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Ganjalizadeh V, Meena GG, Stott MA, Hawkins AR, Schmidt H. Machine learning at the edge for AI-enabled multiplexed pathogen detection. Sci Rep 2023; 13:4744. [PMID: 36959357 PMCID: PMC10034896 DOI: 10.1038/s41598-023-31694-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 03/15/2023] [Indexed: 03/25/2023] Open
Abstract
Multiplexed detection of biomarkers in real-time is crucial for sensitive and accurate diagnosis at the point of use. This scenario poses tremendous challenges for detection and identification of signals of varying shape and quality at the edge of the signal-to-noise limit. Here, we demonstrate a robust target identification scheme that utilizes a Deep Neural Network (DNN) for multiplex detection of single particles and molecular biomarkers. The model combines fast wavelet particle detection with Short-Time Fourier Transform analysis, followed by DNN identification on an AI-specific edge device (Google Coral Dev board). The approach is validated using multi-spot optical excitation of Klebsiella Pneumoniae bacterial nucleic acids flowing through an optofluidic waveguide chip that produces fluorescence signals of varying amplitude, duration, and quality. Amplification-free 3× multiplexing in real-time is demonstrated with excellent specificity, sensitivity, and a classification accuracy of 99.8%. These results show that a minimalistic DNN design optimized for mobile devices provides a robust framework for accurate pathogen detection using compact, low-cost diagnostic devices.
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Affiliation(s)
- Vahid Ganjalizadeh
- School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Gopikrishnan G Meena
- School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Matthew A Stott
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT, 84602, USA
| | - Aaron R Hawkins
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT, 84602, USA
| | - Holger Schmidt
- School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA.
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2
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Tevlek A, Kecili S, Ozcelik OS, Kulah H, Tekin HC. Spheroid Engineering in Microfluidic Devices. ACS OMEGA 2023; 8:3630-3649. [PMID: 36743071 PMCID: PMC9893254 DOI: 10.1021/acsomega.2c06052] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/12/2022] [Indexed: 05/27/2023]
Abstract
Two-dimensional (2D) cell culture techniques are commonly employed to investigate biophysical and biochemical cellular responses. However, these culture methods, having monolayer cells, lack cell-cell and cell-extracellular matrix interactions, mimicking the cell microenvironment and multicellular organization. Three-dimensional (3D) cell culture methods enable equal transportation of nutrients, gas, and growth factors among cells and their microenvironment. Therefore, 3D cultures show similar cell proliferation, apoptosis, and differentiation properties to in vivo. A spheroid is defined as self-assembled 3D cell aggregates, and it closely mimics a cell microenvironment in vitro thanks to cell-cell/matrix interactions, which enables its use in several important applications in medical and clinical research. To fabricate a spheroid, conventional methods such as liquid overlay, hanging drop, and so forth are available. However, these labor-intensive methods result in low-throughput fabrication and uncontrollable spheroid sizes. On the other hand, microfluidic methods enable inexpensive and rapid fabrication of spheroids with high precision. Furthermore, fabricated spheroids can also be cultured in microfluidic devices for controllable cell perfusion, simulation of fluid shear effects, and mimicking of the microenvironment-like in vivo conditions. This review focuses on recent microfluidic spheroid fabrication techniques and also organ-on-a-chip applications of spheroids, which are used in different disease modeling and drug development studies.
