jilin University, Changchun 130012, China
| | - Y T Wang
- Department of Radiology, the First Hospital of Jilin University, Changchun 130012, China
| | - D Dong
- Department of Radiology, the First Hospital of Jilin University, Changchun 130012, China
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13
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Dong D, Zhao YL, Wang C, Tian JS, Zhang YD, Wei RH, Qiao XJ, Guo G, Yin TN, Hu HJ. [Impact of sinonasal anatomic changes after endoscopic anterior skull base surgery on nasal airflow and air conditioning: a computational fluid dynamics study]. Zhonghua Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2023; 58:445-451. [PMID: 37100751 DOI: 10.3760/cma.j.cn115330-20221031-00643] [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] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Objective: To analyze the impact of the sinonasal anatomic changes after endonasal endoscopic anterior skull base surgery on the nasal airflow and heating and humidification by computational fluid dynamics (CFD), and to explore the correlation between the postoperative CFD parameters and the subjective symptoms of the patients. Methods: The clinical data in the Rhinology Department of the First Affiliated Hospital of Zhengzhou University from 2016 to 2021 were retrospectively analyzed. The patients received the endoscopic resection of the anterior skull base tumor were selected as the case group, and the adults whose CT scans had no sinonasal abnormalities were chosen as the control group. The CFD simulation was performed on the sinonasal models after reconstructed from the patients' sinus CT images during the post-surgical follow-up. All the patients were asked to complete the Empty Nose Syndrome 6-Item Questionnaire (ENS6Q) to assess the subjective symptoms. The comparison between two independent groups and the correlation analysis were carried out by using the Mann-Whitney U test and the Spearman correlation test in the SPSS 26.0 software. Results: Nineteen patients (including 8 males and 11 females, from 22 to 67 years old) in the case group and 2 patients (a male of 38 years old and a female of 45 years old) in the control group were enrolled in this study. After the anterior skull base surgery, the high-speed airflow moved to the upper part of the nasal cavity, and the lowest temperature shifted upwards on the choana. Comparing with the control group, the ratio of nasal mucosal surface area to nasal ventilation volume in the case group decreased [0.41 (0.40, 0.41) mm-1 vs 0.32 (0.30, 0.38) mm-1; Z=-2.04, P=0.041], the air flow in the upper and middle part of the nasal cavity increased [61.14 (59.78, 62.51)% vs 78.07 (76.22, 94.43)%; Z=-2.28, P=0.023], the nasal resistance decreased [0.024 (0.022, 0.026) Pa·s/ml vs 0.016 (0.009, 0.018) Pa·s/ml; Z=-2.29, P=0.022], the lowest temperature in the middle of the nasal cavity decreased [28.29 (27.23, 29.35)℃ vs 25.06 (24.07, 25.50)℃; Z=-2.28, P=0.023], the nasal heating efficiency decreased [98.74 (97.95, 99.52)% vs 82.16 (80.24, 86.91)%; Z=-2.28, P=0.023], the lowest relative humidity decreased [(79.62 (76.55, 82.69)% vs 73.28 (71.27, 75.05)%; Z=-2.28, P=0.023], and the nasal humidification efficiency decreased [99.50 (97.69, 101.30)% vs 86.09 (79.33, 87.16)%; Z=-2.28, P=0.023]. The ENS6Q total scores of all patients in the case group were less than 11 points. There was a moderate negative correlation between the proportion of the inferior airflow in the post-surgical nasal cavity negatively and the ENS6Q total scores (rs=-0.50, P=0.029). Conclusions: The sinonasal anatomic changes after the endoscopic anterior skull base surgery alter the nasal airflow patterns, reducing the efficiency of nasal heating and humidification. However, the post-surgical occurrence tendency of the empty nose syndrome is weak.
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Affiliation(s)
- D Dong
- The Rhinology Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Y L Zhao
- The Rhinology Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - C Wang
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - J S Tian
- Chongqing Gonggangzhihui Additive Manufacturing Technology Research Institute, Chongqing 401147, China
| | - Y D Zhang
- School of Mechanics and Safety Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - R H Wei
- School of Mechanics and Safety Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - X J Qiao
- The Rhinology Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - G Guo
- The Rhinology Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - T N Yin
- The Rhinology Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - H J Hu
- The Rhinology Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
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Li H, Wang S, Liu B, Fang M, Cao R, He B, Liu S, Hu C, Dong D, Wang X, Wang H, Tian J. A multi-view co-training network for semi-supervised medical image-based prognostic prediction. Neural Netw 2023; 164:455-463. [PMID: 37182347 DOI: 10.1016/j.neunet.2023.04.030] [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: 11/16/2022] [Revised: 03/07/2023] [Accepted: 04/18/2023] [Indexed: 05/16/2023]
Abstract
Prognostic prediction has long been a hotspot in disease analysis and management, and the development of image-based prognostic prediction models has significant clinical implications for current personalized treatment strategies. The main challenge in prognostic prediction is to model a regression problem based on censored observations, and semi-supervised learning has the potential to play an important role in improving the utilization efficiency of censored data. However, there are yet few effective semi-supervised paradigms to be applied. In this paper, we propose a semi-supervised co-training deep neural network incorporating a support vector regression layer for survival time estimation (Co-DeepSVS) that improves the efficiency in utilizing censored data for prognostic prediction. First, we introduce a support vector regression layer in deep neural networks to deal with censored data and directly predict survival time, and more importantly to calculate the labeling confidence of each case. Then, we apply a semi-supervised multi-view co-training framework to achieve accurate prognostic prediction, where labeling confidence estimation with prior knowledge of pseudo time is conducted for each view. Experimental results demonstrate that the proposed Co-DeepSVS has a promising prognostic ability and surpasses most widely used methods on a multi-phase CT dataset. Besides, the introduction of SVR layer makes the model more robust in the presence of follow-up bias.
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Affiliation(s)
- Hailin Li
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, 100191, China; CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
| | - Siwen Wang
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bo Liu
- Lanzhou University Second Hospital, Lanzhou, 730050, Gansu, China; Department of Radiology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Shandong University, Jinan, 250021, Shandong, China
| | - Mengjie Fang
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, 100191, China; CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
| | - Runnan Cao
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bingxi He
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, 100191, China; CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
| | - Shengyuan Liu
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaoen Hu
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
| | - Di Dong
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ximing Wang
- Department of Radiology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Shandong University, Jinan, 250021, Shandong, China.
| | - Hexiang Wang
- Department of Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China.
| | - Jie Tian
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, 100191, China; CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China.
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15
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Yang Z, Dong D, Qi Z, Jia C, Han L, Chao Y. Genome-wide identification, expression analysis, and transcriptome analysis of the IAA gene family in Zoysia japonica. Mol Biol Rep 2023; 50:4385-4394. [PMID: 36961632 DOI: 10.1007/s11033-022-08154-x] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/23/2022] [Indexed: 03/25/2023]
Abstract
BACKGROUND AUX/IAA is an essential signaling molecule and has great physiological importance in various plants, but its function in Zoysia japonica remains unknown. METHODS AND RESULTS Genome-wide identification and analysis of AUX/IAA genes used bioinformatics methods to investigate the ZjIAA genes' expression of exogenous IAA hydroponics treatment for 2 h by qRT-PCR, control and exogenous IAA treated zoysia were subjected to transcriptome sequencing. ZjIAAs were distributed across the 13 subfamilies by phylogenetic analysis with Oryza sativa and Arabidopsis thaliana. Multiple sequence alignment revealed that the majority of genes were non-canonical ZjIAAs with incomplete domain. The optimal growth concentration of the IAA hormone was 0.05 mM, and the qRT-PCR analysis revealed that eight ZjIAAs were differentially expressed, with seven genes considerably upregulating and one gene significantly downregulating. The result of transcriptome sequencing revealed that 515 differentially expressed genes (DEGs) were identified, with 344 upregulated genes and 171 downregulated genes. A total of 18 genes were annotated as involved in the plant hormone signal transduction pathway. And 8 ZjIAAs exhibited distinct expressions, 7 upregulated, and only one downregulated, according to the qRT-PCR study. CONCLUSIONS Genome-wide identification and analysis increased the understanding of the evolution and function of the IAA family in zoysia. DEGs of control and treatment with 0.05 mM exogenous IAA hormone were investigated by transcriptome sequencing. ZjIAAs had substantial variations in the expression of associated genes, with the majority of genes upregulated and 18 genes implicated in plant hormone signal transduction.
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Affiliation(s)
- Zhuoxiong Yang
- College of Grassland Science, Beijing Forestry University, Beijing, 100083, China
| | - Di Dong
- College of Grassland Science, Beijing Forestry University, Beijing, 100083, China
| | - Zewen Qi
- College of Grassland Science, Beijing Forestry University, Beijing, 100083, China
| | - Chenyan Jia
- Inner Mongolia M-Grass Ecology and Environment (Group) Co., Ltd, Hohhot, 010010, Inner Mongolia, China
| | - Liebao Han
- College of Grassland Science, Beijing Forestry University, Beijing, 100083, China.
| | - Yuehui Chao
- College of Grassland Science, Beijing Forestry University, Beijing, 100083, China.
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16
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Zhang ST, Wang SY, Zhang J, Dong D, Mu W, Xia XE, Fu FF, Lu YN, Wang S, Tang ZC, Li P, Qu JR, Wang MY, Tian J, Liu JH. Artificial intelligence-based computer-aided diagnosis system supports diagnosis of lymph node metastasis in esophageal squamous cell carcinoma: A multicenter study. Heliyon 2023; 9:e14030. [PMID: 36923854 PMCID: PMC10009687 DOI: 10.1016/j.heliyon.2023.e14030] [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: 12/21/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Background This study aimed to develop an artificial intelligence-based computer-aided diagnosis system (AI-CAD) emulating the diagnostic logic of radiologists for lymph node metastasis (LNM) in esophageal squamous cell carcinoma (ESCC) patients, which contributed to clinical treatment decision-making. Methods A total of 689 ESCC patients with PET/CT images were enrolled from three hospitals and divided into a training cohort and two external validation cohorts. 452 CT images from three publicly available datasets were also included for pretraining the model. Anatomic information from CT images was first obtained automatically using a U-Net-based multi-organ segmentation model, and metabolic information from PET images was subsequently extracted using a gradient-based approach. AI-CAD was developed in the training cohort and externally validated in two validation cohorts. Results The AI-CAD achieved an accuracy of 0.744 for predicting pathological LNM in the external cohort and a good agreement with a human expert in two external validation cohorts (kappa = 0.674 and 0.587, p < 0.001). With the aid of AI-CAD, the human expert's diagnostic performance for LNM was significantly improved (accuracy [95% confidence interval]: 0.712 [0.669-0.758] vs. 0.833 [0.797-0.865], specificity [95% confidence interval]: 0.697 [0.636-0.753] vs. 0.891 [0.851-0.928]; p < 0.001) among patients underwent lymphadenectomy in the external validation cohorts. Conclusions The AI-CAD could aid in preoperative diagnosis of LNM in ESCC patients and thereby support clinical treatment decision-making.
