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Kumar V, Banerjee A, Roy K. Breaking the Barriers: Machine-Learning-Based c-RASAR Approach for Accurate Blood-Brain Barrier Permeability Prediction. J Chem Inf Model 2024; 64:4298-4309. [PMID: 38700741 DOI: 10.1021/acs.jcim.4c00433] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2024]
Abstract
The intricate nature of the blood-brain barrier (BBB) poses a significant challenge in predicting drug permeability, which is crucial for assessing central nervous system (CNS) drug efficacy and safety. This research utilizes an innovative approach, the classification read-across structure-activity relationship (c-RASAR) framework, that leverages machine learning (ML) to enhance the accuracy of BBB permeability predictions. The c-RASAR framework seamlessly integrates principles from both read-across and QSAR methodologies, underscoring the need to consider similarity-related aspects during the development of the c-RASAR model. It is crucial to note that the primary goal of this research is not to introduce yet another model for predicting BBB permeability but rather to showcase the refinement in predicting the BBB permeability of organic compounds through the introduction of a c-RASAR approach. This groundbreaking methodology aims to elevate the accuracy of assessing neuropharmacological implications and streamline the process of drug development. In this study, an ML-based c-RASAR linear discriminant analysis (LDA) model was developed using a dataset of 7807 compounds, encompassing both BBB-permeable and -nonpermeable substances sourced from the B3DB database (freely accessible from https://github.com/theochem/B3DB), for predicting BBB permeability in lead discovery for CNS drugs. The model's predictive capability was then validated using three external sets: one containing 276,518 natural products (NPs) from the LOTUS database (accessible from https://lotus.naturalproducts.net/download) for data gap filling, another comprising 13,002 drug-like/drug compounds from the DrugBank database (available from https://go.drugbank.com/), and a third set of 56 FDA-approved drugs to assess the model's reliability. Further diversifying the predictive arsenal, various other ML-based c-RASAR models were also developed for comparison purposes. The proposed c-RASAR framework emerged as a powerful tool for predicting BBB permeability. This research not only advances the understanding of molecular determinants influencing CNS drug permeability but also provides a versatile computational platform for the rapid assessment of diverse compounds, facilitating informed decision-making in drug development and design.
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Affiliation(s)
- Vinay Kumar
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Arkaprava Banerjee
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Kunal Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
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2
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Ma J, Li G, Wang H, Mo C. Comprehensive review of potential drugs with anti-pulmonary fibrosis properties. Biomed Pharmacother 2024; 173:116282. [PMID: 38401514 DOI: 10.1016/j.biopha.2024.116282] [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: 12/06/2023] [Revised: 02/02/2024] [Accepted: 02/17/2024] [Indexed: 02/26/2024] Open
Abstract
Pulmonary fibrosis is a chronic and progressive lung disease characterized by the accumulation of scar tissue in the lungs, which leads to impaired lung function and reduced quality of life. The prognosis for idiopathic pulmonary fibrosis (IPF), which is the most common form of pulmonary fibrosis, is generally poor. The median survival for patients with IPF is estimated to be around 3-5 years from the time of diagnosis. Currently, there are two approved drugs (Pirfenidone and Nintedanib) for the treatment of IPF. However, Pirfenidone and Nintedanib are not able to reverse or cure pulmonary fibrosis. There is a need for new pharmacological interventions that can slow or halt disease progression and cure pulmonary fibrosis. This review aims to provide an updated overview of current and future drug interventions for idiopathic pulmonary fibrosis, and to summarize possible targets of potential anti-pulmonary fibrosis drugs, providing theoretical support for further clinical combination therapy or the development of new drugs.
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Affiliation(s)
- Jie Ma
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China; The Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Gang Li
- Department of Thoracic Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Han Wang
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Center for RNA Science and Therapeutics, School of Medicine, Cleveland, OH, USA
| | - Chunheng Mo
- The Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China.
