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Impact of Training Data, Ground Truth and Shape Variability in the Deep Learning-Based Semantic Segmentation of HeLa Cells Observed with Electron Microscopy. J Imaging 2023; 9:jimaging9030059. [PMID: 36976110 PMCID: PMC10058680 DOI: 10.3390/jimaging9030059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
This paper investigates the impact of the amount of training data and the shape variability on the segmentation provided by the deep learning architecture U-Net. Further, the correctness of ground truth (GT) was also evaluated. The input data consisted of a three-dimensional set of images of HeLa cells observed with an electron microscope with dimensions 8192×8192×517. From there, a smaller region of interest (ROI) of 2000×2000×300 was cropped and manually delineated to obtain the ground truth necessary for a quantitative evaluation. A qualitative evaluation was performed on the 8192×8192 slices due to the lack of ground truth. Pairs of patches of data and labels for the classes nucleus, nuclear envelope, cell and background were generated to train U-Net architectures from scratch. Several training strategies were followed, and the results were compared against a traditional image processing algorithm. The correctness of GT, that is, the inclusion of one or more nuclei within the region of interest was also evaluated. The impact of the extent of training data was evaluated by comparing results from 36,000 pairs of data and label patches extracted from the odd slices in the central region, to 135,000 patches obtained from every other slice in the set. Then, 135,000 patches from several cells from the 8192×8192 slices were generated automatically using the image processing algorithm. Finally, the two sets of 135,000 pairs were combined to train once more with 270,000 pairs. As would be expected, the accuracy and Jaccard similarity index improved as the number of pairs increased for the ROI. This was also observed qualitatively for the 8192×8192 slices. When the 8192×8192 slices were segmented with U-Nets trained with 135,000 pairs, the architecture trained with automatically generated pairs provided better results than the architecture trained with the pairs from the manually segmented ground truths. This suggests that the pairs that were extracted automatically from many cells provided a better representation of the four classes of the various cells in the 8192×8192 slice than those pairs that were manually segmented from a single cell. Finally, the two sets of 135,000 pairs were combined, and the U-Net trained with these provided the best results.
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Allawadhi P, Khurana A, Allwadhi S, Navik US, Joshi K, Banothu AK, Bharani KK. Potential of electric stimulation for the management of COVID-19. Med Hypotheses 2020; 144:110259. [PMID: 33254561 PMCID: PMC7481069 DOI: 10.1016/j.mehy.2020.110259] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 08/28/2020] [Accepted: 09/05/2020] [Indexed: 12/15/2022]
Abstract
The COVID-19 pandemic is the most devastating health emergency that humans have seen over the past century. The war against the disease has been handicapped by unavailability of effective therapeutic options. Till date, there is no clinically approved vaccine or drug for the treatment of COVID-19, and the ongoing search to find a novel therapy is progressing at pandemic pace. Herein, we propose a novel hypothesis based on sound research evidence that electric stimulation can be a potential adjuvant to the currently used symptomatic therapies and antiviral drugs. Based on preclinical evidence, we propose that electric stimulation can improve respiratory functions, inhibit SARS-CoV-2 growth, reduce pain, boost immunity and improve the penetration of antiviral drugs. We envisage that our hypothesis, if used clinically as an adjuvant, may significantly improve the therapeutic outcomes of the current treatment regimen being used around the globe for the management of COVID-19.
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Affiliation(s)
- Prince Allawadhi
- Department of Pharmacy, Vaish Institute of Pharmaceutical Education and Research (VIPER), PBDS-UHS, Rohtak-124001, Haryana, India
| | - Amit Khurana
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Rajendranagar, Hyderabad-500030, Telangana, India; Centre for Biomedical Engineering (CBME), Indian Institute of Technology (IIT), Delhi-110016, India.
| | - Sachin Allwadhi
- Department of Computer Science and Engineering, University Institute of Engineering and Technology (UIET), Maharshi Dayanand University, Rohtak-124001, Haryana, India
| | - Uma Shanker Navik
- Department of Pharmacology, School of Basic and Applied Sciences, Central University of Punjab, Bathinda-151001, Punjab, India
| | - Kamaldeep Joshi
- Department of Computer Science and Engineering, University Institute of Engineering and Technology (UIET), Maharshi Dayanand University, Rohtak-124001, Haryana, India
| | - Anil Kumar Banothu
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Rajendranagar, Hyderabad-500030, Telangana, India
| | - Kala Kumar Bharani
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Rajendranagar, Hyderabad-500030, Telangana, India.