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Key Words
- 18F-FDG PET/CT, 18-fluorine-fluorodeoxyglucose positron-emission tomography/computed tomography
- AI, Artificial intelligence
- AI-CAD, Artificial intelligence-based computer-aided diagnosis
- Artificial intelligence
- CI, Confidence interval
- CT, Computed tomography
- ESCC, Esophageal squamous cell carcinoma
- Esophageal squamous cell carcinoma
- LNM, Lymph node metastasis
- Lymph node metastasis
- OS, Overall survival
- PET/CT
- PFS, Progression-free survival
- SD, Standard deviation
- SLR, Ratio of the SUV value to liver uptake
- SUV, Standardized uptake value
- cN, Clinical N stage
- nCRT, Neoadjuvant chemoradiotherapy
- pN, Pathological N stage
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Affiliation(s)
- Shuai-Tong Zhang
- School of Medical Technology, Beijing Institute of Technology, Beijing, China.,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, China.,CAS Key Laboratory of Molecular Imaging, The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology, Beijing, China
| | - Si-Yun Wang
- Department of PET Center, Guangdong Provincial People's Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jie Zhang
- Department of Radiology, Zhuhai City People's Hospital/Zhuhai Hospital Affiliated to Jinan University, Zhuhai, Guangdong, China
| | - Di Dong
- CAS Key Laboratory of Molecular Imaging, The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Wei Mu
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, China.,Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology, Beijing, China
| | - Xue-Er Xia
- Department of Gastrointestinal Surgery, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Fang-Fang Fu
- Department of Medical Imaging, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Ya-Nan Lu
- Department of Radiology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Shuo Wang
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, China.,Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology, Beijing, China
| | - Zhen-Chao Tang
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, China.,Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology, Beijing, China
| | - Peng Li
- Department of PET Center, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Jin-Rong Qu
- Department of Radiology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Mei-Yun Wang
- Department of Medical Imaging, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Jie Tian
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, China.,CAS Key Laboratory of Molecular Imaging, The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology, Beijing, China
| | - Jian-Hua Liu
- Department of Oncology, Guangdong Provincial People's Hospital, Southern Medical University, Guangzhou, Guangdong, China
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Zhang S, Mu W, Dong D, Wei J, Fang M, Shao L, Zhou Y, He B, Zhang S, Liu Z, Liu J, Tian J. The Applications of Artificial Intelligence in Digestive System Neoplasms: A Review. Health Data Sci 2023; 3:0005. [PMID: 38487199 PMCID: PMC10877701 DOI: 10.34133/hds.0005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 12/05/2022] [Indexed: 03/17/2024]
Abstract
Importance Digestive system neoplasms (DSNs) are the leading cause of cancer-related mortality with a 5-year survival rate of less than 20%. Subjective evaluation of medical images including endoscopic images, whole slide images, computed tomography images, and magnetic resonance images plays a vital role in the clinical practice of DSNs, but with limited performance and increased workload of radiologists or pathologists. The application of artificial intelligence (AI) in medical image analysis holds promise to augment the visual interpretation of medical images, which could not only automate the complicated evaluation process but also convert medical images into quantitative imaging features that associated with tumor heterogeneity. Highlights We briefly introduce the methodology of AI for medical image analysis and then review its clinical applications including clinical auxiliary diagnosis, assessment of treatment response, and prognosis prediction on 4 typical DSNs including esophageal cancer, gastric cancer, colorectal cancer, and hepatocellular carcinoma. Conclusion AI technology has great potential in supporting the clinical diagnosis and treatment decision-making of DSNs. Several technical issues should be overcome before its application into clinical practice of DSNs.
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Affiliation(s)
- Shuaitong Zhang
- School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology, Beijing, China
| | - Wei Mu
- School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology, Beijing, China
| | - Di Dong
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Jingwei Wei
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Mengjie Fang
- School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology, Beijing, China
| | - Lizhi Shao
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Yu Zhou
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Bingxi He
- School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology, Beijing, China
| | - Song Zhang
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Zhenyu Liu
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Jianhua Liu
- Department of Oncology, Guangdong Provincial People's Hospital/Second Clinical Medical College of Southern Medical University/Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Jie Tian
- School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology, Beijing, China
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
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18
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Fang M, Wang Z, Tian J, Dong D. Predicting origin for bone metastatic cancer using deep learning-based pathology. EBioMedicine 2023; 88:104449. [PMID: 36716573 PMCID: PMC9900359 DOI: 10.1016/j.ebiom.2023.104449] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/30/2023] Open
Affiliation(s)
- Mengjie Fang
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, China,Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology, Beijing, China,CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Zipei Wang
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China,School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China,School of Modern Post (School of Automation), Beijing University of Posts and Telecommunications, Beijing, China
| | - Jie Tian
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, China,Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology, Beijing, China,CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Di Dong
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China.
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Nikoloski Z, Alghaith T, Herbst CH, Hamza M, AlSaffer Q, Alluhidan M, Dong D, Alsukait R, Alqasem L, Alazemi N. Responsiveness of the healthcare system in the Kingdom of Saudi Arabia: evidence from a nationally representative survey. BMC Health Serv Res 2022; 22:1524. [PMID: 36517822 PMCID: PMC9749241 DOI: 10.1186/s12913-022-08779-5] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 11/02/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Responsiveness is one of the widely used metrics in assessing the performance of healthcare systems. An analysis of the determinants of health care demand and supply and how the Saudi health system responds to the needs of patients (inpatient and outpatient) is needed; hence the need for this study. METHODS We analysed data from the Saudi Health Systems Responsiveness survey - a nationally representative survey of 10,000 households interviewed in 2017. Using this dataset, we descriptively analysed the level of responsiveness of inpatient and outpatient services (using the standard World Health Organization (WHO) responsiveness dimensions). Based on a logit modelling approach, the relationship between responsiveness and its key determinants was analysed in terms of healthcare demand and supply. RESULTS Over four fifths of respondents are satisfied with the level of inpatient and outpatient responsiveness. Furthermore, we find that those in bad health tend to show lower levels of satisfaction with inpatient and outpatient care. We also find some evidence that age, gender, and to some extent nationality act as correlates of health system responsiveness. Specifically, we find evidence that Saudi nationals are less satisfied with health services compared to foreign nationals. CONCLUSION Based on these findings improving the responsiveness of public healthcare facilities would need to be prioritized. Focusing on patients in worse health and lower socio-economic status should also be one of the main priorities.
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Affiliation(s)
- Zlatko Nikoloski
- grid.13063.370000 0001 0789 5319Department of Health Policy, London School of Economics and Political Science, London, UK
| | | | | | - Mariam Hamza
- grid.431778.e0000 0004 0482 9086World Bank, Washington DC, USA
| | - Quds AlSaffer
- Saudi Health Council, Riyadh, Kingdom of Saudi Arabia
| | | | - Di Dong
- grid.431778.e0000 0004 0482 9086World Bank, Washington DC, USA
| | - Reem Alsukait
- grid.431778.e0000 0004 0482 9086World Bank, Washington DC, USA ,grid.56302.320000 0004 1773 5396Department of Community Health, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Latifah Alqasem
- grid.507413.40000 0001 2178 8237Saudi Arabian Monetary Authority, Riyadh, Kingdom of Saudi Arabia
| | - Nahar Alazemi
- Saudi Health Council, Riyadh, Kingdom of Saudi Arabia
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20
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Li S, Xie H, Zhou L, Dong D, Liu Y, Jia C, Han L, Chao Y, Chen Y. Overexpression of MsSAG113 gene promotes leaf senescence in alfalfa via participating in the hormone regulatory network. Front Plant Sci 2022; 13:1085497. [PMID: 36570962 PMCID: PMC9774027 DOI: 10.3389/fpls.2022.1085497] [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] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Introduction Alfalfa (Medicago sativa) is a kind of high quality leguminous forage species, which was widely cultivated in the world. Leaf senescence is an essential process in plant development and life cycle. Here, we reported the isolation and functional analysis of an alfalfa SENESCENCE-ASSOCIATED GENE113 (MsSAG113), which belongs to the PP2C family and mainly plays a role in promoting plant senescence. Methods In the study, Agrobacterium-mediated, gene expression analysis, next generation sequencing, DNA pull-down, yeast single hybridization and transient expression were used to identify the function of MsSAG113 gene. Results The MsSAG113 gene was isolated from alfalfa, and the transgenic plants were obtained by Agrobacterium-mediated method. Compared with the wildtype, transgenic plants showed premature senescence in leaves, especially when cultivated under dark conditions. Meanwhile, application of exogenous hormones ABA, SA, MeJA, obviously acclerated leaf senescence of transgenic plants. Furthermore, the detached leaves from transgenic plants turned yellow earlier with lower chlorophyll content. Transcriptome analysis identified a total of 1,392 differentially expressed genes (DEGs), involving 13 transcription factor families. Of which, 234 genes were related to phytohormone synthesis, metabolism and transduction. Pull-down assay and yeast one-hybrid assay confirmed that alfalfa zinc finger CCCH domain-containing protein 39 (MsC3H-39) could directly bind the upstream of MsSAG113 gene. In conclusion, the MsSAG113 gene plays a crucial role in promoting leaf senescence in alfalfa via participating in the hormone regulatory network. Discussion This provides an essential basis for further analysis on the regulatory network involving senescence-associated genes in alfalfa.