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Qiu Y, Mo C, Chen L, Ye W, Chen G, Zhu T. Alterations in microbiota of patients with COVID-19: implications for therapeutic interventions. MedComm (Beijing) 2024; 5:e513. [PMID: 38495122 PMCID: PMC10943180 DOI: 10.1002/mco2.513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/19/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recently caused a global pandemic, resulting in more than 702 million people being infected and over 6.9 million deaths. Patients with coronavirus disease (COVID-19) may suffer from diarrhea, sleep disorders, depression, and even cognitive impairment, which is associated with long COVID during recovery. However, there remains no consensus on effective treatment methods. Studies have found that patients with COVID-19 have alterations in microbiota and their metabolites, particularly in the gut, which may be involved in the regulation of immune responses. Consumption of probiotics may alleviate the discomfort caused by inflammation and oxidative stress. However, the pathophysiological process underlying the alleviation of COVID-19-related symptoms and complications by targeting the microbiota remains unclear. In the current study, we summarize the latest research and evidence on the COVID-19 pandemic, together with symptoms of SARS-CoV-2 and vaccine use, with a focus on the relationship between microbiota alterations and COVID-19-related symptoms and vaccine use. This work provides evidence that probiotic-based interventions may improve COVID-19 symptoms by regulating gut microbiota and systemic immunity. Probiotics may also be used as adjuvants to improve vaccine efficacy.
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Affiliation(s)
- Yong Qiu
- Department of AnesthesiologyNational Clinical Research Center for Geriatrics and The Research Units of West China (2018RU012)West China HospitalSichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Center of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduChina
| | - Chunheng Mo
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOEState Key Laboratory of BiotherapyWest China Second University HospitalSichuan UniversityChengduChina
| | - Lu Chen
- Department of AnesthesiologyNational Clinical Research Center for Geriatrics and The Research Units of West China (2018RU012)West China HospitalSichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Center of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduChina
| | - Wanlin Ye
- Department of AnesthesiologyNational Clinical Research Center for Geriatrics and The Research Units of West China (2018RU012)West China HospitalSichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Center of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduChina
| | - Guo Chen
- Department of AnesthesiologyNational Clinical Research Center for Geriatrics and The Research Units of West China (2018RU012)West China HospitalSichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Center of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduChina
| | - Tao Zhu
- Department of AnesthesiologyNational Clinical Research Center for Geriatrics and The Research Units of West China (2018RU012)West China HospitalSichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Center of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduChina
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Morgan AE, Mc Auley MT. Vascular dementia: From pathobiology to emerging perspectives. Ageing Res Rev 2024; 96:102278. [PMID: 38513772 DOI: 10.1016/j.arr.2024.102278] [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: 01/26/2024] [Revised: 03/16/2024] [Accepted: 03/17/2024] [Indexed: 03/23/2024]
Abstract
Vascular dementia (VaD) is the second most common type of dementia. VaD is synonymous with ageing, and its symptoms place a significant burden on the health and wellbeing of older people. Despite the identification of a substantial number of risk factors for VaD, the pathological mechanisms underpinning this disease remain to be fully elucidated. Consequently, a biogerontological imperative exists to highlight the modifiable lifestyle factors which can mitigate against the risk of developing VaD. This review will critically examine some of the factors which have been revealed to modulate VaD risk. The survey commences by providing an overview of the putative mechanisms which are associated with the pathobiology of VaD. Next, the factors which influence the risk of developing VaD are examined. Finally, emerging treatment avenues including epigenetics, the gut microbiome, and pro-longevity pharmaceuticals are discussed. By drawing this key evidence together, it is our hope that it can be used to inform future experimental investigations in this field.
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Affiliation(s)
- Amy Elizabeth Morgan
- School of Health and Sports Sciences, Hope Park, Liverpool Hope University, Liverpool L16 9JD, United Kingdom.
