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Jin Y, Wang J, Tang R, Jiang Y, Xi D. Nucleic Acid-Based Biological Nanopore Sensing Strategies for Tumor Marker Detection. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:21327-21340. [PMID: 39356337 DOI: 10.1021/acs.langmuir.4c02804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2024]
Abstract
Cancer, which is characterized by high mortality rates, poses a significant threat to global human health. Early diagnosis is of paramount importance in managing cancer, and tumor markers have emerged as crucial indicators for achieving this goal. The advent of precision medicine has further emphasized the need for the effective detection of these markers. However, traditional detection methods are hampered by numerous limitations. In recent years, nanopore technology has emerged as a promising alternative, due to its unique physical and chemical properties, which facilitate rapid, label-free, and amplification-free detection. This Review focuses on the direct detection of tumor markers through nucleic acid analysis and indirect detection mediated by nucleic acids and facilitated by biological nanopores. Furthermore, it also discusses the challenges and prospects of applying biological nanopore sensing technology in early cancer diagnosis, underscoring its potential to revolutionize tumor marker detection.
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Affiliation(s)
- Yameng Jin
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Shandong 276005, China
| | - Junxiao Wang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Shandong 276005, China
| | - Ruping Tang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Shandong 276005, China
| | - Yao Jiang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Science, Linyi University, Shandong 276005, China
| | - Dongmei Xi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Science, Linyi University, Shandong 276005, China
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Zhang Y, Hu C, Liu R, He S, Yang J, Yao W, Li Y, Guo X. Protein nanopore-based sensors for public health analyte detection. J Mater Chem B 2024; 12:9845-9862. [PMID: 39258387 DOI: 10.1039/d4tb01149j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
High-throughput and label-free protein nanopore-based sensors are extensively used in DNA sequencing, single-protein analysis, molecular sensing and chemical catalysis with single channel recording. These technologies show great potential for identifying various harmful substances linked to public health by addressing the limitations of current portability and the speed of existing techniques. In this review, we provide an overview of the fundamental principles of nanopore sensing, with a focus on chemical modification and genetic engineering strategies aimed at enhancing the detection sensitivity and identification accuracy of protein nanopores. The engineered protein nanopores enable direct sensing, while the introduction of aptamers and substrates enables indirect sensing, translating the physical structure and chemical properties of analytes into readable signals. These scientific discoveries and engineering efforts have provided new prospects for detecting and monitoring trace hazardous substances.
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Affiliation(s)
- Yanhua Zhang
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
| | - Chan Hu
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
| | - Ronghui Liu
- School of Microelectronics, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China.
| | - Shujun He
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
| | - Jie Yang
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
| | - Wen Yao
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
| | - Yi Li
- School of Microelectronics, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China.
| | - Xinrong Guo
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
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Wang R, Zhang Y, Ma QDY, Wu L. Recent advances of small molecule detection in nanopore sensing. Talanta 2024; 277:126323. [PMID: 38810384 DOI: 10.1016/j.talanta.2024.126323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/04/2024] [Accepted: 05/23/2024] [Indexed: 05/31/2024]
Abstract
Due to its advantages of label-free and highly sensitive, the resistive pulse sensing with a nanopore has recently become even more potent for the discrimination of analytes in single molecule level. Generally, a transient interruption of ion current originated from the captured molecule passing through a nanopore will provide the rich information on the structure, charge and translocation dynamics of the analytes. Therefore, nanopore sensors have been widely used in the fields of DNA sequencing, protein recognition, and the portable detection of varied macromolecules and particles. However, the conventional nanopore devices are still lack of sufficient selectivity and sensitivity to distinguish more metabolic molecules involving ATP, glucose, amino acids and small molecular drugs because it is hard to receive a large number of identifiable signals with the fabricated pores comparable in size to small molecules for nanopore sensing. For all this, a series of innovative strategies developed in the past decades have been summarized in this review, including host-guest recognition, engineering alteration of protein channel, the introduction of nucleic acid aptamers and various delivery carriers integrating signal amplification sections based on the biological and solid nanopore platforms, to achieve the high resolution for the small molecules sensing in micro-nano environment. These works have greatly enhanced the powerful sensing capabilities and extended the potential application of nanopore sensors.