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Affiliation(s)
- Shuwen Li
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Hong Xie
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Lingfang Zhou
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Di Dong
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Yaling Liu
- Inner Mongolia M-Grass Ecology And Environment (Group) Co., Ltd, Hohhot, China
| | - Chenyan Jia
- Inner Mongolia M-Grass Ecology And Environment (Group) Co., Ltd, Hohhot, China
| | - Liebao Han
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Yuehui Chao
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Yinglong Chen
- The University of Western Australia (UWA) Institute of Agriculture, and University of Western Australia School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
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Gong L, Wang M, Shu L, He J, Qin B, Xu J, Su W, Dong D, Hu H, Tian J, Zhou P. Automatic captioning of early gastric cancer using magnification endoscopy with narrow-band imaging. Gastrointest Endosc 2022; 96:929-942.e6. [PMID: 35917877 DOI: 10.1016/j.gie.2022.07.019] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/03/2022] [Accepted: 07/13/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIMS The detection rate for early gastric cancer (EGC) is unsatisfactory, and mastering the diagnostic skills of magnifying endoscopy with narrow-band imaging (ME-NBI) requires rich expertise and experience. We aimed to develop an EGC captioning model (EGCCap) to automatically describe the visual characteristics of ME-NBI images for endoscopists. METHODS ME-NBI images (n = 1886) from 294 cases were enrolled from multiple centers, and corresponding 5658 text data were designed following the simple EGC diagnostic algorithm. An EGCCap was developed using the multiscale meshed-memory transformer. We conducted comprehensive evaluations for EGCCap including the quantitative and quality of performance, generalization, robustness, interpretability, and assistant value analyses. The commonly used metrics were BLEUs, CIDEr, METEOR, ROUGE, SPICE, accuracy, sensitivity, and specificity. Two-sided statistical tests were conducted, and statistical significance was determined when P < .05. RESULTS EGCCap acquired satisfying captioning performance by outputting correctly and coherently clinically meaningful sentences in the internal test cohort (BLEU1 = 52.434, CIDEr = 36.734, METEOR = 27.823, ROUGE = 49.949, SPICE = 35.548) and maintained over 80% performance when applied to other centers or corrupted data. The diagnostic ability of endoscopists improved with the assistance of EGCCap, which was especially significant (P < .05) for junior endoscopists. Endoscopists gave EGCCap an average remarkable score of 7.182, showing acceptance of EGCCap. CONCLUSIONS EGCCap exhibited promising captioning performance and was proven with satisfying generalization, robustness, and interpretability. Our study showed potential value in aiding and improving the diagnosis of EGC and facilitating the development of automated reporting in the future.
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Affiliation(s)
- Lixin Gong
- College of Medicine and Biological Information Engineering School, Northeastern University, Shenyang, China; CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, The State Key Laboratory for Management and Control of Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Min Wang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Lei Shu
- Department of Gastroenterology, No. 1 Hospital of Wuhan, Wuhan, China
| | - Jie He
- Endoscopy Center, Zhongshan Hospital (Xiamen Branch), Fudan University, Xiamen, China; Department of Gastroenterology, The Affiliated Dongnan Hospital of Xiamen University, Zhangzhou, China
| | - Bin Qin
- Department of Gastroenterology, the Second Affiliated Hospital of Xi'an Jiaotong University, Zhangzhou, China
| | - Jiacheng Xu
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Collaborative Innovation Center of Endoscopy, Shanghai, China
| | - Wei Su
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Collaborative Innovation Center of Endoscopy, Shanghai, China
| | - Di Dong
- CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, The State Key Laboratory for Management and Control of Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Hao Hu
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Collaborative Innovation Center of Endoscopy, Shanghai, China; Department of Gastroenterology, Shigatse People's Hospital, Shigatse, China
| | - Jie Tian
- College of Medicine and Biological Information Engineering School, Northeastern University, Shenyang, China; CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, The State Key Laboratory for Management and Control of Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China; Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, China
| | - Pinghong Zhou
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Collaborative Innovation Center of Endoscopy, Shanghai, China
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22
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She Y, He B, Wang F, Zhong Y, Wang T, Liu Z, Yang M, Yu B, Deng J, Sun X, Wu C, Hou L, Zhu Y, Yang Y, Hu H, Dong D, Chen C, Tian J. Deep learning for predicting major pathological response to neoadjuvant chemoimmunotherapy in non-small cell lung cancer: A multicentre study. EBioMedicine 2022; 86:104364. [PMID: 36395737 PMCID: PMC9672965 DOI: 10.1016/j.ebiom.2022.104364] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/15/2022] Open
Abstract
Background This study, based on multicentre cohorts, aims to utilize computed tomography (CT) images to construct a deep learning model for predicting major pathological response (MPR) to neoadjuvant chemoimmunotherapy in non-small cell lung cancer (NSCLC) and further explore the biological basis under its prediction. Methods 274 patients undergoing curative surgery after neoadjuvant chemoimmunotherapy for NSCLC at 4 centres from January 2019 to December 2021 were included and divided into a training cohort, an internal validation cohort, and an external validation cohort. ShuffleNetV2x05-based features of the primary tumour on the CT scans within the 2 weeks preceding neoadjuvant administration were employed to develop a deep learning score for distinguishing MPR and non-MPR. To reveal the underlying biological basis of the deep learning score, a genetic analysis was conducted based on 25 patients with RNA-sequencing data. Findings MPR was achieved in 54.0% (n = 148) patients. The area under the curve (AUC) of the deep learning score to predict MPR was 0.73 (95% confidence interval [CI]: 0.58–0.86) and 0.72 (95% CI: 0.58–0.85) in the internal validation and external validation cohorts, respectively. After integrating the clinical characteristic into the deep learning score, the combined model achieved satisfactory performance in the internal validation (AUC: 0.77, 95% CI: 0.64–0.89) and external validation cohorts (AUC: 0.75, 95% CI: 0.62–0.87). In the biological basis exploration for the deep learning score, a high deep learning score was associated with the downregulation of pathways mediating tumour proliferation and the promotion of antitumour immune cell infiltration in the microenvironment. Interpretation The proposed deep learning model could effectively predict MPR in NSCLC patients treated with neoadjuvant chemoimmunotherapy. Funding This study was supported by National Key Research and Development Program of China, China (2017YFA0205200); National Natural Science Foundation of China, China (91959126, 82022036, 91959130, 81971776, 81771924, 6202790004, 81930053, 9195910169, 62176013, 8210071009); Beijing Natural Science Foundation, China (L182061); Strategic Priority Research Program of Chinese Academy of Sciences, China (XDB38040200); Chinese Academy of Sciences, China (GJJSTD20170004, QYZDJ-SSW-JSC005); Shanghai Hospital Development Center, China (SHDC2020CR3047B); and Science and Technology Commission of Shanghai Municipality, China (21YF1438200).
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23
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Cao R, Tang L, Fang M, Zhong L, Wang S, Gong L, Li J, Dong D, Tian J. Artificial intelligence in gastric cancer: applications and challenges. Gastroenterol Rep (Oxf) 2022; 10:goac064. [PMID: 36457374 PMCID: PMC9707405 DOI: 10.1093/gastro/goac064] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/27/2022] [Accepted: 10/18/2022] [Indexed: 08/10/2023] Open
Abstract
Gastric cancer (GC) is one of the most common malignant tumors with high mortality. Accurate diagnosis and treatment decisions for GC rely heavily on human experts' careful judgments on medical images. However, the improvement of the accuracy is hindered by imaging conditions, limited experience, objective criteria, and inter-observer discrepancies. Recently, the developments of machine learning, especially deep-learning algorithms, have been facilitating computers to extract more information from data automatically. Researchers are exploring the far-reaching applications of artificial intelligence (AI) in various clinical practices, including GC. Herein, we aim to provide a broad framework to summarize current research on AI in GC. In the screening of GC, AI can identify precancerous diseases and assist in early cancer detection with endoscopic examination and pathological confirmation. In the diagnosis of GC, AI can support tumor-node-metastasis (TNM) staging and subtype classification. For treatment decisions, AI can help with surgical margin determination and prognosis prediction. Meanwhile, current approaches are challenged by data scarcity and poor interpretability. To tackle these problems, more regulated data, unified processing procedures, and advanced algorithms are urgently needed to build more accurate and robust AI models for GC.
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Affiliation(s)
| | | | - Mengjie Fang
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, P. R. China
- CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, P. R. China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, P. R. China
| | - Lianzhen Zhong
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, P. R. China
- CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, P. R. China
| | - Siwen Wang
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, P. R. China
- CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, P. R. China
| | - Lixin Gong
- College of Medicine and Biological Information Engineering School, Northeastern University, Shenyang, Liaoning, P. R. China
| | - Jiazheng Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Radiology Department, Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Di Dong
- Corresponding authors. Di Dong, CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, 95 Zhongguancun East Road, Beijing 100190, P. R. China. Tel: +86-13811833760; ; Jie Tian, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, P. R. China. Tel: +86-10-82618465;
| | - Jie Tian
- Corresponding authors. Di Dong, CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, 95 Zhongguancun East Road, Beijing 100190, P. R. China. Tel: +86-13811833760; ; Jie Tian, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, P. R. China. Tel: +86-10-82618465;
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24
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Mistry PK, Kishnani P, Wanner C, Dong D, Bender J, Batista JL, Foster J. Rare lysosomal disease registries: lessons learned over three decades of real-world evidence. Orphanet J Rare Dis 2022; 17:362. [PMID: 36244992 PMCID: PMC9573793 DOI: 10.1186/s13023-022-02517-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 07/29/2022] [Accepted: 09/04/2022] [Indexed: 12/24/2022] Open
Abstract
Lysosomal storage disorders (LSD) are rare diseases, caused by inherited deficiencies of lysosomal enzymes/transporters, that affect 1 in 7000 to 1 in 8000 newborns. Individuals with LSDs face long diagnostic journeys during which debilitating and life-threatening events can occur. Clinical trials and classical descriptions of LSDs typically focus on common manifestations, which are not representative of the vast phenotypic heterogeneity encountered in real-world experience. Additionally, recognizing that there was a limited understanding of the natural history, disease progression, and real-world clinical outcomes of rare LSDs, a collaborative partnership was pioneered 30 years ago to address these gaps. The Rare Disease Registries (RDR) (for Gaucher, Fabry, Mucopolysaccharidosis type I, and Pompe), represent the largest observational database for these LSDs. Over the past thirty years, data from the RDRs have helped to inform scientific understanding and the development of comprehensive monitoring and treatment guidelines by creating a framework for data collection and establishing a standard of care, with an overarching goal to improve the quality of life of affected patients. Here, we highlight the history, process, and impact of the RDRs, and discuss the lessons learned and future directions.
