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Antar S, Abd El-Sattar HKH, Abdel-Rahman MH, F M Ghaleb F. COVID-19 infection segmentation using hybrid deep learning and image processing techniques. Sci Rep 2023; 13:22737. [PMID: 38123587 PMCID: PMC10733411 DOI: 10.1038/s41598-023-49337-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) epidemic has become a worldwide problem that continues to affect people's lives daily, and the early diagnosis of COVID-19 has a critical importance on the treatment of infected patients for medical and healthcare organizations. To detect COVID-19 infections, medical imaging techniques, including computed tomography (CT) scan images and X-ray images, are considered some of the helpful medical tests that healthcare providers carry out. However, in addition to the difficulty of segmenting contaminated areas from CT scan images, these approaches also offer limited accuracy for identifying the virus. Accordingly, this paper addresses the effectiveness of using deep learning (DL) and image processing techniques, which serve to expand the dataset without the need for any augmentation strategies, and it also presents a novel approach for detecting COVID-19 virus infections in lung images, particularly the infection prediction issue. In our proposed method, to reveal the infection, the input images are first preprocessed using a threshold then resized to 128 × 128. After that, a density heat map tool is used for coloring the resized lung images. The three channels (red, green, and blue) are then separated from the colored image and are further preprocessed through image inverse and histogram equalization, and are subsequently fed, in independent directions, into three separate U-Nets with the same architecture for segmentation. Finally, the segmentation results are combined and run through a convolution layer one by one to get the detection. Several evaluation metrics using the CT scan dataset were used to measure the performance of the proposed approach in comparison with other state-of-the-art techniques in terms of accuracy, sensitivity, precision, and the dice coefficient. The experimental results of the proposed approach reached 99.71%, 0.83, 0.87, and 0.85, respectively. These results show that coloring the CT scan images dataset and then dividing each image into its RGB image channels can enhance the COVID-19 detection, and it also increases the U-Net power in the segmentation when merging the channel segmentation results. In comparison to other existing segmentation techniques employing bigger 512 × 512 images, this study is one of the few that can rapidly and correctly detect the COVID-19 virus with high accuracy on smaller 128 × 128 images using the metrics of accuracy, sensitivity, precision, and dice coefficient.
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Affiliation(s)
- Samar Antar
- Computer Science Division, Department of Mathematics, Faculty of Science, Ain Shams University, Abbassia, Cairo, 11566, Egypt
| | | | - Mohammad H Abdel-Rahman
- Computer Science Division, Department of Mathematics, Faculty of Science, Ain Shams University, Abbassia, Cairo, 11566, Egypt
| | - Fayed F M Ghaleb
- Computer Science Division, Department of Mathematics, Faculty of Science, Ain Shams University, Abbassia, Cairo, 11566, Egypt
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2
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Ghassemi N, Shoeibi A, Khodatars M, Heras J, Rahimi A, Zare A, Zhang YD, Pachori RB, Gorriz JM. Automatic diagnosis of COVID-19 from CT images using CycleGAN and transfer learning. Appl Soft Comput 2023; 144:110511. [PMID: 37346824 PMCID: PMC10263244 DOI: 10.1016/j.asoc.2023.110511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 08/23/2022] [Accepted: 06/08/2023] [Indexed: 06/23/2023]
Abstract
The outbreak of the corona virus disease (COVID-19) has changed the lives of most people on Earth. Given the high prevalence of this disease, its correct diagnosis in order to quarantine patients is of the utmost importance in the steps of fighting this pandemic. Among the various modalities used for diagnosis, medical imaging, especially computed tomography (CT) imaging, has been the focus of many previous studies due to its accuracy and availability. In addition, automation of diagnostic methods can be of great help to physicians. In this paper, a method based on pre-trained deep neural networks is presented, which, by taking advantage of a cyclic generative adversarial net (CycleGAN) model for data augmentation, has reached state-of-the-art performance for the task at hand, i.e., 99.60% accuracy. Also, in order to evaluate the method, a dataset containing 3163 images from 189 patients has been collected and labeled by physicians. Unlike prior datasets, normal data have been collected from people suspected of having COVID-19 disease and not from data from other diseases, and this database is made available publicly. Moreover, the method's reliability is further evaluated by calibration metrics, and its decision is interpreted by Grad-CAM also to find suspicious regions as another output of the method and make its decisions trustworthy and explainable.