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Agrawal RK, Pandey V, Barhanpurkar-Naik A, Wani MR, Chattopadhyay K, Singh V. Effect of ultrasonic shot peening duration on microstructure, corrosion behavior and cell response of cp-Ti. ULTRASONICS 2020; 104:106110. [PMID: 32146383 DOI: 10.1016/j.ultras.2020.106110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 11/10/2019] [Accepted: 02/10/2020] [Indexed: 06/10/2023]
Abstract
Surface mechanical attrition treatment (SMAT) of metallic biomaterials has gained significant importance due to its ability to develop nano structure in the surface region. In the present study, the microstructural changes and corrosion behavior of the commercially pure titanium (cp-Ti), following different durations of ultrasonic shot peening (USSP) has been investigated. cp-Ti was shot peened for different durations from 0 to 120 s and the treated samples were examined for microstructural changes in the surface region, cell viability and corrosion behavior. Cell viability was considerably increased after USSP for 60-120 s, exhibiting maximum for the 90 s of USSP. The passivation tendency was also improved with peening duration up to 90 s, however, it declined for longer duration of USSP. The beneficial effects of USSP may be attributed to nano structuring in the surface region and development of higher positive potentials at the USSP treated surface. Transmission Electron Microscope (TEM) examination of the USSPed surface revealed dislocation entanglement and substructure. Also, higher surface volta potential was observed over the USSPed sample exhibiting better cell proliferation. The present work is corollary to previous work of the group and mainly discusses the role of USSP duration, as a process parameter, on the cell viability and corrosion resistance of cp-Ti.
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Affiliation(s)
- Rahul Kumar Agrawal
- Department of Metallurgical Engineering, Indian Institute of Technology (B.H.U.), Varanasi 221005, Uttar Pradesh, India
| | - Vaibhav Pandey
- Department of Metallurgical Engineering, Indian Institute of Technology (B.H.U.), Varanasi 221005, Uttar Pradesh, India
| | | | - Mohan R Wani
- Bone Research Laboratory, National Centre for Cell Science, Pune 411007, Maharashtra, India
| | - Kausik Chattopadhyay
- Department of Metallurgical Engineering, Indian Institute of Technology (B.H.U.), Varanasi 221005, Uttar Pradesh, India
| | - Vakil Singh
- Department of Metallurgical Engineering, Indian Institute of Technology (B.H.U.), Varanasi 221005, Uttar Pradesh, India.
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Haeri M, Wöllert T, Langford GM, Gilbert JL. Voltage-controlled cellular viability of preosteoblasts on polarized cpTi with varying surface oxide thickness. Bioelectrochemistry 2013; 94:53-60. [DOI: 10.1016/j.bioelechem.2013.06.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Revised: 05/31/2013] [Accepted: 06/05/2013] [Indexed: 10/26/2022]
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Haeri M, Wӧllert T, Langford GM, Gilbert JL. Electrochemical control of cell death by reduction-induced intrinsic apoptosis and oxidation-induced necrosis on CoCrMo alloy in vitro. Biomaterials 2012; 33:6295-304. [DOI: 10.1016/j.biomaterials.2012.05.054] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 05/20/2012] [Indexed: 01/01/2023]
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Sensitivity to electrical stimulation of human immunodeficiency virus type 1 and MAGIC-5 cells. AMB Express 2011; 1:23. [PMID: 21906386 PMCID: PMC3222307 DOI: 10.1186/2191-0855-1-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 08/08/2011] [Indexed: 11/15/2022] Open
Abstract
To determine the sensitivities to low electrical potential of human immunodeficiency virus type 1 (HIV-1) and its target cells, HIV-1 and MAGIC-5 cells were directly stimulated with a constant direct current potential of 1.0 V (vs. Ag/AgCl). HIV-1 was incubated for 3 h at 37°C on a poly-L-lysine-coated indium-tin oxide electrode, and then stimulated by an electrical potential. MAGIC-5 cells were seeded onto the electrically stimulated HIV-1 and cultured for 3 days at 37°C. HIV-1-infected cells were measured by multinuclear activation via a galactosidase indicator assay. MAGIC-5 cells were also stimulated by an electrical potential of 1.0 V; cell damage, proliferation and apoptosis were evaluated by trypan blue staining, cell counting and in situ apoptosis detection, respectively. HIV-1 was found to be damaged to a greater extent by electrical stimulation than the cells. In particular, after application of a 1.0-V potential for 3 min, HIV-1LAI and HIV-1KMT infection were inhibited by about 90%, but changes in cell damage, proliferation and apoptosis were virtually undetectable. These results suggested that HIV-1 is significantly more susceptible to low electrical potential than cells. This finding could form the basis of a novel therapeutic strategy against HIV-1 infection.
