1
|
Pham NT, Phan LT, Seo J, Kim Y, Song M, Lee S, Jeon YJ, Manavalan B. Advancing the accuracy of SARS-CoV-2 phosphorylation site detection via meta-learning approach. Brief Bioinform 2023; 25:bbad433. [PMID: 38058187 PMCID: PMC10753650 DOI: 10.1093/bib/bbad433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/30/2023] [Accepted: 11/05/2023] [Indexed: 12/08/2023] Open
Abstract
The worldwide appearance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has generated significant concern and posed a considerable challenge to global health. Phosphorylation is a common post-translational modification that affects many vital cellular functions and is closely associated with SARS-CoV-2 infection. Precise identification of phosphorylation sites could provide more in-depth insight into the processes underlying SARS-CoV-2 infection and help alleviate the continuing COVID-19 crisis. Currently, available computational tools for predicting these sites lack accuracy and effectiveness. In this study, we designed an innovative meta-learning model, Meta-Learning for Serine/Threonine Phosphorylation (MeL-STPhos), to precisely identify protein phosphorylation sites. We initially performed a comprehensive assessment of 29 unique sequence-derived features, establishing prediction models for each using 14 renowned machine learning methods, ranging from traditional classifiers to advanced deep learning algorithms. We then selected the most effective model for each feature by integrating the predicted values. Rigorous feature selection strategies were employed to identify the optimal base models and classifier(s) for each cell-specific dataset. To the best of our knowledge, this is the first study to report two cell-specific models and a generic model for phosphorylation site prediction by utilizing an extensive range of sequence-derived features and machine learning algorithms. Extensive cross-validation and independent testing revealed that MeL-STPhos surpasses existing state-of-the-art tools for phosphorylation site prediction. We also developed a publicly accessible platform at https://balalab-skku.org/MeL-STPhos. We believe that MeL-STPhos will serve as a valuable tool for accelerating the discovery of serine/threonine phosphorylation sites and elucidating their role in post-translational regulation.
Collapse
Affiliation(s)
- Nhat Truong Pham
- Department of Integrative Biotechnology and of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Le Thi Phan
- Department of Integrative Biotechnology and of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Jimin Seo
- Department of Integrative Biotechnology and of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Yeonwoo Kim
- Department of Integrative Biotechnology and of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Minkyung Song
- Department of Integrative Biotechnology and of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology and of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Young-Jun Jeon
- Department of Integrative Biotechnology and of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Balachandran Manavalan
- Department of Integrative Biotechnology and of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| |
Collapse
|
2
|
Pham NT, Rakkiyapan R, Park J, Malik A, Manavalan B. H2Opred: a robust and efficient hybrid deep learning model for predicting 2'-O-methylation sites in human RNA. Brief Bioinform 2023; 25:bbad476. [PMID: 38180830 PMCID: PMC10768780 DOI: 10.1093/bib/bbad476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 01/07/2024] Open
Abstract
2'-O-methylation (2OM) is the most common post-transcriptional modification of RNA. It plays a crucial role in RNA splicing, RNA stability and innate immunity. Despite advances in high-throughput detection, the chemical stability of 2OM makes it difficult to detect and map in messenger RNA. Therefore, bioinformatics tools have been developed using machine learning (ML) algorithms to identify 2OM sites. These tools have made significant progress, but their performances remain unsatisfactory and need further improvement. In this study, we introduced H2Opred, a novel hybrid deep learning (HDL) model for accurately identifying 2OM sites in human RNA. Notably, this is the first application of HDL in developing four nucleotide-specific models [adenine (A2OM), cytosine (C2OM), guanine (G2OM) and uracil (U2OM)] as well as a generic model (N2OM). H2Opred incorporated both stacked 1D convolutional neural network (1D-CNN) blocks and stacked attention-based bidirectional gated recurrent unit (Bi-GRU-Att) blocks. 1D-CNN blocks learned effective feature representations from 14 conventional descriptors, while Bi-GRU-Att blocks learned feature representations from five natural language processing-based embeddings extracted from RNA sequences. H2Opred integrated these feature representations to make the final prediction. Rigorous cross-validation analysis demonstrated that H2Opred consistently outperforms conventional ML-based single-feature models on five different datasets. Moreover, the generic model of H2Opred demonstrated a remarkable performance on both training and testing datasets, significantly outperforming the existing predictor and other four nucleotide-specific H2Opred models. To enhance accessibility and usability, we have deployed a user-friendly web server for H2Opred, accessible at https://balalab-skku.org/H2Opred/. This platform will serve as an invaluable tool for accurately predicting 2OM sites within human RNA, thereby facilitating broader applications in relevant research endeavors.