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Affiliation(s)
- P K Mistry
- Department of Medicine, Yale Liver Center, Yale University School of Medicine, 333 Cedar Street, PO Box 208019, New Haven, CT, 06520, USA.
| | - P Kishnani
- Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, USA
| | - C Wanner
- University Hospital of Würzburg, Würzburg, Germany
| | - D Dong
- Global Operations and Advocacy Lead, Rare Disease Registries, Sanofi, Cambridge, MA, USA
| | - J Bender
- Head of Global Rare Disease Registries, Sanofi, Cambridge, MA, USA
| | - J L Batista
- Epidemiology/Biostatistics, Sanofi, Cambridge, MA, USA
| | - J Foster
- Data Management, Sanofi, Cambridge, MA, USA
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25
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Li Y, Wang M, Guo T, Li S, Teng K, Dong D, Liu Z, Jia C, Chao Y, Han L. Overexpression of abscisic acid-insensitive gene ABI4 from Medicago truncatula, which could interact with ABA2, improved plant cold tolerance mediated by ABA signaling. Front Plant Sci 2022; 13:982715. [PMID: 36212309 PMCID: PMC9545351 DOI: 10.3389/fpls.2022.982715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
ABI4 is considered an important transcription factor with multiple regulatory functions involved in many biological events. However, its role in abiotic stresses, especially low-temperature-induced stress, is poorly understood. In this study, the MtABI4 gene was derived from M. truncatula, a widely used forage grass. Analysis of subcellular localization indicated that ABI4 was localized in the nucleus. Identification of expression characteristics showed that ABI4 was involved in the regulatory mechanisms of multiple hormones and could be induced by the low temperature. IP-MS assay revealed that MtABI4 protein could interact with xanthoxin dehydrogenase protein (ABA2). The two-hybrid yeast assay and the biomolecular fluorescence complementarity assay further supported this finding. Expression analysis demonstrated that overexpression of MtABI4 induced an increase in ABA2 gene expression both in M. truncatula and Arabidopsis, which in turn increased the ABA level in transgenic plants. In addition, the transgenic lines with the overexpression of MtABI4 exhibited enhanced tolerance to low temperature, including lower malondialdehyde content, electrical conductivity, and cell membrane permeability, compared with the wide-type lines after being cultivated for 5 days in 4°C. Gene expression and enzyme activities of the antioxidant system assay revealed the increased activities of SOD, CAT, MDHAR, and GR, and higher ASA/DHA ratio and GSH/GSSG ratio in transgenic lines. Additionally, overexpression of ABI4 also induced the expression of members of the Inducer of CBF expression genes (ICEs)-C-repeat binding transcription factor genes(CBFs)-Cold regulated genes (CORs) low-temperature response module. In summary, under low-temperature conditions, overexpression of ABI4 could enhance the content of endogenous ABA in plants through interactions with ABA2, which in turn reduced low-temperature damage in plants. This provides a new perspective for further understanding the molecular regulatory mechanism of plant response to low temperature and the improvement of plant cold tolerance.
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Affiliation(s)
- Yinruizhi Li
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Mengdi Wang
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Tao Guo
- Chongqing Key Laboratory of Germplasm Innovation and Utilization of Native Plants, Chongqing Landscape and Gardening Research Institute, Chongqing, China
| | - Shuwen Li
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Ke Teng
- Beijing Research and Development Center for Grass and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Di Dong
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Zhuocheng Liu
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Chenyan Jia
- Inner Mongolia Mengcao Ecological Environment (Group) Co., Ltd., Hohhot, China
| | - Yuehui Chao
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Liebao Han
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
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26
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Sheng Y, Dong D, He G, Zhang J. How Noise Can Influence Experience-Based Decision-Making under Different Types of the Provided Information. Int J Environ Res Public Health 2022; 19:10445. [PMID: 36012080 PMCID: PMC9408651 DOI: 10.3390/ijerph191610445] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Pervasive noise undermines many cognitive processes. Across two studies, we examined how noise influences experience-based decision-making and whether the nature of the information provided moderates this influence. Study 1 used the repeated choice paradigm and found that noise can significantly reduce people's performance in experience-based decision-making by increasing the likelihood of choosing the option with the lower expected value. This negative influence can be attenuated when experience-congruent suggestions are provided, but significantly worsened when experience-incongruent suggestions are provided. Study 2 investigated how noise influences decision-making performance in two experience-incongruent conditions differing in error salience. By replicating noise's general negative effect, we found that the noise effect could be attenuated when incongruent suggestions were obvious. We suggest that noise can undermine the information updating and integration process, which is necessary for experience-based decision-making. We also discuss the principles for designing better information aids based on these findings.
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Affiliation(s)
- Youyu Sheng
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing 100000, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing 100000, China
| | - Di Dong
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing 100000, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing 100000, China
| | - Gang He
- Chongqing Changan Automobile Co., Ltd., Chongqing 400000, China
| | - Jingyu Zhang
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing 100000, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing 100000, China
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27
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Kong YX, Dong D, Chen HD, Dai M, Zhuo L, Lou T, Cai ST, Chen JJ, Pan YH, Gao H, Lu ZM, Dong HY, Zhao XH, Luo GH, Chen G. [Comparison of application effects of colonoscopy, fecal immunochemical test and a novel risk-adapted screening approach in colorectal cancer screening in Xuzhou population]. Zhonghua Yu Fang Yi Xue Za Zhi 2022; 56:1074-1079. [PMID: 35922234 DOI: 10.3760/cma.j.cn112150-20211203-01113] [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] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Objective: To compare the application effect of the colonoscopy, fecal immunochemical test (FIT) and novel risk-adapted screening approach in colorectal cancer screening in Xuzhou population. Methods: From May 2018 to April 2019, 4 280 subjects aged 50-74 were recruited from Gulou district, Yunlong district and Quanshan district of Xuzhou. They were randomly assigned to the colonoscopy group (n=863), FIT group (n=1 723) and novel risk-adapted screening approach group (n=1 694) according to the ratio of 1∶2∶2. For the novel risk-adapted screening approach group, after the risk assessment, high-risk subjects were invited to undergo colonoscopy and low-risk subjects were invited to undergo FIT examination. All FIT positive subjects were invited to undergo colonoscopy. Colonoscopy participation rate [(the number of colonoscopies completed/the number of colonoscopies invited to participate)×100%], detection rate of colorectal lesions [(the number of diagnosed patients/the number of colonoscopies completed)×100%], colonoscopy resource load (the number of colonoscopies completed/the number of diagnosed advanced tumors) and FIT resource load in each group were calculated and compared. Results: The age of all subjects was (61±6) years old, including 1 816 males (42.43%). There was no statistically significant difference in the socio-demographic characteristics of the subjects in different screening groups. The colonoscopy participation rate was 22.60% (195/863) in the colonoscopy group, 57.04% (77/135) in the FIT group, and 33.94% (149/439) in the novel risk-adapted screening approach group, respectively. The colonoscopy participation rate was higher in the FIT group than in the colonoscopy group and the novel risk-adapted screening approach group (P<0.001). The colonoscopy participation rate of novel risk-adapted screening group was significantly higher than the colonoscopy group (P<0.001). The detection rates of advanced tumors were 6.67% (13/195), 9.09% (7/77) and 8.72% (13/149), respectively, and the difference was not statistically significant (P>0.05). The colonoscopy resource load (95%CI) was 15 (13-17) in the colonoscopy group, 11 (9-14) in the FIT group and 11 (10-13) in the novel risk-adapted screening approach group, respectively. Among them, the colonoscopy resource load of high-risk individuals in the novel risk-adapted screening approach group was 12 (9-15). FIT resource loads (95%CI) were 207 (196-218) and 88 (83-94) in the FIT group and the novel risk-adapted screening approach group. Conclusion: The combined application of risk-adapted screening approach and FIT may have a good application effect in colorectal cancer screening.
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Affiliation(s)
- Y X Kong
- Cancer Prevention and Control Office, Xuzhou Cancer Hospital, Xuzhou 221000, China
| | - D Dong
- Cancer Prevention and Control Office, Xuzhou Cancer Hospital, Xuzhou 221000, China
| | - H D Chen
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100730, China
| | - M Dai
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100730, China
| | - L Zhuo
- School of Public Health, Xuzhou Medical University, Xuzhou 221004, China
| | - T Lou
- Chronic Disease Prevention and Control Department, Xuzhou Center for Disease Control and Prevention, Xuzhou 221000, China
| | - S T Cai
- School of Management, Xuzhou Medical University, Xuzhou 221004, China
| | - J J Chen
- School of Management, Xuzhou Medical University, Xuzhou 221004, China
| | - Y H Pan
- School of Management, Xuzhou Medical University, Xuzhou 221004, China
| | - H Gao
- School of Public Health, Xuzhou Medical University, Xuzhou 221004, China
| | - Z M Lu
- School of Management, Xuzhou Medical University, Xuzhou 221004, China
| | - H Y Dong
- Chronic Disease Prevention and Control Department, Xuzhou Center for Disease Control and Prevention, Xuzhou 221000, China
| | - X H Zhao
- Cancer Prevention and Control Office, Xuzhou Cancer Hospital, Xuzhou 221000, China
| | - G H Luo
- Cancer Prevention and Control Office, Xuzhou Cancer Hospital, Xuzhou 221000, China
| | - Guohui Chen
- Cancer Prevention and Control Office, Xuzhou Cancer Hospital, Xuzhou 221000, China
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28
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Strickland G, Qu R, Gupta K, Jiang Y, Dong D, Saez C, Weng P, Taketo M, Klugar Y, Myung P. 704 Decomposing a deterministic path to hair follicle dermal niche formation: The intersection of two morphogen gradients. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.05.716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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29
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Zhang L, Zhong L, Li C, Zhang W, Hu C, Dong D, Liu Z, Zhou J, Tian J. Knowledge-guided multi-task attention network for survival risk prediction using multi-center computed tomography images. Neural Netw 2022; 152:394-406. [DOI: 10.1016/j.neunet.2022.04.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 04/02/2022] [Accepted: 04/22/2022] [Indexed: 12/12/2022]
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30
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Liu Y, Duan H, Dong D, Chen J, Zhong L, Zhang L, Cao R, Fan H, Cui Z, Liu P, Kang S, Zhan X, Wang S, Zhao X, Chen C, Tian J. Development of a deep learning-based nomogram for predicting lymph node metastasis in cervical cancer: A multicenter study. Clin Transl Med 2022; 12:e938. [PMID: 35839331 PMCID: PMC9286523 DOI: 10.1002/ctm2.938] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/28/2022] [Accepted: 06/05/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Yujia Liu
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Hui Duan
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Di Dong
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China.,Beijing Key Laboratory of Molecular Imaging, Beijing, China
| | - Jiaming Chen
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Huizhou Municipal central Hospital, Huizhou, China
| | - Lianzhen Zhong
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Liwen Zhang
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Runnan Cao
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Huijian Fan
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhumei Cui
- The affiliated hospital of Qingdao University, Qingdao, China
| | - Ping Liu
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shan Kang
- Department of Gynecology, Fourth Hospital Hebei Medical University, Shijiazhuang, China
| | | | - Shaoguang Wang
- Department of Gynecology, Yantai Yuhuangding Hospital, Yantai, China
| | - Xun Zhao
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Chunlin Chen
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jie Tian
- CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China.,Beijing Key Laboratory of Molecular Imaging, Beijing, China.,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, China.,Zhuhai Precision Medical Center, Zhuhai People's Hospital (Affiliated with Jinan University), Zhuhai, China
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Zhang L, Dong D, Sun Y, Hu C, Sun C, Wu Q, Tian J. Development and Validation of a Deep Learning Model to Screen for Trisomy 21 During the First Trimester From Nuchal Ultrasonographic Images. JAMA Netw Open 2022; 5:e2217854. [PMID: 35727579 PMCID: PMC9214589 DOI: 10.1001/jamanetworkopen.2022.17854] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
IMPORTANCE Accurate screening of trisomy 21 in the first trimester can provide an early opportunity for decision-making regarding reproductive choices. OBJECTIVE To develop and validate a deep learning model for screening fetuses with trisomy 21 based on ultrasonographic images. DESIGN, SETTING, AND PARTICIPANTS This diagnostic study used data from all available cases and controls enrolled at 2 hospitals in China between January 2009 and September 2020. Two-dimensional images of the midsagittal plane of the fetal face in singleton pregnancies with gestational age more than 11 weeks and less than 14 weeks were examined. Observers were blinded to subjective fetus nuchal translucency (NT) marker measurements. A convolutional neural network was developed to construct a deep learning model. Data augmentation was applied to generate more data. Different groups were randomly selected as training and validation sets to assess the robustness of the deep learning model. The fetal NT was shown and measured. Each detection of trisomy 21 was confirmed by chorionic villus sampling or amniocentesis. Data were analyzed from March 1, 2021, to January 3, 2022. MAIN OUTCOMES AND MEASURES The primary outcome was detection of fetuses with trisomy 21. The receiver operating characteristic curve, metrics of accuracy, area under the curve (AUC), sensitivity, and specificity were used for model performance evaluation. RESULTS A total of 822 case and control participants (mean [SD] age, 31.9 [4.6] years) were enrolled in the study, including 550 participants (mean [SD] age, 31.7 [4.7] years) in the training set and 272 participants (mean [SD] age, 32.3 [4.7] years) in the validation set. The deep learning model showed good performance for trisomy 21 screening in the training (AUC, 0.98; 95% CI, 0.97-0.99) and validation (AUC, 0.95; 95% CI, 0.93-0.98) sets. The deep learning model had better detective performance for fetuses with trisomy 21 than the model with NT marker and maternal age (training: AUC, 0.82; 95% CI, 0.77-0.86; validation: AUC, 0.73; 95% CI, 0.66-0.80). CONCLUSIONS AND RELEVANCE These findings suggest that this deep learning model accurately screened fetuses with trisomy 21, which indicates that the model is a potential tool to facilitate universal primary screening for trisomy 21.