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Affiliation(s)
- Runyu Wang
- College of Science, Nanjing University of Posts and Telecommunications, Nanjing, 210046, China
| | - Yinuo Zhang
- College of Integrated Circuit Science and Engineering, Nanjing University of Posts and Telecommunications, Nanjing, 210046, China
| | - Qianli D Y Ma
- College of Integrated Circuit Science and Engineering, Nanjing University of Posts and Telecommunications, Nanjing, 210046, China.
| | - Lingzhi Wu
- College of Science, Nanjing University of Posts and Telecommunications, Nanjing, 210046, China.
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Li Y, Zhang D, Zeng X, Liu C, Wu Y, Fu C. Advances in Aptamer-Based Biosensors for the Detection of Foodborne Mycotoxins. Molecules 2024; 29:3974. [PMID: 39203052 PMCID: PMC11356850 DOI: 10.3390/molecules29163974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 08/14/2024] [Accepted: 08/16/2024] [Indexed: 09/03/2024] Open
Abstract
Foodborne mycotoxins (FBMTs) are toxins produced by food itself or during processing and transportation that pose an enormous threat to public health security. However, traditional instrumental and chemical methods for detecting toxins have shortcomings, such as high operational difficulty, time consumption, and high cost, that limit their large-scale applications. In recent years, aptamer-based biosensors have become a new tool for food safety risk assessment and monitoring due to their high affinity, good specificity, and fast response. In this review, we focus on the progress of single-mode and dual-mode aptasensors in basic research and device applications over recent years. Furthermore, we also point out some problems in the current detection strategies, with the aim of stimulating future toxin detection systems for a transition toward ease of operation and rapid detection.
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Affiliation(s)
- Yangyang Li
- Chongqing Key Laboratory for New Chemical Materials of Shale Gas, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing 408100, China
| | - Dan Zhang
- School of Cable Engineering, Henan Institute of Technology, Xinxiang 453003, China
| | - Xiaoyuan Zeng
- Chongqing Key Laboratory for New Chemical Materials of Shale Gas, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing 408100, China
| | - Cheng Liu
- Chongqing Key Laboratory for New Chemical Materials of Shale Gas, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing 408100, China
| | - Yan Wu
- Chongqing Key Laboratory for New Chemical Materials of Shale Gas, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing 408100, China
| | - Cuicui Fu
- Chongqing Key Laboratory for New Chemical Materials of Shale Gas, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing 408100, China
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Zheng H, Munusamy S, Arora P, Jahani R, Guan X. A highly sensitive nanopore platform for measuring RNase A activity. Talanta 2024; 276:126276. [PMID: 38796995 PMCID: PMC11187776 DOI: 10.1016/j.talanta.2024.126276] [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: 03/20/2024] [Revised: 05/11/2024] [Accepted: 05/16/2024] [Indexed: 05/29/2024]
Abstract
Ribonuclease A (RNase A) plays significant roles in several physiological and pathological conditions and can be used as a valuable diagnostic biomarker for human diseases such as myocardial infarction and cancer. Hence, it is of great importance to develop a rapid and cost-effective method for the highly sensitive detection of RNase A. The significance of RNase A assay is further enhanced by the growing attention from the biotechnology and pharmaceutical industries to develop RNA-based vaccines and drugs in large part as a result of the successful development of mRNA vaccines in the COVID-19 pandemic. Herein, we report a label-free method for the detection of RNase A by monitoring its proteolytic cleavage of an RNA substrate in a nanopore. The method is ultra-sensitive with the limit of detection reaching as low as 30 fg per milliliter. Furthermore, sensor selectivity and the effects of temperature, incubation time, metal ion, salt concentration on sensor sensitivity were also investigated.
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Affiliation(s)
- Haiyan Zheng
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA
| | | | - Pearl Arora
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Rana Jahani
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA
| | - Xiyun Guan
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA.