Collapse
Affiliation(s)
- Nhat Truong Pham
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Rajan Rakkiyapan
- Department of Mathematics, Bharathiar University, Coimbatore - 641046, Tamil Nadu, India
| | - Jongsun Park
- InfoBoss inc. and InfoBoss Research Center, Gangnam-gu, Seoul 06278, Republic of Korea
| | - Adeel Malik
- Institute of Intelligence Informatics Technology, Sangmyung University, Seoul, 03016, Republic of Korea
| | - Balachandran Manavalan
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| |
Collapse
|
3
|
Basith S, Pham NT, Song M, Lee G, Manavalan B. ADP-Fuse: A novel two-layer machine learning predictor to identify antidiabetic peptides and diabetes types using multiview information. Comput Biol Med 2023; 165:107386. [PMID: 37619323 DOI: 10.1016/j.compbiomed.2023.107386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023]
Abstract
Diabetes mellitus has become a major public health concern associated with high mortality and reduced life expectancy and can cause blindness, heart attacks, kidney failure, lower limb amputations, and strokes. A new generation of antidiabetic peptides (ADPs) that act on β-cells or T-cells to regulate insulin production is being developed to alleviate the effects of diabetes. However, the lack of effective peptide-mining tools has hampered the discovery of these promising drugs. Hence, novel computational tools need to be developed urgently. In this study, we present ADP-Fuse, a novel two-layer prediction framework capable of accurately identifying ADPs or non-ADPs and categorizing them into type 1 and type 2 ADPs. First, we comprehensively evaluated 22 peptide sequence-derived features coupled with eight notable machine learning algorithms. Subsequently, the most suitable feature descriptors and classifiers for both layers were identified. The output of these single-feature models, embedded with multiview information, was trained with an appropriate classifier to provide the final prediction. Comprehensive cross-validation and independent tests substantiate that ADP-Fuse surpasses single-feature models and the feature fusion approach for the prediction of ADPs and their types. In addition, the SHapley Additive exPlanation method was used to elucidate the contributions of individual features to the prediction of ADPs and their types. Finally, a user-friendly web server for ADP-Fuse was developed and made publicly accessible (https://balalab-skku.org/ADP-Fuse), enabling the swift screening and identification of novel ADPs and their types. This framework is expected to contribute significantly to antidiabetic peptide identification.
Collapse
Affiliation(s)
- Shaherin Basith
- Department of Physiology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
| | - Nhat Truong Pham
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Minkyung Song
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea; Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| | - Gwang Lee
- Department of Physiology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea; Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea.
| | - Balachandran Manavalan
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| |
Collapse
|
4
|
Pham NT, Bunruangses M, Youplao P, Garhwal A, Ray K, Roy A, Boonkirdram S, Yupapin P, Jalil MA, Ali J, Kaiser S, Mahmud M, Mallik S, Zhao Z. An exploratory simulation study and prediction model on human brain behavior and activity using an integration of deep neural network and biosensor Rabi antenna. Heliyon 2023; 9:e15749. [PMID: 37305516 PMCID: PMC10256856 DOI: 10.1016/j.heliyon.2023.e15749] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 06/13/2023] Open
Abstract
The plasmonic antenna probe is constructed using a silver rod embedded in a modified Mach-Zehnder interferometer (MZI) ad-drop filter. Rabi antennas are formed when space-time control reaches two levels of system oscillation and can be used as human brain sensor probes. Photonic neural networks are designed using brain-Rabi antenna communication, and transmissions are connected via neurons. Communication signals are carried by electron spin (up and down) and adjustable Rabi frequency. Hidden variables and deep brain signals can be obtained by external detection. A Rabi antenna has been developed by simulation using computer simulation technology (CST) software. Additionally, a communication device has been developed that uses the Optiwave program with Finite-Difference Time-Domain (OptiFDTD). The output signal is plotted using the MATLAB program with the parameters of the OptiFDTD simulation results. The proposed antenna oscillates in the frequency range of 192 THz to 202 THz with a maximum gain of 22.4 dBi. The sensitivity of the sensor is calculated along with the result of electron spin and applied to form a human brain connection. Moreover, intelligent machine learning algorithms are proposed to identify high-quality transmissions and predict the behavior of transmissions in the near future. During the process, a root mean square error (RMSE) of 2.3332(±0.2338) was obtained. Finally, it can be said that our proposed model can efficiently predict human mind, thoughts, behavior as well as action/reaction, which can be greatly helpful in the diagnosis of various neuro-degenerative/psychological diseases (such as Alzheimer's, dementia, etc.) and for security purposes.