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Affiliation(s)
- Navid Ghassemi
- Faculty of Electrical Engineering, FPGA Lab, K. N. Toosi University of Technology, Tehran, Iran
- Computer Engineering department, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Afshin Shoeibi
- Faculty of Electrical Engineering, FPGA Lab, K. N. Toosi University of Technology, Tehran, Iran
- Computer Engineering department, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Marjane Khodatars
- Department of Medical Engineering, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Jonathan Heras
- Department of Mathematics and Computer Science, University of La Rioja, La Rioja, Spain
| | - Alireza Rahimi
- Computer Engineering department, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Assef Zare
- Faculty of Electrical Engineering, Gonabad Branch, Islamic Azad University, Gonabad, Iran
| | - Yu-Dong Zhang
- School of Informatics, University of Leicester, Leicester, LE1 7RH, UK
| | - Ram Bilas Pachori
- Department of Electrical Engineering, Indian Institute of Technology Indore, Indore 453552, India
| | - J Manuel Gorriz
- Department of Signal Theory, Networking and Communications, Universidad de Granada, Spain
- Department of Psychiatry, University of Cambridge, UK
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3
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Cong Y, Lee JH, Perry DL, Cooper K, Wang H, Dixit S, Liu DX, Feuerstein IM, Solomon J, Bartos C, Seidel J, Hammoud DA, Adams R, Anthony SM, Liang J, Schuko N, Li R, Liu Y, Wang Z, Tarbet EB, Hischak AMW, Hart R, Isic N, Burdette T, Drawbaugh D, Huzella LM, Byrum R, Ragland D, St Claire MC, Wada J, Kurtz JR, Hensley LE, Schmaljohn CS, Holbrook MR, Johnson RF. Longitudinal analyses using 18F-Fluorodeoxyglucose positron emission tomography with computed tomography as a measure of COVID-19 severity in the aged, young, and humanized ACE2 SARS-CoV-2 hamster models. Antiviral Res 2023; 214:105605. [PMID: 37068595 PMCID: PMC10105383 DOI: 10.1016/j.antiviral.2023.105605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/28/2023] [Accepted: 04/12/2023] [Indexed: 04/19/2023]
Abstract
This study compared disease progression of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in three different models of golden hamsters: aged (≈60 weeks old) wild-type (WT), young (6 weeks old) WT, and adult (14-22 weeks old) hamsters expressing the human-angiotensin-converting enzyme 2 (hACE2) receptor. After intranasal (IN) exposure to the SARS-CoV-2 Washington isolate (WA01/2020), 2-deoxy-2-[fluorine-18]fluoro-D-glucose positron emission tomography with computed tomography (18F-FDG PET/CT) was used to monitor disease progression in near real time and animals were euthanized at pre-determined time points to directly compare imaging findings with other disease parameters associated with coronavirus disease 2019 (COVID-19). Consistent with histopathology, 18F-FDG-PET/CT demonstrated that aged WT hamsters exposed to 105 plaque forming units (PFU) developed more severe and protracted pneumonia than young WT hamsters exposed to the same (or lower) dose or hACE2 hamsters exposed to a uniformly lethal dose of virus. Specifically, aged WT hamsters presented with a severe interstitial pneumonia through 8 d post-exposure (PE), while pulmonary regeneration was observed in young WT hamsters at that time. hACE2 hamsters exposed to 100 or 10 PFU virus presented with a minimal to mild hemorrhagic pneumonia but succumbed to SARS-CoV-2-related meningoencephalitis by 6 d PE, suggesting that this model might allow assessment of SARS-CoV-2 infection on the central nervous system (CNS). Our group is the first to use (18F-FDG) PET/CT to differentiate respiratory disease severity ranging from mild to severe in three COVID-19 hamster models. The non-invasive, serial measure of disease progression provided by PET/CT makes it a valuable tool for animal model characterization.
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Affiliation(s)
- Yu Cong
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Ji Hyun Lee
- Radiology and Imaging Sciences, Clinical Center, National Institute of Health, Bethesda, MD, USA
| | - Donna L Perry
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Kurt Cooper
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Hui Wang
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Saurabh Dixit
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - David X Liu
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Irwin M Feuerstein
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Jeffrey Solomon
- Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Christopher Bartos
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Jurgen Seidel
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Dima A Hammoud
- Center for Infectious Disease Imaging, Radiology and Imaging Sciences, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Ricky Adams
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Scott M Anthony
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Janie Liang
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Nicolette Schuko
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Rong Li
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, USA.
| | - Yanan Liu
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, USA
| | - Zhongde Wang
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, USA
| | - E Bart Tarbet
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, USA
| | - Amanda M W Hischak
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Randy Hart
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Nejra Isic
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Tracey Burdette
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA; Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, USA
| | - David Drawbaugh
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Louis M Huzella
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Russell Byrum
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Danny Ragland
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Marisa C St Claire
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Jonathan R Kurtz
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Lisa E Hensley
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Connie S Schmaljohn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Michael R Holbrook
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA.
| | - Reed F Johnson
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA; SARS-CoV-2 Virology Core Laboratory, Division of Intramural Research, National Institutes of Health, Bethesda, MD, USA.
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Bhattacharjee V, Priya A, Kumari N, Anwar S. DeepCOVNet Model for COVID-19 Detection Using Chest X-Ray Images. WIRELESS PERSONAL COMMUNICATIONS 2023; 130:1399-1416. [PMID: 37168437 PMCID: PMC10088652 DOI: 10.1007/s11277-023-10336-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 02/25/2023] [Indexed: 05/13/2023]
Abstract
COVID-19 is an epidemic disease that has threatened all the people at worldwide scale and eventually became a pandemic It is a crucial task to differentiate COVID-19-affected patients from healthy patient populations. The need for technology enabled solutions is pertinent and this paper proposes a deep learning model for detection of COVID-19 using Chest X-Ray (CXR) images. In this research work, we provide insights on how to build robust deep learning based models for COVID-19 CXR image classification from Normal and Pneumonia affected CXR images. We contribute a methodical escort on preparation of data to produce a robust deep learning model. The paper prepared datasets by refactoring, using images from several datasets for ameliorate training of deep model. These recently published datasets enable us to build our own model and compare by using pre-trained models. The proposed experiments show the ability to work effectively to classify COVID-19 patients utilizing CXR. The empirical work, which uses a 3 convolutional layer based Deep Neural Network called "DeepCOVNet" to classify CXR images into 3 classes: COVID-19, Normal and Pneumonia cases, yielded an accuracy of 96.77% and a F1-score of 0.96 on two different combination of datasets.