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Smith A, Larsen TRB, Zimmerman HK, Virolainen SJ, Meyer JJ, Keranen Burden LM, Burden DL. Design and Construction of a Multi-Tiered Minimal Actin Cortex for Structural Support in Lipid Bilayer Applications. ACS APPLIED BIO MATERIALS 2024; 7:1936-1946. [PMID: 38427377 PMCID: PMC10951949 DOI: 10.1021/acsabm.3c01267] [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: 12/22/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
Artificial lipid bilayers have revolutionized biochemical and biophysical research by providing a versatile interface to study aspects of cell membranes and membrane-bound processes in a controlled environment. Artificial bilayers also play a central role in numerous biosensing applications, form the foundational interface for liposomal drug delivery, and provide a vital structure for the development of synthetic cells. But unlike the envelope in many living cells, artificial bilayers can be mechanically fragile. Here, we develop prototype scaffolds for artificial bilayers made from multiple chemically linked tiers of actin filaments that can be bonded to lipid headgroups. We call the interlinked and layered assembly a multiple minimal actin cortex (multi-MAC). Construction of multi-MACs has the potential to significantly increase the bilayer's resistance to applied stress while retaining many desirable physical and chemical properties that are characteristic of lipid bilayers. Furthermore, the linking chemistry of multi-MACs is generalizable and can be applied almost anywhere lipid bilayers are important. This work describes a filament-by-filament approach to multi-MAC assembly that produces distinct 2D and 3D architectures. The nature of the structure depends on a combination of the underlying chemical conditions. Using fluorescence imaging techniques in model planar bilayers, we explore how multi-MACs vary with electrostatic charge, assembly time, ionic strength, and type of chemical linker. We also assess how the presence of a multi-MAC alters the underlying lateral diffusion of lipids and investigate the ability of multi-MACs to withstand exposure to shear stress.
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Affiliation(s)
- Amanda
J. Smith
- Chemistry Department, Wheaton College, 501 College Ave., Wheaton, Illinois 60187, United States
| | - Theodore R. B. Larsen
- Chemistry Department, Wheaton College, 501 College Ave., Wheaton, Illinois 60187, United States
| | - Harmony K. Zimmerman
- Chemistry Department, Wheaton College, 501 College Ave., Wheaton, Illinois 60187, United States
| | - Samuel J. Virolainen
- Chemistry Department, Wheaton College, 501 College Ave., Wheaton, Illinois 60187, United States
| | - Joshua J. Meyer
- Chemistry Department, Wheaton College, 501 College Ave., Wheaton, Illinois 60187, United States
| | - Lisa M. Keranen Burden
- Chemistry Department, Wheaton College, 501 College Ave., Wheaton, Illinois 60187, United States
| | - Daniel L. Burden
- Chemistry Department, Wheaton College, 501 College Ave., Wheaton, Illinois 60187, United States
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Zhang X, Su Z, Zhao Y, Wu D, Wu Y, Li G. Recent advances of nanopore technique in single cell analysis. Analyst 2024; 149:1350-1363. [PMID: 38312056 DOI: 10.1039/d3an01973j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Single cells and their dynamic behavior are closely related to biological research. Monitoring their dynamic behavior is of great significance for disease prevention. How to achieve rapid and non-destructive monitoring of single cells is a major issue that needs to be solved urgently. As an emerging technology, nanopores have been proven to enable non-destructive and label-free detection of single cells. The structural properties of nanopores enable a high degree of sensitivity and accuracy during analysis. In this article, we summarize and classify the different types of solid-state nanopores that can be used for single-cell detection and illustrate their specific applications depending on the size of the analyte. In addition, their research progress in material transport and microenvironment monitoring is also highlighted. Finally, a brief summary of existing research challenges and future trends in nanopore single-cell analysis is tentatively provided.
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Affiliation(s)
- Xue Zhang
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Zhuoqun Su
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Yan Zhao
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Di Wu
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - Yongning Wu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Guoliang Li
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
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Yang Y, Shi Y, Zhang X, Li G. MNAzyme catalyzed signal amplification-mediated lateral flow biosensor for portable and sensitive detection of mycotoxin in food samples. Anal Bioanal Chem 2024; 416:1057-1067. [PMID: 38117324 DOI: 10.1007/s00216-023-05096-6] [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: 10/15/2023] [Revised: 12/05/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
Here, an enzyme-free lateral flow aptasensor was designed by target-induced strand-displacement effect and followed by the activation of multi-component nucleic acid enzyme (MNAzyme)-mediated cleavage to enable rapid and portable ochratoxin A (OTA) detection. The substrate was prepared as an oligonucleotide strand modified with magnetic beads (MB) and human chorionic gonadotropin (hCG). The interaction of OTA with the aptamer induces the release of blocking DNA, which hybridized with three separated subunits of DNA, forming a sequence-specific MNAzyme catalytic core. This core subsequently initiated an enzyme-free MNAzyme cleavage reaction in the presence of the Mg2+ cofactor, cleaving a special substrate and releasing both the incomplete MNAzyme catalytic core and hCG-DNA probe. The incomplete MNAzyme catalytic core was then recognized by substrates once again, triggering a cascade recycling cleavage and resulting in the generation of a larger number of hCG-DNA probes. After magnetic enrichment, the free hCG-DNA probes flow through the pregnancy test strip (PTS) to the T line, generating a colorimetric readout that unequivocally confirms the presence of the target OTA. This work leverages the efficient enzyme-free cleavage amplification of MNAzyme and the PTS-based portable detection device, presenting a biosensing strategy with significant potential for sensitive and portable OTA detection. This method exhibited remarkable sensitivity and selectivity for OTA detection, boasting a detection limit of 5 nM. The present study successfully demonstrated the practical application of this method on real samples, offering a viable alternative for rapid and portable detection of mycotoxins.