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Affiliation(s)
- Atakan Tevlek
- METU
MEMS Research and Application Center, Ankara 06800, Turkey
| | - Seren Kecili
- The
Department of Bioengineering, Izmir Institute
of Technology, Urla, Izmir 35430, Turkey
| | - Ozge S. Ozcelik
- The
Department of Bioengineering, Izmir Institute
of Technology, Urla, Izmir 35430, Turkey
| | - Haluk Kulah
- METU
MEMS Research and Application Center, Ankara 06800, Turkey
- The
Department of Electrical and Electronics Engineering, Middle East Technical University, Ankara 06800, Turkey
| | - H. Cumhur Tekin
- METU
MEMS Research and Application Center, Ankara 06800, Turkey
- The
Department of Bioengineering, Izmir Institute
of Technology, Urla, Izmir 35430, Turkey
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Gil Rosa B, Akingbade OE, Guo X, Gonzalez-Macia L, Crone MA, Cameron LP, Freemont P, Choy KL, Güder F, Yeatman E, Sharp DJ, Li B. Multiplexed immunosensors for point-of-care diagnostic applications. Biosens Bioelectron 2022; 203:114050. [DOI: 10.1016/j.bios.2022.114050] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/22/2021] [Accepted: 01/25/2022] [Indexed: 12/14/2022]
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Tang M, Chen J, Lei J, Ai Z, Liu F, Hong SL, Liu K. Precise and convenient size barcode on microfluidic chip for multiplex biomarker detection. Analyst 2021; 146:5892-5897. [PMID: 34494037 DOI: 10.1039/d1an01265g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The existing multiplex biomarker detection methods are limited by the high demand for coding material and expensive detection equipment. This paper proposes a convenient and precise coding method based on a wedge-shaped microfluidic chip, which can be further applied in multiplex biomarker detection. The proposed microfluidic chip has a microchannel with continuously varying height, which can naturally separate and code microparticles of different sizes. Our data indicate that this method can be applied to code more than 5 or 7 kinds of microparticles, even when their size discrepancies are smaller than 1 μm. Based on these, multiplex biomarker detection can be implemented by using microparticles of different sizes, hence each kind of microparticle that coats one kind of antibody represents the species of targets. This method is simple and easy to operate, with no clogging or sophisticated coding design, showing its significant potential in the area of point-of-care tests (POCT).
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Affiliation(s)
- Man Tang
- School of Electronic and Electrical Engineering, Wuhan Textile University, Wuhan 430200, People's Republic of China. .,Hubei Engineering and Technology Research Centre for Functional Fibre Fabrication and Testing, Wuhan Textile University, Wuhan 430200, People's Republic of China.,Hubei Province Engineering Research Centre for Intelligent Micro-nano Medical Equipment and Key Technologies, Wuhan 30200, People's Republic of China
| | - Jinyao Chen
- School of Electronic and Electrical Engineering, Wuhan Textile University, Wuhan 430200, People's Republic of China.
| | - Jia Lei
- School of Electronic and Electrical Engineering, Wuhan Textile University, Wuhan 430200, People's Republic of China.
| | - Zhao Ai
- School of Electronic and Electrical Engineering, Wuhan Textile University, Wuhan 430200, People's Republic of China. .,Hubei Engineering and Technology Research Centre for Functional Fibre Fabrication and Testing, Wuhan Textile University, Wuhan 430200, People's Republic of China.,Hubei Province Engineering Research Centre for Intelligent Micro-nano Medical Equipment and Key Technologies, Wuhan 30200, People's Republic of China
| | - Feng Liu
- School of Electronic and Electrical Engineering, Wuhan Textile University, Wuhan 430200, People's Republic of China. .,Hubei Engineering and Technology Research Centre for Functional Fibre Fabrication and Testing, Wuhan Textile University, Wuhan 430200, People's Republic of China.,Hubei Province Engineering Research Centre for Intelligent Micro-nano Medical Equipment and Key Technologies, Wuhan 30200, People's Republic of China
| | - Shao-Li Hong
- School of Electronic and Electrical Engineering, Wuhan Textile University, Wuhan 430200, People's Republic of China. .,Hubei Engineering and Technology Research Centre for Functional Fibre Fabrication and Testing, Wuhan Textile University, Wuhan 430200, People's Republic of China.,Hubei Province Engineering Research Centre for Intelligent Micro-nano Medical Equipment and Key Technologies, Wuhan 30200, People's Republic of China
| | - Kan Liu
- School of Electronic and Electrical Engineering, Wuhan Textile University, Wuhan 430200, People's Republic of China. .,Hubei Engineering and Technology Research Centre for Functional Fibre Fabrication and Testing, Wuhan Textile University, Wuhan 430200, People's Republic of China.,Hubei Province Engineering Research Centre for Intelligent Micro-nano Medical Equipment and Key Technologies, Wuhan 30200, People's Republic of China