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Affiliation(s)
- Liwen Zhang
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Di Dong
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital, Jinan University, Zhuhai, China
| | - Yongqing Sun
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University. Beijing Maternal and Child Health Care Hospital, China
| | - Chaoen Hu
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Congxin Sun
- Department of Ultrasound, Shijiazhuang Obstetrics and Gynecology Hospital, Shijiazhuang, China
| | - Qingqing Wu
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University. Beijing Maternal and Child Health Care Hospital, China
| | - Jie Tian
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, China
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Dong D, Yang Z, Ma Y, Li S, Wang M, Li Y, Liu Z, Han L, Chao Y. Expression of a Chlorophyll b Reductase Gene from Zoysia japonica Causes Changes in Leaf Color and Chlorophyll Morphology in Agrostis stolonifera. Int J Mol Sci 2022; 23:6032. [PMID: 35682725 PMCID: PMC9181577 DOI: 10.3390/ijms23116032] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/19/2022] [Accepted: 05/24/2022] [Indexed: 01/27/2023] Open
Abstract
The NYC-like (NOL) enzyme is considered as an essential enzyme for chlorophyll b degradation, which catalyzes the formation of 7-hydroxymethyl chlorophyll a from chlorophyll b. The ZjNOL gene was cloned from Zoysia japonica with a completed coding sequence of 981-bp in length, encoding 326 amino acids. ZjNOL was localized on the stroma side of the thylakoid membrane, and co-localized with ZjNYC in the chloroplasts. Multiple photoregulatory elements and hormone regulatory elements were identified in the promoter region of the ZjNOL gene, and the expression level of the ZjNOL gene was dramatically up-regulated in senescence leaves, which were regulated by a variety of plant hormones. ZjNOL's ectopic expression in creeping bentgrass produced yellow leaves, thicker cortex, and smaller vascular column cells. Additionally, transgenic plants exhibited morphological alterations in their chloroplast structure, and the number of grana and thylakoids per grana stack reduced dramatically. Transgenic plants also had a lower photosynthetic rate and Fm/Fv than the control. The transgenic plants displayed a decreased chlorophyll content and a greater rate of ion leakage. The properties and activities of ZjNOL will serve as a foundation for future research into gene functions and regulatory processes.
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Affiliation(s)
| | | | | | | | | | | | | | - Liebao Han
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (D.D.); (Z.Y.); (Y.M.); (S.L.); (M.W.); (Y.L.); (Z.L.)
| | - Yuehui Chao
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (D.D.); (Z.Y.); (Y.M.); (S.L.); (M.W.); (Y.L.); (Z.L.)
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Hu S, Zhu Y, Dong D, Wang B, Zhou Z, Wang C, Tian J, Peng Y. Chest Radiographs Using a Context-Fusion Convolution Neural Network (CNN): Can It Distinguish the Etiology of Community-Acquired Pneumonia (CAP) in Children? J Digit Imaging 2022; 35:1079-1090. [PMID: 35585465 PMCID: PMC9116701 DOI: 10.1007/s10278-021-00543-1] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/02/2021] [Accepted: 11/11/2021] [Indexed: 11/25/2022] Open
Abstract
Clinical symptoms and inflammatory markers cannot reliably distinguish the etiology of CAP, and chest radiographs have abundant information related with CAP. Hence, we developed a context-fusion convolution neural network (CNN) to explore the application of chest radiographs to distinguish the etiology of CAP in children. This retrospective study included 1769 cases of pediatric pneumonia (viral pneumonia, n = 487; bacterial pneumonia, n = 496; and mycoplasma pneumonia, n = 786). The chest radiographs of the first examination, C-reactive protein (CRP), and white blood cell (WBC) were collected for analysis. All patients were stochastically divided into training, validation, and test cohorts in a 7:1:2 ratio. Automatic lung segmentation and hand-crafted pneumonia lesion segmentation were performed, from which three image-based models including a full-lung model, a local-lesion model, and a context-fusion model were built; two clinical characteristics were used to build a clinical model, while a logistic regression model combined the best CNN model and two clinical characteristics. Our experiments showed that the context-fusion model which integrated the features of the full-lung and local-lesion had better performance than the full-lung model and local-lesion model. The context-fusion model had area under curves of 0.86, 0.88, and 0.93 in identifying viral, bacterial, and mycoplasma pneumonia on the test cohort respectively. The addition of clinical characteristics to the context-fusion model obtained slight improvement. Mycoplasma pneumonia was more easily identified compared with the other two types. Using chest radiographs, we developed a context-fusion CNN model with good performance for noninvasively diagnosing the etiology of community-acquired pneumonia in children, which would help improve early diagnosis and treatment.
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Affiliation(s)
- Shasha Hu
- Department of Radiology, National Center for Children' Health, Beijing Children's Hospital, Capital Medical University, Beijing, 100045, China
| | - Yongbei Zhu
- CAS Key Laboratory of Molecular Imaging, State Key Laboratory of Management and Control for Complex Systems, Beijing Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, 100191, China
| | - Di Dong
- CAS Key Laboratory of Molecular Imaging, State Key Laboratory of Management and Control for Complex Systems, Beijing Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bei Wang
- Department of Radiology, National Center for Children' Health, Beijing Children's Hospital, Capital Medical University, Beijing, 100045, China
| | - Zuofu Zhou
- Department of Radiology, Fujian Provincial Maternity and Children's Hospital, Fujian Medical University, Fuzhou, 350000, China
| | - Chi Wang
- Department of Radiology, National Center for Children' Health, Beijing Children's Hospital, Capital Medical University, Beijing, 100045, China
| | - Jie Tian
- CAS Key Laboratory of Molecular Imaging, State Key Laboratory of Management and Control for Complex Systems, Beijing Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China.
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, 100191, China.
| | - Yun Peng
- Department of Radiology, National Center for Children' Health, Beijing Children's Hospital, Capital Medical University, Beijing, 100045, China.
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Dong D, Tukker A, Steubing B, van Oers L, Rechberger H, Alonso Aguilar-Hernandez G, Li H, Van der Voet E. Assessing China's potential for reducing primary copper demand and associated environmental impacts in the context of energy transition and "Zero waste" policies. Waste Manag 2022; 144:454-467. [PMID: 35462290 DOI: 10.1016/j.wasman.2022.04.006] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/16/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
To conserve resources and enhance the environmental performance, China has launched the "Zero waste" concept, focused on reutilization of solid waste and recovery of materials, including copper. Although several studies have assessed the copper demand and recycling, there is a lack of understanding on how different waste management options would potentially reduce primary copper demand and associated environmental impacts in China in the context of energy transition. This study addresses this gap in view of a transition to low-carbon energy system and the optimization of copper waste management combining MFA and LCA approaches. Six types of waste streams (C&DW, ELV, WEEE, IEW, MSW, ICW) are investigated in relation to various "Zero waste" strategies including reduction, reuse (repair, remanufacturing or refurbishment), recycling and transition from informal to formal waste management. Under present Chinese policies, reuse and recycling of copper containing products will lead to a somewhat lower dependency on primary copper in 2100 (11187Gg), as well as lower total GHG emissions (64869 Gg CO2-eq.) and cumulative energy demand (1.18x10^12 MJ). Maximizing such "Zero waste" options may lead to a further reduction, resulting in 65% potential reduction of primary copper demand, around 55% potential reduction of total GHG emissions and total cumulative energy demand in 2100. Several policy actions are proposed to provide insights into future waste management in China as well as some of the challenges involved.