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Affiliation(s)
- Yan Yang
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiao Tong University, Lanzhou, 730070, China
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Yiheng Shi
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Xianlong Zhang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Guoliang Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China.
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da Silva AAR, da Silva Júnior JJ, Cavalcanti MIDS, Machado DC, Medeiros PL, Rodrigues CG. Alphatoxin Nanopore Detection of Aflatoxin, Ochratoxin and Fumonisin in Aqueous Solution. Toxins (Basel) 2023; 15:toxins15030183. [PMID: 36977074 PMCID: PMC10058818 DOI: 10.3390/toxins15030183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/23/2023] [Accepted: 02/26/2023] [Indexed: 03/08/2023] Open
Abstract
Mycotoxins are toxic and carcinogenic metabolites produced by groups of filamentous fungi that colonize food crops. Aflatoxin B1 (AFB1), ochratoxin A (OTA) and fumonisin B1 (FB1) are among the most relevant agricultural mycotoxins, as they can induce various toxic processes in humans and animals. To detect AFB1, OTA and FB1 in the most varied matrices, chromatographic and immunological methods are primarily used; however, these techniques are time-consuming and expensive. In this study, we demonstrate that unitary alphatoxin nanopore can be used to detect and differentiate these mycotoxins in aqueous solution. The presence of AFB1, OTA or FB1 inside the nanopore induces reversible blockage of the ionic current flowing through the nanopore, with distinct characteristics of blockage that are unique to each of the three toxins. The process of discrimination is based on the residual current ratio calculation and analysis of the residence time of each mycotoxin inside the unitary nanopore. Using a single alphatoxin nanopore, the mycotoxins could be detected at the nanomolar level, indicating that alphatoxin nanopore is a promising molecular tool for discriminatory analysis of mycotoxins in aqueous solution.
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Affiliation(s)
- Artur Alves Rodrigues da Silva
- Education and Health Center, Federal University of Campina Grande, Rua Aprígio Veloso, 882, Universitário, Campina Grande 58429-900, Brazil
- Postgraduate Program in Therapeutic Innovation, Federal University of Pernambuco, Avenida Professor Moraes Rego, s/n, Cidade Universitária, Recife 50670-901, Brazil
| | - Janilson José da Silva Júnior
- Department of Biophysics and Radiobiology, Federal University of Pernambuco, Avenida Professor Moraes Rego, s/n, Cidade Universitária, Recife 50670-901, Brazil
| | - Maria Isabel dos Santos Cavalcanti
- Department of Biophysics and Radiobiology, Federal University of Pernambuco, Avenida Professor Moraes Rego, s/n, Cidade Universitária, Recife 50670-901, Brazil
| | - Dijanah Cota Machado
- Department of Biophysics and Radiobiology, Federal University of Pernambuco, Avenida Professor Moraes Rego, s/n, Cidade Universitária, Recife 50670-901, Brazil
| | - Paloma Lys Medeiros
- Department of Biophysics and Radiobiology, Federal University of Pernambuco, Avenida Professor Moraes Rego, s/n, Cidade Universitária, Recife 50670-901, Brazil
| | - Claudio Gabriel Rodrigues
- Postgraduate Program in Therapeutic Innovation, Federal University of Pernambuco, Avenida Professor Moraes Rego, s/n, Cidade Universitária, Recife 50670-901, Brazil
- Department of Biophysics and Radiobiology, Federal University of Pernambuco, Avenida Professor Moraes Rego, s/n, Cidade Universitária, Recife 50670-901, Brazil
- Correspondence: ; Tel.: +55-81-2126-8535
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Recent advances on CRISPR/Cas system-enabled portable detection devices for on-site agri-food safety assay. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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