Collapse
Affiliation(s)
- Nhat Truong Pham
- Computational Biology and Bioinformatics Laboratory, Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Montree Bunruangses
- Department of Computer Engineering, Faculty of Industrial Education, Rajamangala University of Technology Phra Nakhon, Bangkok 10300, Thailand
| | - Phichai Youplao
- Department of Electrical Engineering, Faculty of Industry and Technology, Rajamangala University of Technology Isan Sakon Nakhon Campus, 199 Village no. 3, Phungkon, Sakon Nakhon 47160, Thailand
| | - Anita Garhwal
- Asia Metropolitan University, 6, Jalan Lembah, Bandar Baru Seri Alam 81750, Masai, Johor, Malaysia
| | - Kanad Ray
- Amity School of Applied Sciences, Amity University Rajasthan, Jaipur, India
- Facultad de CienciasFisico-Matematicas, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y AV. 18 sur, Col. San Manuel Ciudad Universitaria, Pueble Pue. 72570, Mexico
- Faubert Lab, Ecole d'optométrie, Université de Montréal, Montréal, QC H3T1P1, Canada
| | - Arup Roy
- School of Computing and Information Technology, Reva University, Bengaluru, Karnataka 560064, India
| | - Sarawoot Boonkirdram
- Program of Electrical and Electronics, Faculty of Industrial Technology, Sakon Nakhon Rajabhat University, 680 Nittayo, Mueang, Sakon Nakhon 47000, Thailand
| | - Preecha Yupapin
- Department of Electrical Technology, School of Industrial Technology, Sakonnakhon Technical College, Institute of Vocational Education Northeastern 2, Sakonnakhon 47000, Thailand
| | - Muhammad Arif Jalil
- Department of Physics, Faculty of Science, Unversiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Jalil Ali
- Department of Electrical Engineering, Faculty of Industry and Technology, Rajamangala University of Technology Isan Sakon Nakhon Campus, 199 Village no. 3, Phungkon, Sakon Nakhon 47160, Thailand
| | - Shamim Kaiser
- Institute of Information Technology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Mufti Mahmud
- Nottingham Trent University, Clifton Lane, NG11 8NS, Nottingham, United Kingdom
| | - Saurav Mallik
- Department of Environmental Health, Harvard T H Chan School of Public Health, Boston, MA 02115, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| |
Collapse
|
5
|
Hu J, Yu W, Pang C, Jin J, Pham NT, Manavalan B, Wei L. DrugormerDTI: Drug Graphormer for drug-target interaction prediction. Comput Biol Med 2023; 161:106946. [PMID: 37244151 DOI: 10.1016/j.compbiomed.2023.106946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/29/2023] [Accepted: 04/15/2023] [Indexed: 05/29/2023]
Abstract
Drug-target interactions (DTI) prediction is a crucial task in drug discovery. Existing computational methods accelerate the drug discovery in this respect. However, most of them suffer from low feature representation ability, significantly affecting the predictive performance. To address the problem, we propose a novel neural network architecture named DrugormerDTI, which uses Graph Transformer to learn both sequential and topological information through the input molecule graph and Resudual2vec to learn the underlying relation between residues from proteins. By conducting ablation experiments, we verify the importance of each part of the DrugormerDTI. We also demonstrate the good feature extraction and expression capabilities of our model via comparing the mapping results of the attention layer and molecular docking results. Experimental results show that our proposed model performs better than baseline methods on four benchmarks. We demonstrate that the introduction of Graph Transformer and the design of residue are appropriate for drug-target prediction.
Collapse
Affiliation(s)
- Jiayue Hu
- School of Software, Shandong University, Jinan, China; Joint SDU-NTU Centre for Artificial Intelligence Research (C-FAIR), Shandong University, Jinan, China
| | - Wang Yu
- School of Software, Shandong University, Jinan, China; Joint SDU-NTU Centre for Artificial Intelligence Research (C-FAIR), Shandong University, Jinan, China
| | - Chao Pang
- School of Software, Shandong University, Jinan, China; Joint SDU-NTU Centre for Artificial Intelligence Research (C-FAIR), Shandong University, Jinan, China
| | - Junru Jin
- School of Software, Shandong University, Jinan, China; Joint SDU-NTU Centre for Artificial Intelligence Research (C-FAIR), Shandong University, Jinan, China
| | - Nhat Truong Pham
- Computational Biology and Bioinformatics Laboratory, Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, 16419, Gyeonggi-do, South Korea
| | - Balachandran Manavalan
- Computational Biology and Bioinformatics Laboratory, Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, 16419, Gyeonggi-do, South Korea.
| | - Leyi Wei
- School of Software, Shandong University, Jinan, China; Joint SDU-NTU Centre for Artificial Intelligence Research (C-FAIR), Shandong University, Jinan, China.