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Affiliation(s)
| | - Ankita Priya
- Birla Institute of Technology Mesra, Ranchi, 835215 India
| | - Nandini Kumari
- Birla Institute of Technology Mesra, Ranchi, 835215 India
- Department of Data Science & Computer Application, Manipal Institute of Technology, Manipal, Manipal Academy of Higher Education, Manipal, 576104 Karnataka India
| | - Shamama Anwar
- Birla Institute of Technology Mesra, Ranchi, 835215 India
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5
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Wen R, Zhang M, Xu R, Gao Y, Liu L, Chen H, Wang X, Zhu W, Lin H, Liu C, Zeng X. COVID-19 imaging, where do we go from here? Bibliometric analysis of medical imaging in COVID-19. Eur Radiol 2023; 33:3133-3143. [PMID: 36892649 PMCID: PMC9996554 DOI: 10.1007/s00330-023-09498-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/08/2022] [Accepted: 01/29/2023] [Indexed: 03/10/2023]
Abstract
OBJECTIVES We conducted a systematic and comprehensive bibliometric analysis of COVID-19-related medical imaging to determine the current status and indicate possible future directions. METHODS This research provides an analysis of Web of Science Core Collection (WoSCC) indexed articles on COVID-19 and medical imaging published between 1 January 2020 and 30 June 2022, using the search terms "COVID-19" and medical imaging terms (such as "X-ray" or "CT"). Publications based solely on COVID-19 themes or medical image themes were excluded. CiteSpace was used to identify the predominant topics and generate a visual map of countries, institutions, authors, and keyword networks. RESULTS The search included 4444 publications. The journal with the most publications was European Radiology, and the most co-cited journal was Radiology. China was the most frequently cited country in terms of co-authorship, with the Huazhong University of Science and Technology being the institution contributing with the highest number of relevant co-authorships. Research trends and leading topics included: assessment of initial COVID-19-related clinical imaging features, differential diagnosis using artificial intelligence (AI) technology and model interpretability, diagnosis systems construction, COVID-19 vaccination, complications, and predicting prognosis. CONCLUSIONS This bibliometric analysis of COVID-19-related medical imaging helps clarify the current research situation and developmental trends. Subsequent trends in COVID-19 imaging are likely to shift from lung structure to function, from lung tissue to other related organs, and from COVID-19 to the impact of COVID-19 on the diagnosis and treatment of other diseases. Key Points • We conducted a systematic and comprehensive bibliometric analysis of COVID-19-related medical imaging from 1 January 2020 to 30 June 2022. • Research trends and leading topics included assessment of initial COVID-19-related clinical imaging features, differential diagnosis using AI technology and model interpretability, diagnosis systems construction, COVID-19 vaccination, complications, and predicting prognosis. • Future trends in COVID-19-related imaging are likely to involve a shift from lung structure to function, from lung tissue to other related organs, and from COVID-19 to the impact of COVID-19 on the diagnosis and treatment of other diseases.
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Affiliation(s)
- Ru Wen
- Medical College, Guizhou University, Guizhou, 550000, People's Republic of China.,Department of Radiology, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gao Tan Yan St, 400038, Chongqing, People's Republic of China.,Department of Medical Imaging, Guizhou Provincial People Hospital, No.83, East Zhongshan Road, Nanming District, Guizhou Province, 550000, Guiyang City, People's Republic of China
| | - Mudan Zhang
- Guizhou Medical University, Guiyang, Guizhou Province, 550000, People's Republic of China
| | - Rui Xu
- Department of Medical Imaging, Guizhou Provincial People Hospital, No.83, East Zhongshan Road, Nanming District, Guizhou Province, 550000, Guiyang City, People's Republic of China
| | - Yingming Gao
- College of Life Science, Guizhou University, Guiyang, Guizhou Province, 550000, People's Republic of China
| | - Lin Liu
- Department of Respiratory Medicine, Guizhou Provincial People Hospital, Guiyang City, Guizhou Province, 550000, People's Republic of China
| | - Hui Chen
- Department of Radiology, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gao Tan Yan St, 400038, Chongqing, People's Republic of China
| | - Xingang Wang
- Department of Radiology, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gao Tan Yan St, 400038, Chongqing, People's Republic of China
| | - Wenyan Zhu
- Medical Department, Yidu Cloud (Beijing) Technology Co., Ltd., Beijing, 100191, People's Republic of China
| | - Huafang Lin
- Medical Department, Yidu Cloud (Beijing) Technology Co., Ltd., Beijing, 100191, People's Republic of China
| | - Chen Liu
- Department of Radiology, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gao Tan Yan St, 400038, Chongqing, People's Republic of China.
| | - Xianchun Zeng
- Department of Medical Imaging, Guizhou Provincial People Hospital, No.83, East Zhongshan Road, Nanming District, Guizhou Province, 550000, Guiyang City, People's Republic of China.
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Chamberlin JH, Smith C, Schoepf UJ, Nance S, Elojeimy S, O'Doherty J, Baruah D, Burt JR, Varga-Szemes A, Kabakus IM. A deep convolutional neural network ensemble for composite identification of pulmonary nodules and incidental findings on routine PET/CT. Clin Radiol 2023; 78:e368-e376. [PMID: 36863883 DOI: 10.1016/j.crad.2023.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/19/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023]
Abstract
AIM To evaluate primary and secondary pathologies of interest using an artificial intelligence (AI) platform, AI-Rad Companion, on low-dose computed tomography (CT) series from integrated positron-emission tomography (PET)/CT to detect CT findings that might be overlooked. MATERIALS AND METHODS One hundred and eighty-nine sequential patients who had undergone PET/CT were included. Images were evaluated using an ensemble of convolutional neural networks (AI-Rad Companion, Siemens Healthineers, Erlangen, Germany). The primary outcome was detection of pulmonary nodules for which the accuracy, identity, and intra-rater reliability was calculated. For secondary outcomes (binary detection of coronary artery calcium, aortic ectasia, vertebral height loss), accuracy and diagnostic performance were calculated. RESULTS The overall per-nodule accuracy for detection of lung nodules was 0.847. The overall sensitivity and specificity for detection of lung nodules was 0.915 and 0.781. The overall per-patient accuracy for AI detection of coronary artery calcium, aortic ectasia, and vertebral height loss was 0.979, 0.966, and 0.840, respectively. The sensitivity and specificity for coronary artery calcium was 0.989 and 0.969. The sensitivity and specificity for aortic ectasia was 0.806 and 1. CONCLUSION The neural network ensemble accurately assessed the number of pulmonary nodules and presence of coronary artery calcium and aortic ectasia on low-dose CT series of PET/CT. The neural network was highly specific for the diagnosis of vertebral height loss, but not sensitive. The use of the AI ensemble can help radiologists and nuclear medicine physicians to catch CT findings that might be overlooked.
