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Dubey S, Verma DK, Kumar M. Real-time infectious disease endurance indicator system for scientific decisions using machine learning and rapid data processing. PeerJ Comput Sci 2024; 10:e2062. [PMID: 39145255 PMCID: PMC11323025 DOI: 10.7717/peerj-cs.2062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/25/2024] [Indexed: 08/16/2024]
Abstract
The SARS-CoV-2 virus, which induces an acute respiratory illness commonly referred to as COVID-19, had been designated as a pandemic by the World Health Organization due to its highly infectious nature and the associated public health risks it poses globally. Identifying the critical factors for predicting mortality is essential for improving patient therapy. Unlike other data types, such as computed tomography scans, x-radiation, and ultrasounds, basic blood test results are widely accessible and can aid in predicting mortality. The present research advocates the utilization of machine learning (ML) methodologies for predicting the likelihood of infectious disease like COVID-19 mortality by leveraging blood test data. Age, LDH (lactate dehydrogenase), lymphocytes, neutrophils, and hs-CRP (high-sensitivity C-reactive protein) are five extremely potent characteristics that, when combined, can accurately predict mortality in 96% of cases. By combining XGBoost feature importance with neural network classification, the optimal approach can predict mortality with exceptional accuracy from infectious disease, along with achieving a precision rate of 90% up to 16 days before the event. The studies suggested model's excellent predictive performance and practicality were confirmed through testing with three instances that depended on the days to the outcome. By carefully analyzing and identifying patterns in these significant biomarkers insightful information has been obtained for simple application. This study offers potential remedies that could accelerate decision-making for targeted medical treatments within healthcare systems, utilizing a timely, accurate, and reliable method.
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Affiliation(s)
- Shivendra Dubey
- Computer Science and Engineering, Jaypee University of Engineering and Technology, Guna, Madhya Pradesh, India
| | - Dinesh Kumar Verma
- Computer Science and Engineering, Jaypee University of Engineering and Technology, Guna, Madhya Pradesh, India
| | - Mahesh Kumar
- Computer Science and Engineering, Jaypee University of Engineering and Technology, Guna, Madhya Pradesh, India
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Nguyen A, Zhao H, Myagmarsuren D, Srinivasan S, Wu D, Chen J, Piszczek G, Schuck P. Modulation of biophysical properties of nucleocapsid protein in the mutant spectrum of SARS-CoV-2. eLife 2024; 13:RP94836. [PMID: 38941236 PMCID: PMC11213569 DOI: 10.7554/elife.94836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024] Open
Abstract
Genetic diversity is a hallmark of RNA viruses and the basis for their evolutionary success. Taking advantage of the uniquely large genomic database of SARS-CoV-2, we examine the impact of mutations across the spectrum of viable amino acid sequences on the biophysical phenotypes of the highly expressed and multifunctional nucleocapsid protein. We find variation in the physicochemical parameters of its extended intrinsically disordered regions (IDRs) sufficient to allow local plasticity, but also observe functional constraints that similarly occur in related coronaviruses. In biophysical experiments with several N-protein species carrying mutations associated with major variants, we find that point mutations in the IDRs can have nonlocal impact and modulate thermodynamic stability, secondary structure, protein oligomeric state, particle formation, and liquid-liquid phase separation. In the Omicron variant, distant mutations in different IDRs have compensatory effects in shifting a delicate balance of interactions controlling protein assembly properties, and include the creation of a new protein-protein interaction interface in the N-terminal IDR through the defining P13L mutation. A picture emerges where genetic diversity is accompanied by significant variation in biophysical characteristics of functional N-protein species, in particular in the IDRs.
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Affiliation(s)
- Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Dulguun Myagmarsuren
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Sanjana Srinivasan
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
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Qayyum A, Tahir A, Butt MA, Luke A, Abbas HT, Qadir J, Arshad K, Assaleh K, Imran MA, Abbasi QH. Dental caries detection using a semi-supervised learning approach. Sci Rep 2023; 13:749. [PMID: 36639724 PMCID: PMC9839770 DOI: 10.1038/s41598-023-27808-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Early diagnosis of dental caries progression can prevent invasive treatment and enable preventive treatment. In this regard, dental radiography is a widely used tool to capture dental visuals that are used for the detection and diagnosis of caries. Different deep learning (DL) techniques have been used to automatically analyse dental images for caries detection. However, most of these techniques require large-scale annotated data to train DL models. On the other hand, in clinical settings, such medical images are scarcely available and annotations are costly and time-consuming. To this end, we present an efficient self-training-based method for caries detection and segmentation that leverages a small set of labelled images for training the teacher model and a large collection of unlabelled images for training the student model. We also propose to use centroid cropped images of the caries region and different augmentation techniques for the training of self-supervised models that provide computational and performance gains as compared to fully supervised learning and standard self-supervised learning methods. We present a fully labelled dental radiographic dataset of 141 images that are used for the evaluation of baseline and proposed models. Our proposed self-supervised learning strategy has provided performance improvement of approximately 6% and 3% in terms of average pixel accuracy and mean intersection over union, respectively as compared to standard self-supervised learning. Data and code will be made available to facilitate future research.
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Affiliation(s)
- Adnan Qayyum
- James Watt School of Engineering, University of Glasgow, Glasgow, UK
- Information Technology University of the Punjab, Lahore, Pakistan
| | - Ahsen Tahir
- James Watt School of Engineering, University of Glasgow, Glasgow, UK
- Department of Electrical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | | | - Alexander Luke
- Department of Clinical Sciences, College of Dentistry, Ajman University, Ajman, UAE
- Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, UAE
| | - Hasan Tahir Abbas
- James Watt School of Engineering, University of Glasgow, Glasgow, UK
| | - Junaid Qadir
- Department of Computer Science and Engineering, College of Engineering, Qatar University, Doha, Qatar
| | - Kamran Arshad
- Artificial Intelligence Research Center (AIRC), College of Engineering and Information Technology, Ajman University, Ajman, UAE
| | - Khaled Assaleh
- Artificial Intelligence Research Center (AIRC), College of Engineering and Information Technology, Ajman University, Ajman, UAE
| | - Muhammad Ali Imran
- James Watt School of Engineering, University of Glasgow, Glasgow, UK
- Artificial Intelligence Research Center (AIRC), College of Engineering and Information Technology, Ajman University, Ajman, UAE
| | - Qammer H Abbasi
- James Watt School of Engineering, University of Glasgow, Glasgow, UK.
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