| |
Collapse
|
6
|
Charoenkwan P, Schaduangrat N, Pham NT, Manavalan B, Shoombuatong W. Pretoria: An effective computational approach for accurate and high-throughput identification of CD8+ t-cell epitopes of eukaryotic pathogens. Int J Biol Macromol 2023; 238:124228. [PMID: 36996953 DOI: 10.1016/j.ijbiomac.2023.124228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/11/2023] [Accepted: 03/25/2023] [Indexed: 03/31/2023]
Abstract
T-cells recognize antigenic epitopes present on major histocompatibility complex (MHC) molecules, triggering an adaptive immune response in the host. T-cell epitope (TCE) identification is challenging because of the extensive number of undetermined proteins found in eukaryotic pathogens, as well as MHC polymorphisms. In addition, conventional experimental approaches for TCE identification are time-consuming and expensive. Thus, computational approaches that can accurately and rapidly identify CD8+ T-cell epitopes (TCEs) of eukaryotic pathogens based solely on sequence information may facilitate the discovery of novel CD8+ TCEs in a cost-effective manner. Here, Pretoria (Predictor of CD8+ TCEs of eukaryotic pathogens) is proposed as the first stack-based approach for accurate and large-scale identification of CD8+ TCEs of eukaryotic pathogens. In particular, Pretoria enabled the extraction and exploration of crucial information embedded in CD8+ TCEs by employing a comprehensive set of 12 well-known feature descriptors extracted from multiple groups, including physicochemical properties, composition-transition-distribution, pseudo-amino acid composition, and amino acid composition. These feature descriptors were then utilized to construct a pool of 144 different machine learning (ML)-based classifiers based on 12 popular ML algorithms. Finally, the feature selection method was used to effectively determine the important ML classifiers for the construction of our stacked model. The experimental results indicated that Pretoria is an accurate and effective computational approach for CD8+ TCE prediction; it was superior to several conventional ML classifiers and the existing method in terms of the independent test, with an accuracy of 0.866, MCC of 0.732, and AUC of 0.921. Additionally, to maximize user convenience for high-throughput identification of CD8+ TCEs of eukaryotic pathogens, a user-friendly web server of Pretoria (http://pmlabstack.pythonanywhere.com/Pretoria) was developed and made freely available.
Collapse
Affiliation(s)
- Phasit Charoenkwan
- Modern Management and Information Technology, College of Arts, Media and Technology, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nalini Schaduangrat
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Nhat Truong Pham
- Computational Biology and Bioinformatics Laboratory, Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea
| | - Balachandran Manavalan
- Computational Biology and Bioinformatics Laboratory, Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Republic of Korea.
| | - Watshara Shoombuatong
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.
| |
Collapse
|
7
|
Mustaqeem, El Saddik A, Alotaibi FS, Pham NT. AAD-Net: Advanced end-to-end speech signal system for human emotion detection & recognition using attention-based deep echo state network. Knowl Based Syst 2023. [DOI: 10.1016/j.knosys.2023.110525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
|
8
|
Nguyen LH, Pham NT, Do VH, Nguyen LT, Nguyen TT, Nguyen H, Nguyen ND, Nguyen TT, Nguyen SD, Bhatti A, Lim CP. Fruit-CoV: An efficient vision-based framework for speedy detection and diagnosis of SARS-CoV-2 infections through recorded cough sounds. Expert Syst Appl 2023; 213:119212. [PMID: 36407848 PMCID: PMC9639421 DOI: 10.1016/j.eswa.2022.119212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 10/20/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
COVID-19 is an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This deadly virus has spread worldwide, leading to a global pandemic since March 2020. A recent variant of SARS-CoV-2 named Delta is intractably contagious and responsible for more than four million deaths globally. Therefore, developing an efficient self-testing service for SARS-CoV-2 at home is vital. In this study, a two-stage vision-based framework, namely Fruit-CoV, is introduced for detecting SARS-CoV-2 infections through recorded cough sounds. Specifically, audio signals are converted into Log-Mel spectrograms, and the EfficientNet-V2 network is used to extract their visual features in the first stage. In the second stage, 14 convolutional layers extracted from the large-scale Pretrained Audio Neural Networks for audio pattern recognition (PANNs) and the Wavegram-Log-Mel-CNN are employed to aggregate feature representations of the Log-Mel spectrograms and the waveform. Finally, the combined features are used to train a binary classifier. In this study, a dataset provided by the AICovidVN 115M Challenge is employed for evaluation. It includes 7,371 recorded cough sounds collected throughout Vietnam, India, and Switzerland. Experimental results indicate that the proposed model achieves an Area Under the Receiver Operating Characteristic Curve (AUC) score of 92.8% and ranks first on the final leaderboard of the AICovidVN 115M Challenge. Our code is publicly available.