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Affiliation(s)
- J H Chamberlin
- Division of Thoracic Imaging, Department of Radiology and Radiological Science, Medical University of South Carolina, Charleston, SC, USA
| | - C Smith
- Division of Thoracic Imaging, Department of Radiology and Radiological Science, Medical University of South Carolina, Charleston, SC, USA
| | - U J Schoepf
- Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Medical University of South Carolina, Charleston, SC, USA
| | - S Nance
- Division of Thoracic Imaging, Department of Radiology and Radiological Science, Medical University of South Carolina, Charleston, SC, USA
| | - S Elojeimy
- Division of Nuclear Medicine, Department of Radiology and Radiological Science, Medical University of South Carolina, Charleston, SC, USA
| | - J O'Doherty
- Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Medical University of South Carolina, Charleston, SC, USA; Siemens Medical Solutions, Malvern, PA, USA
| | - D Baruah
- Division of Thoracic Imaging, Department of Radiology and Radiological Science, Medical University of South Carolina, Charleston, SC, USA
| | - J R Burt
- Division of Thoracic Imaging, Department of Radiology and Radiological Science, Medical University of South Carolina, Charleston, SC, USA
| | - A Varga-Szemes
- Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Medical University of South Carolina, Charleston, SC, USA
| | - I M Kabakus
- Division of Thoracic Imaging, Department of Radiology and Radiological Science, Medical University of South Carolina, Charleston, SC, USA; Division of Cardiovascular Imaging, Department of Radiology and Radiological Science, Medical University of South Carolina, Charleston, SC, USA; Division of Nuclear Medicine, Department of Radiology and Radiological Science, Medical University of South Carolina, Charleston, SC, USA.
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Asnawi MH, Pravitasari AA, Darmawan G, Hendrawati T, Yulita IN, Suprijadi J, Nugraha FAL. Lung and Infection CT-Scan-Based Segmentation with 3D UNet Architecture and Its Modification. Healthcare (Basel) 2023; 11:healthcare11020213. [PMID: 36673581 PMCID: PMC9859364 DOI: 10.3390/healthcare11020213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
COVID-19 is the disease that has spread over the world since December 2019. This disease has a negative impact on individuals, governments, and even the global economy, which has caused the WHO to declare COVID-19 as a PHEIC (Public Health Emergency of International Concern). Until now, there has been no medicine that can completely cure COVID-19. Therefore, to prevent the spread and reduce the negative impact of COVID-19, an accurate and fast test is needed. The use of chest radiography imaging technology, such as CXR and CT-scan, plays a significant role in the diagnosis of COVID-19. In this study, CT-scan segmentation will be carried out using the 3D version of the most recommended segmentation algorithm for bio-medical images, namely 3D UNet, and three other architectures from the 3D UNet modifications, namely 3D ResUNet, 3D VGGUNet, and 3D DenseUNet. These four architectures will be used in two cases of segmentation: binary-class segmentation, where each architecture will segment the lung area from a CT scan; and multi-class segmentation, where each architecture will segment the lung and infection area from a CT scan. Before entering the model, the dataset is preprocessed first by applying a minmax scaler to scale the pixel value to a range of zero to one, and the CLAHE method is also applied to eliminate intensity in homogeneity and noise from the data. Of the four models tested in this study, surprisingly, the original 3D UNet produced the most satisfactory results compared to the other three architectures, although it requires more iterations to obtain the maximum results. For the binary-class segmentation case, 3D UNet produced IoU scores, Dice scores, and accuracy of 94.32%, 97.05%, and 99.37%, respectively. For the case of multi-class segmentation, 3D UNet produced IoU scores, Dice scores, and accuracy of 81.58%, 88.61%, and 98.78%, respectively. The use of 3D segmentation architecture will be very helpful for medical personnel because, apart from helping the process of diagnosing someone with COVID-19, they can also find out the severity of the disease through 3D infection projections.
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Affiliation(s)
- Mohammad Hamid Asnawi
- Department of Statistics, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung 45363, Indonesia
| | - Anindya Apriliyanti Pravitasari
- Department of Statistics, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung 45363, Indonesia
- Correspondence:
| | - Gumgum Darmawan
- Department of Statistics, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung 45363, Indonesia
| | - Triyani Hendrawati
- Department of Statistics, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung 45363, Indonesia
| | - Intan Nurma Yulita
- Department of Computer Science, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung 45363, Indonesia
| | - Jadi Suprijadi
- Department of Statistics, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung 45363, Indonesia
| | - Farid Azhar Lutfi Nugraha
- Department of Statistics, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung 45363, Indonesia
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Dofuor AK, Quartey NKA, Osabutey AF, Boateng BO, Lutuf H, Osei JHN, Ayivi-Tosuh SM, Aiduenu AF, Ekloh W, Loh SK, Opoku MJ, Aidoo OF. The Global Impact of COVID-19: Historical Development, Molecular Characterization, Drug Discovery and Future Directions. CLINICAL PATHOLOGY (THOUSAND OAKS, VENTURA COUNTY, CALIF.) 2023; 16:2632010X231218075. [PMID: 38144436 PMCID: PMC10748929 DOI: 10.1177/2632010x231218075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/16/2023] [Indexed: 12/26/2023]
Abstract
In December 2019, an outbreak of a respiratory disease called the coronavirus disease 2019 (COVID-19) caused by a new coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began in Wuhan, China. The SARS-CoV-2, an encapsulated positive-stranded RNA virus, spread worldwide with disastrous consequences for people's health, economies, and quality of life. The disease has had far-reaching impacts on society, including economic disruption, school closures, and increased stress and anxiety. It has also highlighted disparities in healthcare access and outcomes, with marginalized communities disproportionately affected by the SARS-CoV-2. The symptoms of COVID-19 range from mild to severe. There is presently no effective cure. Nevertheless, significant progress has been made in developing COVID-19 vaccine for different therapeutic targets. For instance, scientists developed multifold vaccine candidates shortly after the COVID-19 outbreak after Pfizer and AstraZeneca discovered the initial COVID-19 vaccines. These vaccines reduce disease spread, severity, and mortality. The addition of rapid diagnostics to microscopy for COVID-19 diagnosis has proven crucial. Our review provides a thorough overview of the historical development of COVID-19 and molecular and biochemical characterization of the SARS-CoV-2. We highlight the potential contributions from insect and plant sources as anti-SARS-CoV-2 and present directions for future research.