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5
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Zhu S, Zhang X, Zhou Z, Han Y, Xiang N, Ni Z. Microfluidic impedance cytometry for single-cell sensing: Review on electrode configurations. Talanta 2021; 233:122571. [PMID: 34215067 DOI: 10.1016/j.talanta.2021.122571] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
Single-cell analysis has gained considerable attention for disease diagnosis, drug screening, and differentiation monitoring. Compared to the well-established flow cytometry, which uses fluorescent-labeled antibodies, microfluidic impedance cytometry (MIC) offers a simple, label-free, and noninvasive method for counting, classifying, and monitoring cells. Superior features including a small footprint, low reagent consumption, and ease of use have also been reported. The MIC device detects changes in the impedance signal caused by cells passing through the sensing/electric field zone, which can extract information regarding the size, shape, and dielectric properties of these cells. According to recent studies, electrode configuration has a remarkable effect on detection accuracy, sensitivity, and throughput. With the improvement in microfabrication technology, various electrode configurations have been reported for improving detection accuracy and throughput. However, the various electrode configurations of MIC devices have not been reviewed. In this review, the theoretical background of the impedance technique for single-cell analysis is introduced. Then, two-dimensional, three-dimensional, and liquid electrode configurations are discussed separately; their sensing mechanisms, fabrication processes, advantages, disadvantages, and applications are also described in detail. Finally, the current limitations and future perspectives of these electrode configurations are summarized. The main aim of this review is to offer a guide for researchers on the ongoing advancement in electrode configuration designs.
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Affiliation(s)
- Shu Zhu
- School of Mechanical Engineering, And Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Xiaozhe Zhang
- School of Mechanical Engineering, And Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Zheng Zhou
- School of Mechanical Engineering, And Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Yu Han
- School of Mechanical Engineering, And Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Nan Xiang
- School of Mechanical Engineering, And Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China.
| | - Zhonghua Ni
- School of Mechanical Engineering, And Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China.
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Wang N, Liu R, Asmare N, Chu CH, Civelekoglu O, Sarioglu AF. Closed-loop feedback control of microfluidic cell manipulation via deep-learning integrated sensor networks. LAB ON A CHIP 2021; 21:1916-1928. [PMID: 34008660 DOI: 10.1039/d1lc00076d] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Microfluidic technologies have long enabled the manipulation of flow-driven cells en masse under a variety of force fields with the goal of characterizing them or discriminating the pathogenic ones. On the other hand, a microfluidic platform is typically designed to function under optimized conditions, which rarely account for specimen heterogeneity and internal/external perturbations. In this work, we demonstrate a proof-of-principle adaptive microfluidic system that consists of an integrated network of distributed electrical sensors for on-chip tracking of cells and closed-loop feedback control that modulates chip parameters based on the sensor data. In our system, cell flow speed is measured at multiple locations throughout the device, the data is interpreted in real-time via deep learning-based algorithms, and a proportional-integral feedback controller updates a programmable pressure pump to maintain a desired cell flow speed. We validate the adaptive microfluidic system with both static and dynamic targets and also observe a fast convergence of the system under continuous external perturbations. With an ability to sustain optimal processing conditions in unsupervised settings, adaptive microfluidic systems would be less prone to artifacts and could eventually serve as reliable standardized biomedical tests at the point of care.
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Affiliation(s)
- Ningquan Wang
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Ruxiu Liu
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Norh Asmare
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Chia-Heng Chu
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Ozgun Civelekoglu
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - A Fatih Sarioglu
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA. and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA and Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, GA 30332, USA
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