Collapse
Affiliation(s)
- Long H Nguyen
- Faculty of Information Technology, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Nhat Truong Pham
- Division of Computational Mechatronics, Institute for Computational Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Electrical and Electronics Engineering, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | | | - Liu Tai Nguyen
- Faculty of Information Technology, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Thanh Tin Nguyen
- Human Computer Interaction Lab, Sejong University, Seoul, South Korea
| | - Hai Nguyen
- Khoury College of Computer Sciences, Northeastern University, Boston, USA
| | - Ngoc Duy Nguyen
- Institute for Intelligent Systems Research and Innovation, Deakin University, Victoria, Australia
| | - Thanh Thi Nguyen
- School of Information Technology, Deakin University, Victoria, Australia
| | - Sy Dzung Nguyen
- Laboratory for Computational Mechatronics, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, Vietnam
- Faculty of Mechanical-Electrical and Computer Engineering, Van Lang University, Ho Chi Minh City, Vietnam
| | - Asim Bhatti
- Institute for Intelligent Systems Research and Innovation, Deakin University, Victoria, Australia
| | - Chee Peng Lim
- Institute for Intelligent Systems Research and Innovation, Deakin University, Victoria, Australia
| |
Collapse
|
9
|
Sonasang S, Jamsai M, Jalil MA, Pham NT, Ray K, Angkawisittpan N, Yupapin P, Boonkirdram S, Palomino-Ovando MA, Toledo-Solano M, Misaghian K, Lugo JE. Multiband Rabi antenna using nest microstrip add-drop filter (NMADF) for relativistic sensing applications. Heliyon 2023; 9:e13611. [PMID: 36879752 PMCID: PMC9984424 DOI: 10.1016/j.heliyon.2023.e13611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/26/2022] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
A microstrip circuit is designed, constructed, and tested based on the nest microstrip add-drop filters (NMADF). The multi-level system oscillation is generated by the wave-particle behaviors of AC driven along the microstrip ring circular path. The continuous successive filtering is applied via the device input port. The higher-order harmonic oscillations can be filtered, from which the two-level system known as a Rabi oscillation is achieved. The outside microstrip ring energy is coupled to the inside rings, from which the multiband Rabi oscillations can be formed within the inner rings. The resonant Rabi frequencies can be applied for multi-sensing probes. The relationship between electron density and Rabi oscillation frequency of each microstrip ring output can be obtained and used for multi-sensing probe applications. The relativistic sensing probe can be obtained by the warp speed electron distribution at the resonant Rabi frequency respecting the resonant ring radii. These are available for relativistic sensing probe usage. The obtained experimental results have shown that there are 3-center Rabi frequencies obtained, which can be used for 3-sensing probes simultaneously. The sensing probe speeds of 1.1c, 1.4c, and 1.5c are obtained using the microstrip ring radii of 14.20, 20.12, and 34.49 mm, respectively. The best sensor sensitivity of 1.30 ms is achieved. The relativistic sensing platform can be used for many applications.
Collapse
Affiliation(s)
- Somchat Sonasang
- Electronics Technology, Faculty of Industrial Technology, Nakon Phanom University, Nakon Phanom 48000, Thailand
| | - M Jamsai
- Department of Electrical Engineering, Faculty of Industry and Technology, Rajamagala University of Technology Isan Sakon Nakhon Campus, Sakon Nakhon 47160, Thailand
| | - M A Jalil
- Department of Physics, Universiti Teknologi Malaysia, 81310 Skuda, Johor, Malaysia
| | - Nhat Truong Pham
- Institute for Computational Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - K Ray
- Amity School of Applied Sciences, Amity University Rajasthan, Jaipur, India.,Facultad de CienciasFisico-Matematicas, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y AV. 18 sur, Col. San Manuel Ciudad Universitaria, Pueble Pue 72570, Mexico.,Faubert Lab, School of Optometry, Université de Montréal, Montréal, QC H3T1P1, Canada
| | - Niwat Angkawisittpan
- Research Unit for Computational Electromagnetics and Optical Systems, Faculty of Engineering, Mahasarakham University, Maha Sarakham 44150, Thailand
| | - Preecha Yupapin
- Department of Electrical Technology, School of Industrial Technology, Sakonnakhon Technical College, Institute of Vocational Education Northeastern 2, Sakonnakhon 47000, Thailand