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Affiliation(s)
- Aboagye Kwarteng Dofuor
- Department of Biological Sciences, School of Natural and Environmental Sciences, University of Environment and Sustainable Development, Somanya, Ghana
| | - Naa Kwarley-Aba Quartey
- Department of Food Science and Technology, Faculty of Biosciences, College of Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Belinda Obenewa Boateng
- Coconut Research Program, Oil Palm Research Institute, Council for Scientific and Industrial Research, Sekondi-Takoradi, Ghana
| | - Hanif Lutuf
- Crop Protection Division, Oil Palm Research Institute, Council for Scientific and Industrial Research, Kade, Ghana
| | - Joseph Harold Nyarko Osei
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Selina Mawunyo Ayivi-Tosuh
- Department of Biochemistry, School of Life Sciences, Northeast Normal University, Changchun, Jilin Province, China
| | - Albert Fynn Aiduenu
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Accra, Ghana
| | - William Ekloh
- Department of Biochemistry, School of Biological Sciences, College of Agriculture and Natural Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Seyram Kofi Loh
- Department of Built Environment, School of Sustainable Development, University of Environment and Sustainable Development, Somanya, Ghana
| | - Maxwell Jnr Opoku
- Department of Biological Sciences, School of Natural and Environmental Sciences, University of Environment and Sustainable Development, Somanya, Ghana
| | - Owusu Fordjour Aidoo
- Department of Biological Sciences, School of Natural and Environmental Sciences, University of Environment and Sustainable Development, Somanya, Ghana
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9
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Rasmusen HK, Aarøe M, Madsen CV, Gudmundsdottir HL, Mertz KH, Mikkelsen AD, Dall CH, Brushøj C, Andersen JL, Vall-Lamora MHD, Bovin A, Magnusson SP, Thune JJ, Pecini R, Pedersen L. The COVID-19 in athletes (COVA) study: a national study on cardio-pulmonary involvement of SARS-CoV-2 infection among elite athletes. Eur Clin Respir J 2022; 10:2149919. [PMID: 36518348 PMCID: PMC9744211 DOI: 10.1080/20018525.2022.2149919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Abstract
Background COVID-19 can cause cardiopulmonary involvement. Physical activity and cardiac complications can worsen prognosis, while pulmonary complications can reduce performance. Aims To determine the prevalence and clinical implications of SARS-CoV-2 cardiopulmonary involvement in elite athletes. Methods An observational study between 1 July 2020 and 30 June 2021 with the assessment of coronary biomarkers, electrocardiogram, echocardiography, Holter-monitoring, spirometry, and chest X-ray in Danish elite athletes showed that PCR-tested positive for SARS-CoV-2. The cohort consisted of male football players screened weekly (cohort I) and elite athletes on an international level only tested if they had symptoms, were near-contact, or participated in international competitions (cohort II). All athletes were categorized into two groups based on symptoms and duration of COVID-19: Group 1 had no cardiopulmonary symptoms and duration ≤7 days, and; Group 2 had cardiopulmonary symptoms or disease duration >7 days. Results In total 121 athletes who tested positive for SARS-CoV-2 were investigated. Cardiac involvement was identified in 2/121 (2%) and pulmonary involvement in 15/121 (12%) participants. In group 1, 87 (72%), no athletes presented with signs of cardiac involvement, and 8 (7%) were diagnosed with radiological COVID-19-related findings or obstructive lung function. In group 2, 34 (28%), two had myocarditis (6%), and 8 (24%) were diagnosed with radiological COVID-19-related findings or obstructive lung function. Conclusions These clinically-driven data show no signs of cardiac involvement among athletes who tested positive for SARS-CoV-2 infection without cardiopulmonary symptoms and duration <7 days. Athletes with cardiopulmonary symptoms or prolonged duration of COVID-19 display, exercise-limiting cardiopulmonary involvement.
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Affiliation(s)
- Hanne Kruuse Rasmusen
- Department of Cardiology, Copenhagen University Hospital – Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | - Mikkel Aarøe
- Department of Cardiology, Copenhagen University Hospital – Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | - Christoffer Valdorff Madsen
- Department of Cardiology, Copenhagen University Hospital – Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | | | - Kenneth Hudlebusch Mertz
- Institute of Sports medicine, Copenhagen University Hospital – Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | - Astrid Duus Mikkelsen
- Department of Cardiology, Copenhagen University Hospital – Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | - Christian Have Dall
- Department of Cardiology, Copenhagen University Hospital – Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | - Christoffer Brushøj
- Institute of Sports medicine, Copenhagen University Hospital – Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | - Jesper Løvind Andersen
- Institute of Sports medicine, Copenhagen University Hospital – Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | | | - Ann Bovin
- Department of Cardiology, Vejle Hospital, Part of Lillebaelt Hospital, Vejle, Denmark
| | - S. Peter Magnusson
- Institute of Sports medicine, Copenhagen University Hospital – Bispebjerg and Frederiksberg, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jens Jakob Thune
- Department of Cardiology, Copenhagen University Hospital – Bispebjerg and Frederiksberg, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Redi Pecini
- Department of Cardiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Lars Pedersen
- Department of Respiratory Medicine and Infectious Diseases, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark
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10
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Polat H. A modified DeepLabV3+ based semantic segmentation of chest computed tomography images for COVID-19 lung infections. INTERNATIONAL JOURNAL OF IMAGING SYSTEMS AND TECHNOLOGY 2022; 32:1481-1495. [PMID: 35941930 PMCID: PMC9349869 DOI: 10.1002/ima.22772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/19/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Coronavirus disease (COVID-19) affects the lives of billions of people worldwide and has destructive impacts on daily life routines, the global economy, and public health. Early diagnosis and quantification of COVID-19 infection have a vital role in improving treatment outcomes and interrupting transmission. For this purpose, advances in medical imaging techniques like computed tomography (CT) scans offer great potential as an alternative to RT-PCR assay. CT scans enable a better understanding of infection morphology and tracking of lesion boundaries. Since manual analysis of CT can be extremely tedious and time-consuming, robust automated image segmentation is necessary for clinical diagnosis and decision support. This paper proposes an efficient segmentation framework based on the modified DeepLabV3+ using lower atrous rates in the Atrous Spatial Pyramid Pooling (ASPP) module. The lower atrous rates make receptive small to capture intricate morphological details. The encoder part of the framework utilizes a pre-trained residual network based on dilated convolutions for optimum resolution of feature maps. In order to evaluate the robustness of the modified model, a comprehensive comparison with other state-of-the-art segmentation methods was also performed. The experiments were carried out using a fivefold cross-validation technique on a publicly available database containing 100 single-slice CT scans from >40 patients with COVID-19. The modified DeepLabV3+ achieved good segmentation performance using around 43.9 M parameters. The lower atrous rates in the ASPP module improved segmentation performance. After fivefold cross-validation, the framework achieved an overall Dice similarity coefficient score of 0.881. The results demonstrate that several minor modifications to the DeepLabV3+ pipeline can provide robust solutions for improving segmentation performance and hardware implementation.