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Affiliation(s)
- Di Dong
- Institute of Environmental Sciences (CML), Leiden University, Leiden, the Netherlands; Institute of Ecology and Sustainable Development, Shanghai Academy of Social Sciences, Shanghai 200020, China.
| | - Arnold Tukker
- Institute of Environmental Sciences (CML), Leiden University, Leiden, the Netherlands; Netherlands Organization for Applied Scientific Research TNO, The Hague, the Netherlands
| | - Bernhard Steubing
- Institute of Environmental Sciences (CML), Leiden University, Leiden, the Netherlands
| | - Lauran van Oers
- Institute of Environmental Sciences (CML), Leiden University, Leiden, the Netherlands
| | - Helmut Rechberger
- TU Wien, Institute for Water Quality and Resource Management, Vienna, Austria
| | | | - Huajiao Li
- School of Economics and Management, China University of Geosciences, Beijing 100083, China; Key Laboratory of Carrying Capacity Assessment for Resource and the Environment, Ministry of Natural Resources, Beijing 100083, China
| | - Ester Van der Voet
- Institute of Environmental Sciences (CML), Leiden University, Leiden, the Netherlands
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Malkin J, Finkelstein E, Baid D, Alqunaibet A, Almudarra S, Herbst CH, Dong D, Alsukait R, El-Saharty S, Algwizani A. Impact of noncommunicable diseases on direct medical costs and worker productivity, Saudi Arabia. East Mediterr Health J 2022; 28:296-301. [DOI: 10.26719/emhj/22.015] [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] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 10/06/2021] [Indexed: 11/09/2022]
Abstract
Background: The prevalence of noncommunicable diseases (NCDs) has been increasing in Saudi Arabia. Aims: Our objective was to estimate the effect of NCDs on direct medical costs and workforce productivity in Saudi Arabia. Methods: To estimate direct medical costs, we estimated the unit cost of treating 10 NCDs, then multiplied the unit cost by disease prevalence and summed across diseases. To estimate workforce productivity losses, we multiplied gross domestic product per person in the labour force by the loss in productivity from each NCD and the prevalence in the labour force of each NCD. Results: We estimated annual direct medical costs of 11.8 billion international dollars (Int$) for the 10 NCDs assessed (13.6% of total annual health expenditure). We estimated workforce productivity losses of Int$ 75.7 billion (4.5% of gross domestic product). Conclusion: The economic burden of NCDs in Saudi Arabia – particularly the effect on worker productivity – is substantial.
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Fang M, Tian J, Dong D. Non-invasively predicting response to neoadjuvant chemotherapy in gastric cancer via deep learning radiomics. EClinicalMedicine 2022; 46:101380. [PMID: 35434584 PMCID: PMC9006631 DOI: 10.1016/j.eclinm.2022.101380] [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] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 03/15/2022] [Indexed: 12/02/2022] Open
Affiliation(s)
- Mengjie Fang
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Beijing Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, No.95 Zhongguancun East Road, Beijing 100190, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, China
| | - Jie Tian
- CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Beijing Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, No.95 Zhongguancun East Road, Beijing 100190, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, China
| | - Di Dong
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Beijing Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, No.95 Zhongguancun East Road, Beijing 100190, China
- Corresponding author at: CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Beijing Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, No.95 Zhongguancun East Road, Beijing 100190, China.
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Gao B, Dong D, Zhang H, Liu Z, Payabvash S, Chen BT. Editorial: Radiomics Advances Precision Medicine. Front Oncol 2022; 12:853948. [PMID: 35311125 PMCID: PMC8924066 DOI: 10.3389/fonc.2022.853948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 01/27/2022] [Indexed: 11/25/2022] Open
Affiliation(s)
- Bo Gao
- Department of Radiology, The Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | - Di Dong
- Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Huimao Zhang
- Department of Radiology, First Hospital of Jilin University, Changchun, China
| | - Zaiyi Liu
- Department of Radiology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Seyedmehdi Payabvash
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, United States
| | - Bihong T Chen
- Department of Radiology, City of Hope Comprehensive Cancer Center, Duarte, CA, United States
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Li Y, Wang M, Teng K, Dong D, Liu Z, Zhang T, Han L. Transcriptome profiling revealed candidate genes, pathways and transcription factors related to nitrogen utilization and excessive nitrogen stress in perennial ryegrass. Sci Rep 2022; 12:3353. [PMID: 35233054 PMCID: PMC8888628 DOI: 10.1038/s41598-022-07329-7] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 02/10/2022] [Indexed: 11/09/2022] Open
Abstract
Ryegrass (Lolium perenne L.), a high-quality forage grass, is a good nutrient source for herbivorous livestock. However, improving nitrogen use efficiency and avoiding nitrate toxicity caused by excessive nitrogen are continual challenges in ryegrass production. The molecular mechanism underlying the response of ryegrass to nitrogen, especially excessive nitrogen, remains unclear. In this study, the transcriptomic changes under different nitrogen levels were investigated in perennial ryegrass by high-throughput next-generation RNA sequencing. Phenotypic characterization showed that treatment with half of the standard N concentration (N0.5) led to a better growth state than the other three treatments. The treatments with the standard N concentration (N1) and treatments with ten times higher than the standard N concentration (N10) contained excessive nitrogen, which placed stress on plant growth. Analysis of differentially expressed genes indicated that 345 and 104 genes are involved in the regulation of nitrogen utilization and excessive nitrogen stress, respectively. KEGG enrichment analysis suggested that "photosynthesis-antenna proteins" may respond positively to appropriate nitrogen conditions, whereas "steroid biosynthesis", "carotenoid biosynthesis" and "C5-branched dibasic acid metabolism" were identified as the top significantly enriched pathways in response to excessive nitrogen. Additionally, 21 transcription factors (TFs) related to nitrogen utilization were classified into 10 families, especially the AP2-EREBP and MYB TF families. Four TFs related to excessive nitrogen stress were identified, including LOBs, NACs, AP2-EREBPs and HBs. The expression patterns of these selected genes were also analyzed. These results provide new insight into the regulatory mechanism of ryegrass in response to nitrogen utilization and excessive nitrogen stress.
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Affiliation(s)
- Yinruizhi Li
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Mengdi Wang
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Ke Teng
- Beijing Research and Development Center for Grass and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Di Dong
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Zhuocheng Liu
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Tiejun Zhang
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Liebao Han
- Turfgrass Research Institute, College of Grassland Science, Beijing Forestry University, Beijing, China.
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Bisanzio D, Reithinger R, Alqunaibet A, Almudarra S, Alsukait RF, Dong D, Zhang Y, El-Saharty S, Herbst CH. Estimating the effect of non-pharmaceutical interventions to mitigate COVID-19 spread in Saudi Arabia. BMC Med 2022; 20:51. [PMID: 35125108 PMCID: PMC8818364 DOI: 10.1186/s12916-022-02232-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 01/03/2022] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND The Kingdom of Saudi Arabia (KSA) quickly controlled the spread of SARS-CoV-2 by implementing several non-pharmaceutical interventions (NPIs), including suspension of international and national travel, local curfews, closing public spaces (i.e., schools and universities, malls and shops), and limiting religious gatherings. The KSA also mandated all citizens to respect physical distancing and to wear face masks. However, after relaxing some restrictions during June 2020, the KSA is now planning a strategy that could allow resuming in-person education and international travel. The aim of our study was to evaluate the effect of NPIs on the spread of the COVID-19 and test strategies to open schools and resume international travel. METHODS We built a spatial-explicit individual-based model to represent the whole KSA population (IBM-KSA). The IBM-KSA was parameterized using country demographic, remote sensing, and epidemiological data. A social network was created to represent contact heterogeneity and interaction among age groups of the population. The IBM-KSA also simulated the movement of people across the country based on a gravity model. We used the IBM-KSA to evaluate the effect of different NPIs adopted by the KSA (physical distancing, mask-wearing, and contact tracing) and to forecast the impact of strategies to open schools and resume international travels. RESULTS The IBM-KSA results scenarios showed the high effectiveness of mask-wearing, physical distancing, and contact tracing in controlling the spread of the disease. Without NPIs, the KSA could have reported 4,824,065 (95% CI: 3,673,775-6,335,423) cases by June 2021. The IBM-KSA showed that mandatory mask-wearing and physical distancing saved 39,452 lives (95% CI: 26,641-44,494). In-person education without personal protection during teaching would have resulted in a high surge of COVID-19 cases. Compared to scenarios with no personal protection, enforcing mask-wearing and physical distancing in schools reduced cases, hospitalizations, and deaths by 25% and 50%, when adherence to these NPIs was set to 50% and 70%, respectively. The IBM-KSA also showed that a quarantine imposed on international travelers reduced the probability of outbreaks in the country. CONCLUSIONS This study showed that the interventions adopted by the KSA were able to control the spread of SARS-CoV-2 in the absence of a vaccine. In-person education should be resumed only if NPIs could be applied in schools and universities. International travel can be resumed but with strict quarantine rules. The KSA needs to keep strict NPIs in place until a high fraction of the population is vaccinated in order to reduce hospitalizations and deaths.
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Affiliation(s)
- Donal Bisanzio
- RTI International, Washington, D.C., USA. .,Epidemiology and Public Health Division, School of Medicine, University of Nottingham, Nottingham, UK.
| | | | | | | | - Reem F Alsukait
- College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia.,World Bank, Washington, D.C., USA
| | - Di Dong
- World Bank, Washington, D.C., USA
| | - Yi Zhang
- World Bank, Washington, D.C., USA
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Gong L, Xu M, Fang M, He B, Li H, Fang X, Dong D, Tian J. The potential of prostate gland radiomic features in identifying the gleason score. Comput Biol Med 2022; 144:105318. [DOI: 10.1016/j.compbiomed.2022.105318] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/17/2022]
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Dong D, Zhao Y, Teng K, Tan P, Liu Z, Yang Z, Han L, Chao Y. Expression of ZjPSY, a Phytoene Synthase Gene from Zoysia japonica Affects Plant Height and Photosynthetic Pigment Contents. Plants (Basel) 2022; 11:395. [PMID: 35161377 PMCID: PMC8840084 DOI: 10.3390/plants11030395] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Phytoene synthase (PSY) is a key limiting enzyme in the carotenoid biosynthesis pathway for regulating phytoene synthesis. In this study, ZjPSY was isolated and identified from Zoysia japonica, an important lawn grass species. ZjPSY cDNA was 1230 bp in length, corresponding to 409 amino acids. ZjPSY showed higher expression in young leaves and was downregulated after GA3, ABA, SA, and MeJA treatments, exhibiting a sensitivity to plant hormones. Regulatory elements of light and plant hormone were found in the upstream of ZjPSY CDS. Expression of ZjPSY in Arabidopsis thaliana protein led to carotenoid accumulation and altered expression of genes involved in the carotenoid pathway. Under no-treatment condition, salt treatment, and drought treatment, transgenic plants exhibited yellowing, dwarfing phenotypes. The carotenoid content of transgenic plants was significantly higher than that of wild-type under salt stress and no-treatment condition. Yeast two-hybrid screening identified a novel interacting partner ZjJ2 (DNAJ homologue 2), which encodes heat-shock protein 40 (HSP40). Taken together, this study suggested that ZjPSY may affect plant height and play an important role in carotenoid synthesis. These results broadened the understanding of carotenoid synthesis pathways and laid a foundation for the exploration and utilization of the PSY gene.