| | - Sarawoot Boonkirdram
- Program of Electrical and Electronics, Faculty of Industrial Technology, Sakon Nakhon Rajabhat University, 680 Nittayo, Mueang, Sakon Nakhon 47000, Thailand
| | - Martha Alicia Palomino-Ovando
- Facultad de CienciasFisico-Matematicas, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y AV. 18 sur, Col. San Manuel Ciudad Universitaria, Pueble Pue 72570, Mexico
| | - Miller Toledo-Solano
- CONACYT-Facultad de CienciasFisico-Matematicas, Benemérita Universidad Autónoma de Pueble, Av. San Claudio y Av. 18 sur, Col. San Manuel Ciudad Universitaria, Puebla Pue, 72570, Mexico
| | - Khashayar Misaghian
- Faubert Lab, School of Optometry, Université de Montréal, Montréal, QC H3T1P1, Canada.,Sage-Sentinel Smart Solutions, 1919-1 Tancha, Onna-son Kunigamigun, Okinawa, 904-0495, Japan
| | - J E Lugo
- Facultad de CienciasFisico-Matematicas, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y AV. 18 sur, Col. San Manuel Ciudad Universitaria, Pueble Pue 72570, Mexico.,Faubert Lab, School of Optometry, Université de Montréal, Montréal, QC H3T1P1, Canada.,Sage-Sentinel Smart Solutions, 1919-1 Tancha, Onna-son Kunigamigun, Okinawa, 904-0495, Japan
| |
Collapse
|
10
|
Van HD, Thi XAT, Le Thi VL, Van TT, Pham NT, Phong NT, Gagnon AS, Pham QB, Anh DT. Zoning the suitability of the western Mekong Delta for paddy rice cultivation and aquaculture under current and future environmental conditions. Environ Monit Assess 2022; 194:767. [PMID: 36255502 DOI: 10.1007/s10661-022-10180-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/06/2021] [Indexed: 06/16/2023]
Abstract
Ca Mau and Kien Giang, the two provinces of the Mekong Delta bordering the Gulf of Thailand, are facing major environmental challenges affecting the agriculture and aquaculture sectors upon which many livelihoods in this region depend on. This study maps the suitability of these two provinces for paddy rice cultivation and shrimp farming according to soil characteristics and current and future environmental conditions for variables found to significantly influence the yield of those two sectors, i.e., the level of saltwater intrusion, water availability for rainfed agriculture, and the length of the growing period. Future environmental conditions were simulated using the MIKE 11 hydrodynamic model forced by four hydrodynamic scenarios, each one representing different extents of saltwater intrusion during both the dry and rainy seasons, while also considering the availability of water resources for rainfed agriculture. The suitability zoning was performed using a GIS-based analytic hierarchy process (AHP) approach, resulting in the categorisation of the land according to four suitability levels for each sector. The analysis reveals that paddy rice cultivation will become more suitable to Kien Giang province while shrimp farming will be more suitable to Ca Mau province if the simulated future environmental conditions materialise. A suitability analysis is essential for optimal utilisation of the land. The approach presented in this study will inform the regional economic development master plan and provide guidance to other delta regions experiencing severe environmental changes and wishing to consider potential future climatic and sea level changes, and their associated impacts, in their land use planning.
Collapse
Affiliation(s)
- Hue Doan Van
- Southern Institute of Water Resources Research, Ho Chi Minh City, Vietnam
| | - Xuan Ai Tien Thi
- Southern Institute of Water Resources Research, Ho Chi Minh City, Vietnam
| | - Van Linh Le Thi
- Southern Institute of Water Resources Research, Ho Chi Minh City, Vietnam
| | - Thanh To Van
- Dau Tieng-Phuoc Hoa Irrigation Exploitation Company, Tay Ninh, Tay Ninh Province, Vietnam
| | - Nhat Truong Pham
- Division of Computational Mechatronics, Institute for Computational Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Electrical and Electronics Engineering, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Nguyen Tan Phong
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Alexandre S Gagnon
- School of Biological and Environmental Science, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - Quoc Bao Pham
- Faculty of Natural Sciences, Institute of Earth Sciences, University of Silesia in Katowice, Będzińska street 60, 41-200, Sosnowiec, Poland
| | - Duong Tran Anh
- HUTECH University, 475A Dien Bien Phu Street, Binh Thanh District, Ho Chi Minh City, Vietnam.