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Affiliation(s)
- Hasan Polat
- Department of Electrical and EnergyBingol UniversityBingölTurkey
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11
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Gecgel O, Ramanujam A, Botte GG. Selective Electrochemical Detection of SARS-CoV-2 Using Deep Learning. Viruses 2022; 14:v14091930. [PMID: 36146738 PMCID: PMC9502341 DOI: 10.3390/v14091930] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
COVID-19 has been in the headlines for the past two years. Diagnosing this infection with minimal false rates is still an issue even with the advent of multiple rapid antigen tests. Enormous data are being collected every day that could provide insight into reducing the false diagnosis. Machine learning (ML) and deep learning (DL) could be the way forward to process these data and reduce the false diagnosis rates. In this study, ML and DL approaches have been applied to the data set collected using an ultra-fast COVID-19 diagnostic sensor (UFC-19). The ability of ML and DL to specifically detect SARS-CoV-2 signals against SARS-CoV, MERS-CoV, Human CoV, and Influenza was investigated. UFC-19 is an electrochemical sensor that was used to test these virus samples and the obtained current response dataset was used to diagnose SARS-CoV-2 using different algorithms. Our results indicate that the convolution neural networks algorithm could diagnose SARS-CoV-2 samples with a sensitivity of 96.15%, specificity of 98.17%, and accuracy of 97.20%. Combining this DL model with the existing UFC-19 could selectively identify SARS-CoV-2 presence within two minutes.
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12
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Polat H. Multi-task semantic segmentation of CT images for COVID-19 infections using DeepLabV3+ based on dilated residual network. Phys Eng Sci Med 2022; 45:443-455. [PMID: 35286619 PMCID: PMC8919169 DOI: 10.1007/s13246-022-01110-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 11/28/2022]
Abstract
COVID-19 is a deadly outbreak that has been declared a public health emergency of international concern. The massive damage of the disease to public health, social life, and the global economy increases the importance of alternative rapid diagnosis and follow-up methods. RT-PCR assay, which is considered the gold standard in diagnosing the disease, is complicated, expensive, time-consuming, prone to contamination, and may give false-negative results. These drawbacks reinforce the trend toward medical imaging techniques such as computed tomography (CT). Typical visual signs such as ground-glass opacity (GGO) and consolidation of CT images allow for quantitative assessment of the disease. In this context, it is aimed at the segmentation of the infected lung CT images with the residual network-based DeepLabV3+, which is a redesigned convolutional neural network (CNN) model. In order to evaluate the robustness of the proposed model, three different segmentation tasks as Task-1, Task-2, and Task-3 were applied. Task-1 represents binary segmentation as lung (infected and non-infected tissues) and background. Task-2 represents multi-class segmentation as lung (non-infected tissue), COVID (GGO, consolidation, and pleural effusion irregularities are gathered under a single roof), and background. Finally, the segmentation in which each lesion type is considered as a separate class is defined as Task-3. COVID-19 imaging data for each segmentation task consists of 100 CT single-slice scans from over 40 diagnosed patients. The performance of the model was evaluated using Dice similarity coefficient (DSC), intersection over union (IoU), sensitivity, specificity, and accuracy by performing five-fold cross-validation. The average DSC performance for three different segmentation tasks was obtained as 0.98, 0.858, and 0.616, respectively. The experimental results demonstrate that the proposed method has robust performance and great potential in evaluating COVID-19 infection.
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Affiliation(s)
- Hasan Polat
- Department of Electrical and Energy, Bingol University, Selahaddin-i Eyyübi Mah. Aydınlık Cad No:1, 12000, Bingöl, Turkey.
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13
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A Deep Learning-Based Diagnosis System for COVID-19 Detection and Pneumonia Screening Using CT Imaging. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12104825] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a global threat impacting the lives of millions of people worldwide. Automated detection of lung infections from Computed Tomography scans represents an excellent alternative; however, segmenting infected regions from CT slices encounters many challenges. Objective: Developing a diagnosis system based on deep learning techniques to detect and quantify COVID-19 infection and pneumonia screening using CT imaging. Method: Contrast Limited Adaptive Histogram Equalization pre-processing method was used to remove the noise and intensity in homogeneity. Black slices were also removed to crop only the region of interest containing the lungs. A U-net architecture, based on CNN encoder and CNN decoder approaches, is then introduced for a fast and precise image segmentation to obtain the lung and infection segmentation models. For better estimation of skill on unseen data, a fourfold cross-validation as a resampling procedure has been used. A three-layered CNN architecture, with additional fully connected layers followed by a Softmax layer, was used for classification. Lung and infection volumes have been reconstructed to allow volume ratio computing and obtain infection rate. Results: Starting with the 20 CT scan cases, data has been divided into 70% for the training dataset and 30% for the validation dataset. Experimental results demonstrated that the proposed system achieves a dice score of 0.98 and 0.91 for the lung and infection segmentation tasks, respectively, and an accuracy of 0.98 for the classification task. Conclusions: The proposed workflow aimed at obtaining good performances for the different system’s components, and at the same time, dealing with reduced datasets used for training.
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14
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Lampejo T. Pneumocystis pneumonia: An important consideration when investigating artificial intelligence-based methods in the radiological diagnosis of COVID-19. Clin Imaging 2022; 85:118-119. [PMID: 33810937 PMCID: PMC7997693 DOI: 10.1016/j.clinimag.2021.02.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 02/23/2021] [Indexed: 12/31/2022]
Affiliation(s)
- Temi Lampejo
- Imperial College Healthcare NHS Trust, London, United Kingdom.