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Affiliation(s)
- Di Dong
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (D.D.); (K.T.); (Z.L.); (Z.Y.)
| | - Yuhong Zhao
- Animal Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi 860000, China;
| | - Ke Teng
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (D.D.); (K.T.); (Z.L.); (Z.Y.)
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100083, China
| | - Penghui Tan
- Beijing Chaoyang Foreign Language School, Beijing 100101, China;
| | - Zhuocheng Liu
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (D.D.); (K.T.); (Z.L.); (Z.Y.)
| | - Zhuoxiong Yang
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (D.D.); (K.T.); (Z.L.); (Z.Y.)
| | - Liebao Han
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (D.D.); (K.T.); (Z.L.); (Z.Y.)
| | - Yuehui Chao
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (D.D.); (K.T.); (Z.L.); (Z.Y.)
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Malkin JD, Finkelstein EA, Baid D, Alqunaibet A, Almudarra S, Herbst CH, Dong D, Alsukait R, El-Saharty S, Algwizani A. Impact of noncommunicable diseases on direct medical costs and worker productivity, Saudi Arabia. East Mediterr Health J 2022. [DOI: 10.26719/emhj.22.015] [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: 11/09/2022]
Abstract
Background: The prevalence of noncommunicable diseases (NCDs) has been increasing in Saudi Arabia. Aim: Our objective was to estimate the effect of NCDs on direct medical costs and workforce productivity in Saudi Arabia. Methods: To estimate direct medical costs, we estimated the unit cost of treating 10 NCDs, then multiplied the unit cost by disease prevalence and summed across diseases. To estimate workforce productivity losses, we multiplied gross domestic product per person in the labour force by the loss in productivity from each NCD and the prevalence in the labour force of each NCD. Results: We estimated annual direct medical costs of 11.8 billion international dollars (Int$) for the 10 NCDs assessed (13.6% of total annual health expenditure). We estimated workforce productivity losses of Int$ 75.7 billion (4.5% of gross domestic product). Conclusion: The economic burden of NCDs in Saudi Arabia – particularly the effect on worker productivity – is substantial.
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Li C, Qin Y, Zhang W, Jiang H, Song B, Bashir MR, Xu H, Duan T, Fang M, Zhong L, Meng L, Dong D, Hu Z, Tian J, Hu J. Deep learning-based AI model for signet-ring cell carcinoma diagnosis and chemotherapy response prediction in gastric cancer. Med Phys 2022; 49:1535-1546. [PMID: 35032039 DOI: 10.1002/mp.15437] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 01/19/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 02/05/2023] Open
Abstract
PURPOSE We aimed to develop a noninvasive artificial intelligence (AI) model to diagnose signet-ring cell carcinoma (SRCC) of gastric cancer (GC) and identify patients with SRCC who could benefit from postoperative chemotherapy based on preoperative contrast-enhanced computed tomography (CT). METHODS A total of 855 GC patients with 855 single GCs were included, of which 249 patients were diagnosed as SRCC by histopathologic examinations. The AI model was generated with clinical, hand-crafted radiomic, and deep learning features. Model diagnostic performance was measured by area under the receiver operating characteristic curve (AUC), sensitivity, and specificity, while predictive performance was measured by Kaplan-Meier curves. RESULTS In the test cohort (n = 257), the AUC, sensitivity, and specificity of our AI model for diagnosing SRCC were 0.786 (95% CI: 0.721-0.845), 77.3%, and 69.2%, respectively. For the entire cohort, patients with AI-predicted high risk had a significantly shorter median OS compared with those with low risk (median overall survival (OS), 38.8 vs. 64.2 months, p = 0.009). Importantly, in pathologically-confirmed advanced SRCC patients, AI-predicted high-risk status was indicative of a shorter overall survival (median overall survival (OS), 31.0 vs. 54.4 months, p = 0.036) and marked chemotherapy resistance, whereas AI-predicted low-risk status had substantial chemotherapy benefit (median OS [without vs. with chemotherapy], 26.0 vs. not reached, p = 0.013). CONCLUSIONS The CT-based AI model demonstrated good performance for diagnosing SRCC, stratifying patient prognosis, and predicting chemotherapy responses. Advanced SRCC patients with AI-predicted low-risk status may benefit substantially from adjuvant chemotherapy. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Cong Li
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.,CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Beijing Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yun Qin
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Weihan Zhang
- Department of Gastrointestinal Surgery and Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, 610041, China
| | - Hanyu Jiang
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Bin Song
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Mustafa R Bashir
- Department of Radiology, Duke University Medical Center, Durham, North Carolina, 27710, USA.,Center for Advanced Magnetic Resonance Development, Duke University Medical Center, Durham, North Carolina, 27710, USA.,Department of Medicine (Gastroenterology), Duke University Medical Center, Durham, North Carolina, 27710, USA
| | - Heng Xu
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Ting Duan
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Mengjie Fang
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.,CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Beijing Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
| | - Lianzhen Zhong
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.,CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Beijing Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
| | - Lingwei Meng
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.,CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Beijing Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
| | - Di Dong
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.,CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Beijing Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
| | - Zhenhua Hu
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.,CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Beijing Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jie Tian
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.,CAS Key Laboratory of Molecular Imaging, the State Key Laboratory of Management and Control for Complex Systems, Beijing Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China.,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, 100191, China.,Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, China
| | - Jiankun Hu
- Department of Gastrointestinal Surgery and Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, 610041, China
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Cao R, Fang M, Li H, Tian J, Dong D. Semi-supervised Long-tail Endoscopic Image Classification. Chinese Medical Sciences Journal 2022; 37:171-180. [PMID: 36321172 DOI: 10.24920/004135] [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: 11/06/2022]
Abstract
Objective To explore the semi-supervised learning (SSL) algorithm for long-tail endoscopic image classification with limited annotations. Method We explored semi-supervised long-tail endoscopic image classification in HyperKvasir, the largest gastrointestinal public dataset with 23 diverse classes. Semi-supervised learning algorithm FixMatch was applied based on consistency regularization and pseudo-labeling. After splitting the training dataset and the test dataset at a ratio of 4:1, we sampled 20%, 50%, and 100% labeled training data to test the classification with limited annotations. Results The classification performance was evaluated by micro-average and macro-average evaluation metrics, with the Mathews correlation coefficient (MCC) as the overall evaluation. SSL algorithm improved the classification performance, with MCC increasing from 0.8761 to 0.8850, from 0.8983 to 0.8994, and from 0.9075 to 0.9095 with 20%, 50%, and 100% ratio of labeled training data, respectively. With a 20% ratio of labeled training data, SSL improved both the micro-average and macro-average classification performance; while for the ratio of 50% and 100%, SSL improved the micro-average performance but hurt macro-average performance. Through analyzing the confusion matrix and labeling bias in each class, we found that the pseudo-based SSL algorithm exacerbated the classifier's preference for the head class, resulting in improved performance in the head class and degenerated performance in the tail class. Conclusion SSL can improve the classification performance for semi-supervised long-tail endoscopic image classification, especially when the labeled data is extremely limited, which may benefit the building of assisted diagnosis systems for low-volume hospitals. However, the pseudo-labeling strategy may amplify the effect of class imbalance, which hurts the classification performance for the tail class.
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Perez-Saez J, Lee EC, Wada NI, Alqunaibet AM, Almudarra SS, Alsukait RF, Dong D, Zhang Y, El Saharty S, Herbst CH, Lessler J. Effect of non-pharmaceutical interventions in the early phase of the COVID-19 epidemic in Saudi Arabia. PLOS Glob Public Health 2022; 2:e0000237. [PMID: 36962205 PMCID: PMC10021433 DOI: 10.1371/journal.pgph.0000237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 04/13/2022] [Indexed: 11/19/2022]
Abstract
Non-pharmaceutical interventions have been widely employed to control the COVID-19 pandemic. Their associated effect on SARS-CoV-2 transmission have however been unequally studied across regions. Few studies have focused on the Gulf states despite their potential role for global pandemic spread, in particular in the Kingdom of Saudi Arabia through religious pilgrimages. We study the association between NPIs and SARS-CoV-2 transmission in the Kingdom of Saudi Arabia during the first pandemic wave between March and October 2020. We infer associations between NPIs introduction and lifting through a spatial SEIR-type model that allows for inferences of region-specific changes in transmission intensity. We find that reductions in transmission were associated with NPIs implemented shortly after the first reported case including Isolate and Test with School Closure (region-level mean estimates of the reduction in R0 ranged from 25-41%), Curfew (20-70% reduction), and Lockdown (50-60% reduction), although uncertainty in the estimates was high, particularly for the Isolate and Test with School Closure NPI (95% Credible Intervals from 1% to 73% across regions). Transmission was found to increase progressively in most regions during the last part of NPI relaxation phases. These results can help informing the policy makers in the planning of NPI scenarios as the pandemic evolves with the emergence of SARS-CoV-2 variants and the availability of vaccination.