| |
Collapse
|
11
|
Pham TNH, Nguyen TH, Tam NM, Y Vu T, Pham NT, Huy NT, Mai BK, Tung NT, Pham MQ, V Vu V, Ngo ST. Improving ligand-ranking of AutoDock Vina by changing the empirical parameters. J Comput Chem 2021; 43:160-169. [PMID: 34716930 DOI: 10.1002/jcc.26779] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/10/2021] [Accepted: 10/14/2021] [Indexed: 01/09/2023]
Abstract
AutoDock Vina (Vina) achieved a very high docking-success rate, p ^ , but give a rather low correlation coefficient, R , for binding affinity with respect to experiments. This low correlation can be an obstacle for ranking of ligand-binding affinity, which is the main objective of docking simulations. In this context, we evaluated the dependence of Vina R coefficient upon its empirical parameters. R is affected more by changing the gauss2 and rotation than other terms. The docking-success rate p ^ is sensitive to the alterations of the gauss1, gauss2, repulsion, and hydrogen bond parameters. Based on our benchmarks, the parameter set1 has been suggested to be the most optimal. The testing study over 800 complexes indicated that the modified Vina provided higher correlation with experiment R set 1 = 0.556 ± 0.025 compared with R Default = 0.493 ± 0.028 obtained by the original Vina and R Vina 1.2 = 0.503 ± 0.029 by Vina version 1.2. Besides, the modified Vina can be also applied more widely, giving R ≥ 0.500 for 32/48 targets, compared with the default package, giving R ≥ 0.500 for 31/48 targets. In addition, validation calculations for 1036 complexes obtained from version 2019 of PDBbind refined structures showed that the set1 of parameters gave higher correlation coefficient ( R set 1 = 0.617 ± 0.017 ) than the default package ( R Default = 0.543 ± 0.020 ) and Vina version 1.2 ( R Vina 1.2 = 0.540 ± 0.020 ). The version of Vina with set1 of parameters can be downloaded at https://github.com/sontungngo/mvina. The outcomes would enhance the ranking of ligand-binding affinity using Autodock Vina.
Collapse
Affiliation(s)
- T Ngoc Han Pham
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam.,Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Nguyen Minh Tam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam.,Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Thien Y Vu
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Nhat Truong Pham
- Faculty of Electrical and Electronics Engineering, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Nguyen Truong Huy
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Binh Khanh Mai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Nguyen Thanh Tung
- Institute of Materials Science, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Minh Quan Pham
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Van V Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam.,Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| |
Collapse
|
12
|
Baudon E, Poon LL, Dao TD, Pham NT, Cowling BJ, Peyre M, Nguyen KV, Peiris M. Detection of Novel Reassortant Influenza A (H3N2) and H1N1 2009 Pandemic Viruses in Swine in Hanoi, Vietnam. Zoonoses Public Health 2014; 62:429-34. [PMID: 25363845 DOI: 10.1111/zph.12164] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Indexed: 01/13/2023]
Abstract
From May to September 2013, monthly samples were collected from swine in a Vietnamese slaughterhouse for influenza virus isolation and serological testing. A(H1N1)pdm09 viruses and a novel H3N2 originating from reassortment between A(H1N1)pdm09 and novel viruses of the North American triple reassortant lineage were isolated. Serological results showed low seroprevalence for the novel H3N2 virus and higher seroprevalence for A(H1N1)pdm09 viruses. In addition, serology suggested that other swine influenza viruses are also circulating in Vietnamese swine.
Collapse
Affiliation(s)
- E Baudon
- School of Public Health, The University of Hong Kong, Hong Kong, China.,CIRAD, UPR AGIRs, Montpellier, France
| | - L L Poon
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - T D Dao
- National Institute of Veterinary Research, Hanoi, Vietnam
| | - N T Pham
- National Institute of Veterinary Research, Hanoi, Vietnam
| | - B J Cowling
- School of Public Health, The University of Hong Kong, Hong Kong, China
| | - M Peyre
- CIRAD, UPR AGIRs, Montpellier, France
| | - K V Nguyen
- National Institute of Veterinary Research, Hanoi, Vietnam
| | - M Peiris
- School of Public Health, The University of Hong Kong, Hong Kong, China
| |
Collapse
|
13
|
Pham NT, McHale G, Newton MI, Carroll BJ, Rowan SM. Application of the quartz crystal microbalance to the evaporation of colloidal suspension droplets. Langmuir 2004; 20:841-847. [PMID: 15773113 DOI: 10.1021/la0357007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
An investigation into the evaporation of sessile droplets of latex and clay particle suspensions is presented in this work. The quartz crystal microbalance (QCM) has been used to study the interfacial phenomena during the drying process of these droplets. Characteristic changes of the crystal oscillating frequency and crystal resistance (damping of the oscillating energy) have been observed and related to the different stages of the evaporation process. Measurements have been made for latex particle sizes from 1.9 to 10 microm and for rough and polished crystals using drops from 0.3 to 1.5 microL. The behavior of the QCM is shown to depend strongly on the size of particles present and on the morphology of the crystal surface. One of the most striking features is a drastic damping of the oscillation energy and corresponding rise in frequency observed during the final stages of evaporation, particularly for the clay suspensions.