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15
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Kuo KM, Talley PC, Chang CS. The Accuracy of Machine Learning Approaches Using Non-image Data for the Prediction of COVID-19: A Meta-Analysis. Int J Med Inform 2022; 164:104791. [PMID: 35594810 PMCID: PMC9098530 DOI: 10.1016/j.ijmedinf.2022.104791] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/08/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022]
Abstract
Objective COVID-19 is a novel, severely contagious disease with enormous negative impact on humanity as well as the world economy. An expeditious, feasible tool for detecting COVID-19 remains yet elusive. Recently, there has been a surge of interest in applying machine learning techniques to predict COVID-19 using non-image data. We have therefore undertaken a meta-analysis to quantify the diagnostic performance of machine learning models facilitating the prediction of COVID-19. Materials and methods A comprehensive electronic database search for the period between January 1st, 2021 and December 3rd, 2021 was undertaken in order to identify eligible studies relevant to this meta-analysis. Summary sensitivity, specificity, and the area under receiver operating characteristic curves were used to assess potential diagnostic accuracy. Risk of bias was assessed by means of a revised Quality Assessment of Diagnostic Studies. Results A total of 30 studies, including 34 models, met all of the inclusion criteria. Summary sensitivity, specificity, and area under receiver operating characteristic curves were 0.86, 0.86, and 0.91, respectively. The purpose of machine learning models, class imbalance, and feature selection are significant covariates useful in explaining the between-study heterogeneity, in terms of both sensitivity and specificity. Conclusions Our study findings show that non-image data can be used to predict COVID-19 with an acceptable performance. Further, class imbalance and feature selection are suggested to be incorporated whenever building models for the prediction of COVID-19, thus improving further diagnostic performance.
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16
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Soni V, Khosla A, Singh P, Nguyen VH, Le QV, Selvasembian R, Hussain CM, Thakur S, Raizada P. Current perspective in metal oxide based photocatalysts for virus disinfection: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 308:114617. [PMID: 35121465 PMCID: PMC8803534 DOI: 10.1016/j.jenvman.2022.114617] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 05/09/2023]
Abstract
Nanotechnology holds huge potential for the prevention of various viral outbreaks that have increased at a disquieting rate over the past decades. Metal oxide nanomaterials with oxidative capability are the effective materials that provide platforms as well as tools for the well understanding of the mechanism, its detection, and treatment of various viral diseases like measles, influenza, herpes, ebola, current COVID-19 etc. In this inclusive review, we survey various previous research articles on different notable photoactive transition metal oxides that possess enough potential to act as antiviral agents for the deactivation of harmful viruses. We investigated and highlighted the plausible photocatalytic oxidative mechanism of photoactive transition metal oxides in degrading viral coatings, genomic RNA using suitable free radical generation. The key finding of the present review article including the discovery of a vision on the suitable photocatalytic transition metal oxides that have been proven to be excellent against harmful viruses and consequently combatting deadly CoV-2 in the environment. This review intends to provide conclusive remarks and a realistic outlook on other advanced photocatalytic metal oxides as a potential solution in battling other similar upcoming pandemics.
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Affiliation(s)
- Vatika Soni
- School of Advanced Chemical Sciences, Shoolini University, Solan, Himachal Pradesh 173229, India
| | - Atul Khosla
- School of Management, Faculty of Management Sciences, Shoolini University, Solan, HP, India, 173229
| | - Pardeep Singh
- School of Advanced Chemical Sciences, Shoolini University, Solan, Himachal Pradesh 173229, India
| | - Van-Huy Nguyen
- School of Advanced Chemical Sciences, Shoolini University, Solan, Himachal Pradesh 173229, India
| | - Quyet Van Le
- Department of Materials Science and Engineering, Korea University, 145, Anam-ro Seongbuk-gu, Seoul 02841, South Korea
| | | | - Chaudhery Mustansar Hussain
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, N J, 07102, USA
| | - Sourbh Thakur
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100, Gliwice, Poland
| | - Pankaj Raizada
- School of Advanced Chemical Sciences, Shoolini University, Solan, Himachal Pradesh 173229, India.
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17
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Fathi Karkan S, Maleki Baladi R, Shahgolzari M, Gholizadeh M, Shayegh F, Arashkia A. The evolving direct and indirect platforms for the detection of SARS-CoV-2. J Virol Methods 2022; 300:114381. [PMID: 34843826 PMCID: PMC8626143 DOI: 10.1016/j.jviromet.2021.114381] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/26/2021] [Accepted: 11/25/2021] [Indexed: 01/08/2023]
Abstract
Diagnosis of SARS-CoV-2 by standard screening measures can reduce the chance of COVID-19 spread before the symptoms become severe. Detecting viral RNA and antigens, anti-viral antibodies, and CT-scan are the most routine diagnostic methods. Accordingly, several diagnostic platforms including thermal and isothermal amplifications, CRISPR/Cas‑based approaches, digital PCR, ELISA, NGS, and point-of-care testing methods with variable sensitivities, have been developed that may facilitate managing and preventing the further spread of the infection. Here, we summarized the currently available direct and indirect testing platforms in research and clinical settings, including recent progress in the methods to detect viral RNA, antigens, and specific antibodies. This summary may help in selecting the effective method for a special application sucha as routine laboratory diagnosis, point-of-care tests or tracing the the virus spread and mutations.
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Affiliation(s)
- Sonia Fathi Karkan
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran,Department of Medical Nanotechnology, Tabriz Medical University, Tabriz, Iran
| | - Reza Maleki Baladi
- Young Researchers and Elite Club, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | - Mehdi Shahgolzari
- Department of Medical Nanotechnology, Tabriz Medical University, Tabriz, Iran
| | - Monireh Gholizadeh
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran,Department of Immunology, Pasteur Institute of Iran, Tehran, Iran
| | - Fahimeh Shayegh
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Arash Arashkia
- Deaprtment of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran.