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Affiliation(s)
- Javier Perez-Saez
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Elizabeth C Lee
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Nikolas I Wada
- Johns Hopkins Novel Coronavirus Research Compendium, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | | | | | - Reem F Alsukait
- Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
- Health, Nutrition and Population Global Practice, World Bank Group, Washington DC, United States of America
| | - Di Dong
- Health, Nutrition and Population Global Practice, World Bank Group, Washington DC, United States of America
| | - Yi Zhang
- Health, Nutrition and Population Global Practice, World Bank Group, Washington DC, United States of America
| | - Sameh El Saharty
- Health, Nutrition and Population Global Practice, World Bank Group, Washington DC, United States of America
| | - Christopher H Herbst
- Health, Nutrition and Population Global Practice, World Bank Group, Washington DC, United States of America
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States of America
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Liu Z, Yang Y, Ji S, Dong D, Li Y, Wang M, Han L, Chen X. Effects of Elevation and Distance from Highway on the Abundance and Community Structure of Bacteria in Soil along Qinghai-Tibet Highway. Int J Environ Res Public Health 2021; 18:ijerph182413137. [PMID: 34948747 PMCID: PMC8701971 DOI: 10.3390/ijerph182413137] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/27/2021] [Accepted: 12/04/2021] [Indexed: 11/21/2022]
Abstract
In recent years, highway construction in the Qinghai-Tibet Plateau (QTP) has developed rapidly. When the highway passes through grassland, the soil, vegetation, and ecological environment along the line are disturbed. However, the impact on soil bacteria is still unclear. Soil bacteria play an important role in the ecological environment. The Qinghai-Tibet Highway (QTH) was selected as the research object to explore the changes in bacterial community structure, vegetation, soil, and other indicators. The results showed that the highway-related activities increased the degradation of vegetation along the road, significantly changed the physical and chemical properties of soil, and caused heavy metal pollution. These environmental factors affected the diversity and community structure of soil bacteria. This kind of disturbance shows a trend of gradually increasing from near to far from the highway. Gemmatimonas, Terrimonas, Nitrospira and Bacillus are more tolerant to environmental changes along the highway, while Barnesiella, and Blastococcus are more sensitive. The content of nitrate decreased and the content of ammonium nitrogen increased in the disturbed area, increasing the abundance of nitrifying bacteria. Therefore, the main factor of the disturbance of the QTH on the grassland is the decline of soil nutrient content, and the supplement of soil nutrients such as carbon and nitrogen should be taken into account in the process of ecological restoration of grassland along the line.
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Affiliation(s)
- Zhuocheng Liu
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (Z.L.); (S.J.); (D.D.); (Y.L.); (M.W.)
- Environmental Protection and Soil and Water Conservation Research Center, China Academy of Transportation Sciences, Beijing 100029, China;
| | - Yangang Yang
- Environmental Protection and Soil and Water Conservation Research Center, China Academy of Transportation Sciences, Beijing 100029, China;
| | - Shuangxuan Ji
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (Z.L.); (S.J.); (D.D.); (Y.L.); (M.W.)
- Environmental Protection and Soil and Water Conservation Research Center, China Academy of Transportation Sciences, Beijing 100029, China;
| | - Di Dong
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (Z.L.); (S.J.); (D.D.); (Y.L.); (M.W.)
| | - Yinruizhi Li
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (Z.L.); (S.J.); (D.D.); (Y.L.); (M.W.)
| | - Mengdi Wang
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (Z.L.); (S.J.); (D.D.); (Y.L.); (M.W.)
| | - Liebao Han
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China; (Z.L.); (S.J.); (D.D.); (Y.L.); (M.W.)
- Correspondence: (L.H.); (X.C.)
| | - Xueping Chen
- Environmental Protection and Soil and Water Conservation Research Center, China Academy of Transportation Sciences, Beijing 100029, China;
- Correspondence: (L.H.); (X.C.)
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Cao R, Gong L, Dong D. Pathological diagnosis and prognosis of Gastric cancer through a multi-instance learning method. EBioMedicine 2021; 73:103671. [PMID: 34740103 PMCID: PMC8577320 DOI: 10.1016/j.ebiom.2021.103671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 10/20/2021] [Indexed: 11/24/2022] Open
Affiliation(s)
- Runnan Cao
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China.
| | - Lixin Gong
- College of Medicine and Biological Information Engineering School, Northeastern University, Shenyang 110016, China.
| | - Di Dong
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, The State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China.
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Zhang G, Hui H, Ning B, Dong D, Tian J, He W. Self-Attention Based Virtual Staining for Bright-field Images of Label-free Human Carotid Atherosclerotic Plaque Tissue Section. Annu Int Conf IEEE Eng Med Biol Soc 2021; 2021:3492-3495. [PMID: 34891992 DOI: 10.1109/embc46164.2021.9630026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Histological analysis of carotid atherosclerotic plaque tissue specimens is a widely used method for studying the diagnosis of ischemic heart disease and stroke. Understanding the physiological and pathological mechanisms of carotid atherosclerotic plaque is of great significance for the effective prevention and treatment of plaque formation and rupture. In this work, we adapted a self-attention generative adversarial model to virtually stain label-free human carotid atherosclerotic plaque tissue sections into corresponding H&E stained sections. The self-attention mechanism and multi-layer structure are introduced into the residual steps of the generator and in the discriminator. Our method achieved the best performance (SSIM, PSNR, and LPIPS of 0.53, 20.29, and 0.30, respectively) in comparison with other state-of-the-art methods.Clinical Relevance - The proposed approach allows for the virtual staining of unlabeled human carotid plaque tissue images. It identifies the histopathological features of atherosclerotic plaques in the same tissue sample which could facilitate the development of personalized prevention and other interventional treatments for carotid atherosclerosis.
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49
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Wang S, Dong D, Li H, Feng C, Wang Y, Tian J. Cross-Phase Adversarial Domain Adaptation for Deep Disease-free Survival Prediction with Gastric Cancer CT Images. Annu Int Conf IEEE Eng Med Biol Soc 2021; 2021:3501-3504. [PMID: 34891994 DOI: 10.1109/embc46164.2021.9631004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Predicting gastric cancer disease-free survival (DFS) and identifying patients probably with high risk are imperative for more appropriate clinical treatment plans. Compared with CT-based radiomics researches adopting linear Cox proportional hazards models, deep neural networks can perform nonlinear transformations and investigate complex associations of image features with prognosis. Exploring shared information between post-contrast CT (with better visual enhancement) and pre-contrast CT (with few side effects and contraindications) is another challenge. In this work, a cross-phase adversarial domain adaptation (CPADA) framework is proposed to adapt a deep DFS prediction network (DDFS-Net) from arterial phase to pre-contrast phase. The DDFS-Net is designed for feature learning and trained by optimizing the average negative log function of Cox partial likelihood. The CPADA maps the feature space of pre-contrast phase (target) to arterial phase (source) in an adversarial manner by measuring Wasserstein distance. The proposed methods are evaluated on a dataset of 249 gastric cancer patients by concordance index, receiver operating characteristic curves, and Kaplan-Meier survival curves. The results demonstrate that our DDFS-Net outperforms linear survival analysis methods, and the CPADA works better than supervised learning and direct transfer schemes.Clinical Relevance-This work enables preoperative DFS prediction and risk stratification in gastric cancer. It is feasible and effective to infer a patient's risk of failure given a pre-contrast CT image by DDFS-Net adapted by CPADA.
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He B, Dong D, She Y, Zhou C, Fang M, Zhu Y, Zhang H, Huang Z, Jiang T, Tian J, Chen C. Predicting response to immunotherapy in advanced non-small-cell lung cancer using tumor mutational burden radiomic biomarker. J Immunother Cancer 2021; 8:jitc-2020-000550. [PMID: 32636239 PMCID: PMC7342823 DOI: 10.1136/jitc-2020-000550] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2020] [Indexed: 12/20/2022] Open
Abstract
Background Tumor mutational burden (TMB) is a significant predictor of immune checkpoint inhibitors (ICIs) efficacy. This study investigated the correlation between deep learning radiomic biomarker and TMB, including its predictive value for ICIs treatment response in patients with advanced non-small-cell lung cancer (NSCLC). Methods CT images from 327 patients with TMB data (TMB median=6.067 mutations per megabase (range: 0 to 42.151)) were retrospectively collected and randomly divided into a training (n=236), validation (n=26), and test cohort (n=65). We used 3D-densenet to estimate the target tumor area, which used 1020 deep learning features to distinguish High-TMB from Low-TMB patients and establish the TMB radiomic biomarker (TMBRB). The TMBRB was developed in the training cohort combined with validation cohort and evaluated in the test cohort. The predictive value of TMBRB was assessed in a cohort of 123 NSCLC patients who had received ICIs (survival median=462 days (range: 16 to 1128)). Results TMBRB discriminated between High-TMB and Low-TMB patients in the training cohort (area under the curve (AUC): 0.85, 95% CI: 0.84 to 0.87))and test cohort (AUC: 0.81, 95% CI: 0.77 to 0.85). In this study, the predictive value of TMBRB was better than that of a histological subtype (AUC of training cohort: 0.75, 95% CI: 0.72 to 0.77; AUC of test cohort: 0.71, 95% CI: 0.66 to 0.76) or Radiomic model (AUC of training cohort: 0.75, 95% CI: 0.72 to 0.77; AUC of test cohort: 0.74, 95% CI: 0.69 to 0.79). When predicting immunotherapy efficacy, TMBRB divided patients into a high- and low-risk group with distinctly different overall survival (OS; HR: 0.54, 95% CI: 0.31 to 0.95; p=0.030) and progression-free survival (PFS; HR: 1.78, 95% CI: 1.07 to 2.95; p=0.023). Moreover, TMBRB had a better predictive ability when combined with the Eastern Cooperative Oncology Group performance status (OS: p=0.007; PFS: p=0.003). Visual analysis revealed that tumor microenvironment was important for predicting TMB. Conclusion By combining deep learning technology and CT images, we developed an individual non-invasive biomarker that could distinguish High-TMB from Low-TMB, which might inform decisions on the use of ICIs in patients with advanced NSCLC.
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Affiliation(s)
- Bingxi He
- School of Electronic Electrical and Communication Engineering, University of the Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Di Dong
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China.,School of Artificial Intelligence, University of the Chinese Academy of Sciences, Beijing, China
| | - Yunlang She
- Department of Thoracic Surgery, Tongji University Affiliated Shanghai Pulmonary Hospital, Shanghai, China
| | - Caicun Zhou
- Department of Medical Oncology, Tongji University Affiliated Shanghai Pulmonary Hospital, Shang hai, China
| | - Mengjie Fang
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Yongbei Zhu
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China.,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, China
| | - Henghui Zhang
- Department of Medicine, Beijing Genecast Biotechnology Co, Beijing, China
| | - Zhipei Huang
- School of Electronic Electrical and Communication Engineering, University of the Chinese Academy of Sciences, Beijing, China
| | - Tao Jiang
- Department of Medical Oncology, Tongji University Affiliated Shanghai Pulmonary Hospital, Shang hai, China
| | - Jie Tian
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China .,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Medicine and Engineering, Beihang University, Beijing, China.,Engineering Research Center of Molecular and Neuro Imaging of Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, China.,Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Chang Chen
- Department of Thoracic Surgery, Tongji University Affiliated Shanghai Pulmonary Hospital, Shanghai, China
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