Collapse
Affiliation(s)
- N T Pham
- School of Science, The Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, United Kingdom.
| | | | | | | | | |
Collapse
|
14
|
Abstract
This work is devoted to a kinetics study of cadmium electrochemical cementation on zinc powder under ultrasonic low-frequency field (20 kHz). Compared to mechanical stirring with a Rushton turbine and for the same suspension quality, ultrasound lead to a lower kinetics during the major part of the reaction but to final conversion rate near 100%. Pointing out a thermal modification in the deposit morphology due to acoustic cavitation, gives explanation to these processes changes. Besides several acting parameter effects, such as temperature, metallic ion concentrations or ultrasonic power have been observed and analysed.
Collapse
Affiliation(s)
- M Aurousseau
- UMR 5631 CNRS-INPG-UJF, BP 75, Cedex 38402 Saint Martin d'Héres, France.
| | | | | |
Collapse
|
15
|
Abstract
AIMS To evaluate the role of nitric oxide (NO) in ocular involvement during systemic toxoplasmosis. METHODS C57B1/6 mice were infected with Toxoplasma gondii strain ME49. The synthesis of NO was inhibited by an intraperitoneal injection of aminoguanidine every 8 hours, starting on the day of infection. Control infected mice received phosphate buffered saline vehicle alone. After 14 days, the ocular lesions were evaluated by histopathological examination. The expression of NO synthase induced in the spleen by toxoplasma infection was evaluated by immunostaining. The production of NO by the spleen cells of infected mice was measured by the colorimetric assay of Griess in the supernatant of cultures stimulated with toxoplasma antigen or concanavalin A. RESULTS The inhibition of NO production in T gondii infected mice resulted in a marked increase in the symptoms of ocular inflammation. We observed a strong induction of NO synthase expression in the spleen of infected animals. In culture, the spleen cells from these mice produced high levels of NO in response to T gondii antigens. This elevation of NO synthesis was suppressed in the presence of aminoguanidine. CONCLUSION This study indicates that NO plays a crucial role in the protection against T gondii infection as reflected by the severity of the ocular involvement.
Collapse
Affiliation(s)
- S Hayashi
- Laboratory of Immunology, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892-1858, USA
| | | | | | | | | | | |
Collapse
|
16
|
Pham NT, Hart LL. Use of ursodeoxycholic acid in primary biliary cirrhosis. Ann Pharmacother 1993; 27:1472-4. [PMID: 8305782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- N T Pham
- Division of Clinical Pharmacy, School of Pharmacy, University of California, San Francisco 94143
| | | |
Collapse
|
17
|
Matsuoka M, Pham NT, Tsukamoto H. Differential effects of interleukin-1 alpha, tumor necrosis factor alpha, and transforming growth factor beta 1 on cell proliferation and collagen formation by cultured fat-storing cells. Liver 1989; 9:71-8. [PMID: 2785237 DOI: 10.1111/j.1600-0676.1989.tb00382.x] [Citation(s) in RCA: 139] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fat-storing cells (FSCs), perisinusoidal cells which normally participate in metabolism of vitamin A, have been suggested to participate in collagen synthesis in fibrotic liver. However, key mediators which regulate collagen metabolism in FSCs are yet to be elucidated. In fibroblasts, Interleukin-1 (IL-1), Tumor Necrosis Factor alpha (TNF alpha), and Transforming Growth Factor beta (TGF beta) have been shown to induce diverse modulations of collagen metabolism and cell proliferation. In the present study, these cytokines were tested for their abilities to regulate collagen formation and proliferation by cultured rat FSCs. FSCs primary culture was established and incubated in the absence or presence of various concentrations of IL-1 alpha, TNF alpha, and TGF beta 1. Tritiated proline and thymidine were used to examine collagen formation and cell proliferation. IL-1 alpha (2.5-10 U/ml) had a concentration-dependent stimulatory effect on FSC proliferation with a maximal response of 160% compared to that of untreated FSCs. This mitogenic effect resulted in slight but significant increases (15-20%) in the net collagen formation. However, when this parameter was standardized relative to DNA content, significant inhibition of both collagen and noncollagen protein formation by IL-1 alpha was demonstrated. TNF alpha also exhibited a similar mitogenic effect but induced a more selective inhibition of collagen formation. In contrast, TGF beta 1 (0.01-1 ng/ml) specifically enhanced collagen formation by 60-80%, as also evidenced by significant increases in the ratio of [3H]hydroxyproline to [3H]proline incorporated in newly formed proteins.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- M Matsuoka
- Hepatopancreatic Research Laboratory, VA Medical Center, Martinez
| | | | | |
Collapse
|