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18
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Tayara H, Abdelbaky I, To Chong K. Recent omics-based computational methods for COVID-19 drug discovery and repurposing. Brief Bioinform 2021; 22:6355836. [PMID: 34423353 DOI: 10.1093/bib/bbab339] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/09/2021] [Indexed: 12/22/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the main reason for the increasing number of deaths worldwide. Although strict quarantine measures were followed in many countries, the disease situation is still intractable. Thus, it is needed to utilize all possible means to confront this pandemic. Therefore, researchers are in a race against the time to produce potential treatments to cure or reduce the increasing infections of COVID-19. Computational methods are widely proving rapid successes in biological related problems, including diagnosis and treatment of diseases. Many efforts in recent months utilized Artificial Intelligence (AI) techniques in the context of fighting the spread of COVID-19. Providing periodic reviews and discussions of recent efforts saves the time of researchers and helps to link their endeavors for a faster and efficient confrontation of the pandemic. In this review, we discuss the recent promising studies that used Omics-based data and utilized AI algorithms and other computational tools to achieve this goal. We review the established datasets and the developed methods that were basically directed to new or repurposed drugs, vaccinations and diagnosis. The tools and methods varied depending on the level of details in the available information such as structures, sequences or metabolic data.
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Affiliation(s)
- Hilal Tayara
- School of international Engineering and Science, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Ibrahim Abdelbaky
- Artificial Intelligence Department, Faculty of Computers and Artificial Intelligence, Benha University, Banha 13518, Egypt
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju, Jeollabukdo 54896, Republic of Korea.,Advances Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, Republic of Korea
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19
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Eleftheriadis GK, Genina N, Boetker J, Rantanen J. Modular design principle based on compartmental drug delivery systems. Adv Drug Deliv Rev 2021; 178:113921. [PMID: 34390776 DOI: 10.1016/j.addr.2021.113921] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/21/2021] [Accepted: 08/09/2021] [Indexed: 12/28/2022]
Abstract
The current manufacturing solutions for oral solid dosage forms are fundamentally based on technologies from the 19th century. This approach is well suited for mass production of one-size-fits-all products; however, it does not allow for a straight-forward personalization and mass customization of the pharmaceutical end-product. In order to provide better therapies to the patients, a need for innovative manufacturing concepts and product design principles has been rising. Additive manufacturing opens up a possibility for compartmentalization of drug products, including design of spatially separated multidrug and functional excipient compartments. This compartmentalized solution can be further expanded to modular design thinking. Modular design is referring to combination of building blocks containing a given amount of drug compound(s) and related functional excipients into a larger final product. Implementation of modular design principles is paving the way for implementing the emerging personalization potential within health sciences by designing compartmental and reactive product structures that can be manufactured based on the individual needs of each patient. This review will introduce the existing compartmentalized product design principles and discuss the integration of these into edible electronics allowing for innovative control of drug release.
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Affiliation(s)
| | - Natalja Genina
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Johan Boetker
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Jukka Rantanen
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark.
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20
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Lee S, Lam SH, Hernandes Rocha TA, Fleischman RJ, Staton CA, Taylor R, Limkakeng AT. Machine Learning and Precision Medicine in Emergency Medicine: The Basics. Cureus 2021; 13:e17636. [PMID: 34646684 PMCID: PMC8485701 DOI: 10.7759/cureus.17636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2021] [Indexed: 12/28/2022] Open
Abstract
As machine learning (ML) and precision medicine become more readily available and used in practice, emergency physicians must understand the potential advantages and limitations of the technology. This narrative review focuses on the key components of machine learning, artificial intelligence, and precision medicine in emergency medicine (EM). Based on the content expertise, we identified articles from EM literature. The authors provided a narrative summary of each piece of literature. Next, the authors provided an introduction of the concepts of ML, artificial intelligence as an extension of ML, and precision medicine. This was followed by concrete examples of their applications in practice and research. Subsequently, we shared our thoughts on how to consume the existing research in these subjects and conduct high-quality research for academic emergency medicine. We foresee that the EM community will continue to adapt machine learning, artificial intelligence, and precision medicine in research and practice. We described several key components using our expertise.
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Affiliation(s)
- Sangil Lee
- Emergency Medicine, University of Iowa Carver College of Medicine, Iowa City, USA
| | - Samuel H Lam
- Emergency Medicine, Sutter Medical Center, Sacramento, USA
| | | | | | - Catherine A Staton
- Division of Emergency Medicine, Department of Surgery, Duke University School of Medicine, Durham, USA
| | - Richard Taylor
- Department of Emergency Medicine, Yale University, New Haven, USA
| | - Alexander T Limkakeng
- Division of Emergency Medicine, Department of Surgery, Duke University School of Medicine, Durham, USA
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Benameur N, Mahmoudi R, Zaid S, Arous Y, Hmida B, Migaou A, Bedoui MH. Lack of AI-based method for pneumocystis pneumonia classification in radiological diagnosis of SARS-CoV-2. Clin Imaging 2021; 79:94-95. [PMID: 33895561 PMCID: PMC8059283 DOI: 10.1016/j.clinimag.2021.03.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Narjes Benameur
- University of Tunis El Manar, Higher Institute of Medical Technologies of Tunis, Laboratory of Biophysics and Medical Technology, Tunis, Tunisia.
| | - Ramzi Mahmoudi
- Université de Monastir, Laboratoire Technologie Imagerie Médicale, LTIM-LR12ES06, Faculté de Médecine de Monastir, 5019 Monastir, Tunisia; Université Paris-Est, Laboratoire d'Informatique Gaspard-Monge, Unité Mixte CNRS-UMLV-ESIEE UMR8049, ESIEE Paris Cité Descartes, BP99, 93162 Noisy Le Grand, France
| | - Soraya Zaid
- Service Imagerie, Centre Hospitalier Escartons, Briancon, France
| | - Younes Arous
- Radiology Service, Military Hospital of Instruction of Tunis, Tunisia
| | - Badii Hmida
- Radiologie Service, UR12SP40, CHU Fattouma Bourguiba, 5019 Monastir, Tunisia
| | - Asma Migaou
- AHU Service de Pneumo-Allergologie, CHU Fattouma Bourguiba, 5019 Monastir, Tunisia
| | - Mohamed Hedi Bedoui
- Université de Monastir, Laboratoire Technologie Imagerie Médicale, LTIM-LR12ES06, Faculté de Médecine de Monastir, 5019 Monastir, Tunisia
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