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TOMINAGA M, NAGAISHI S, KUMAGAI E, HARADA S, TANIGUCHI I. Effects of the Expansion Time of Alternating Potential Loading and Temperature on Cell Membrane Damage in HeLa Cells Cultured on an Electrode Surface. ELECTROCHEMISTRY 2008. [DOI: 10.5796/electrochemistry.76.538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Kumagai E, Tominaga M, Nagaishi S, Harada S. Effect of electrical stimulation on human immunodeficiency virus type-1 infectivity. Appl Microbiol Biotechnol 2007; 77:947-53. [PMID: 17940763 DOI: 10.1007/s00253-007-1214-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2007] [Revised: 09/12/2007] [Accepted: 09/16/2007] [Indexed: 10/22/2022]
Abstract
We examined the effects of electrical stimulation on HIV-1-adsorbed MAGIC-5 (MAGIC-5/HIV-1) cells and unadsorbed MAGIC-5 (MAGIC-5) cells. When MAGIC-5 cells were stimulated by a constant d.c. potential of 1.0 V (vs Ag/Agcl) immediately after HIV-1(LAI) infection, infectivity was more affected by electrical stimulation than by cell membrane damage. In particular, after application of potential at 1.0 V for 5 min, about 1% of the membranes of the MAGIC-5/HIV-1(LAI) cells were damaged, but the infectivities of both HIV-1(LAI) and HIV-1(NL43-luc) cells decreased about 37 and 44%, respectively (p < 0.05). After application of potential at 1.0 V for 5 min, the mean fluorescence intensities (MFIs) of highly reactive oxygen species (hROS) and nitric oxide (NO) in MAGIC-5/HIV-1(NL43-Luc) cells were significantly increased compared with that of unstimulated MAGIC-5/HIV-1(NL43-Luc) cells (p < 0.01). However, the MFIs of hROS and NO in MAGIC-5 cells were also increased, to the same level, by electrical stimulation for 5 min. These results suggest that HIV-1 adsorbed onto or invading cells is damaged by direct or indirect effects of electrical stimulation, resulting in a decrease in HIV-1 infectivity. It is also suggested that hROS and NO induced by electrical stimulation are important factors for inhibiting HIV-1 infection.
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Affiliation(s)
- Etsuko Kumagai
- Department of Health Science, Kumamoto University School of Medicine, 4-24-1 Kuhonji, Kumamoto 862-0976, Japan.
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Tominaga M, Nagaishi S, Kirihara M, Kumagai E, Harada S, Taniguchi I. Frequency change-induced alternative potential waveform dependence of membrane damage to cells cultured on an electrode surface. J Biotechnol 2007; 129:498-501. [PMID: 17368608 DOI: 10.1016/j.jbiotec.2007.01.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Accepted: 01/24/2007] [Indexed: 10/23/2022]
Abstract
In the present study, alternative potential stimulation with rectangular pulse, sine and triangular waveforms at 10 and 100Hz was applied to cells cultured on an ITO electrode. As a result, we found that the alternating potential waveform dependence induced by the frequency on membrane damage of cells cultured on an electrode surface. The cell membrane damage was promoted by a rectangular pulse wave in comparison with sine and triangular waves, when alternating electrical potentials of 0 to +1.0V at 100Hz were loaded. In contrast, this waveform dependence was not observed when the frequency was 10Hz. Furthermore, it was found that cell membrane damage was induced at positive potentials more than +0.8V under the present experimental conditions.
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Affiliation(s)
- Masato Tominaga
- Graduate School of Science and Technology, Kumamoto University, 2-39-1, Kumamoto 860-8555, Japan.
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