| | - Mark Tomás Mc Auley
- School of Science, Engineering and Environment, University of Salford Manchester, Salford M5 4NT, United Kingdom
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Fanning JP, Campbell BCV, Bulbulia R, Gottesman RF, Ko SB, Floyd TF, Messé SR. Perioperative stroke. Nat Rev Dis Primers 2024; 10:3. [PMID: 38238382 DOI: 10.1038/s41572-023-00487-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 01/23/2024]
Abstract
Ischaemic or haemorrhagic perioperative stroke (that is, stroke occurring during or within 30 days following surgery) can be a devastating complication following surgery. Incidence is reported in the 0.1-0.7% range in adults undergoing non-cardiac and non-neurological surgery, in the 1-5% range in patients undergoing cardiac surgery and in the 1-10% range following neurological surgery. However, higher rates have been reported when patients are actively assessed and in high-risk populations. Prognosis is significantly worse than stroke occurring in the community, with double the 30-day mortality, greater disability and diminished quality of life among survivors. Considering the annual volume of surgeries performed worldwide, perioperative stroke represents a substantial burden. Despite notable differences in aetiology, patient populations and clinical settings, existing clinical recommendations for perioperative stroke are extrapolated mainly from stroke in the community. Perioperative in-hospital stroke is unique with respect to the stroke occurring in other settings, and it is essential to apply evidence from other settings with caution and to identify existing knowledge gaps in order to effectively guide patient care and future research.
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Affiliation(s)
- Jonathon P Fanning
- Critical Care Research Group, The Prince Charles Hospital, Brisbane, Queensland, Australia.
- Anaesthesia & Perfusion Services, The Prince Charles Hospital, Brisbane, Queensland, Australia.
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia.
- The George Institute for Global Health, Sydney, New South Wales, Australia.
- Nuffield Department of Population Health, University of Oxford, Oxford, UK.
| | - Bruce C V Campbell
- Department of Neurology, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Richard Bulbulia
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Department of Vascular Surgery, Gloucestershire Hospitals NHS Foundation Trust, Gloucester, UK
| | | | - Sang-Bae Ko
- Department of Neurology and Department of Critical Care Medicine, Seoul National University Hospital, Seoul, Korea
| | - Thomas F Floyd
- Department of Anaesthesiology & Pain Management, Department of Cardiovascular and Thoracic Surgery, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Steven R Messé
- Department of Neurology, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
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6
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Mo C, Yan M, Tang XX, Shichino S, Bagnato G. Editorial: Cellular and molecular mechanisms of lung regeneration, repair, and fibrosis. Front Cell Dev Biol 2024; 11:1346875. [PMID: 38259517 PMCID: PMC10801291 DOI: 10.3389/fcell.2023.1346875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Affiliation(s)
- Chunheng Mo
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Mengli Yan
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
- Institute of Hematology, Henan Key Laboratory of Stem Cell Differentiation and Modification, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Henan University People’s Hospital, Zhengzhou, Henan, China
| | - Xiao Xiao Tang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangzhou Laboratory, Bio-Island, Guangzhou, China
| | - Shigeyuki Shichino
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Gianluca Bagnato
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
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Zhang S, Zhang L, Wang L, Wang H, Wu J, Cai H, Mo C, Yang J. Machine learning identified MDK score has prognostic value for idiopathic pulmonary fibrosis based on integrated bulk and single cell expression data. Front Genet 2023; 14:1246983. [PMID: 38075691 PMCID: PMC10704369 DOI: 10.3389/fgene.2023.1246983] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 11/10/2023] [Indexed: 03/09/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease that poses a significant challenge to medical professionals due to its increasing incidence and prevalence coupled with the limited understanding of its underlying molecular mechanisms. In this study, we employed a novel approach by integrating five expression datasets from bulk tissue with single-cell datasets; they underwent pseudotime trajectory analysis, switch gene selection, and cell communication analysis. Utilizing the prognostic information derived from the GSE47460 dataset, we identified 22 differentially expressed switch genes that were correlated with clinical indicators as important genes. Among these genes, we found that the midkine (MDK) gene has the potential to serve as a marker of Idiopathic pulmonary fibrosis because its cellular communicating genes are differentially expressed in the epithelial cells. We then utilized midkine and its cellular communication-related genes to calculate the midkine score. Machine learning models were further constructed through midkine and related genes to predict Idiopathic pulmonary fibrosis disease through the bulk gene expression datasets. The midkine score demonstrated a correlation with clinical indexes, and the machine learning model achieved an AUC of 0.94 and 0.86 in the Idiopathic pulmonary fibrosis classification task based on lung tissue samples and peripheral blood mononuclear cell samples, respectively. Our findings offer valuable insights into the pathogenesis of Idiopathic pulmonary fibrosis, providing new therapeutic directions and target genes for further investigation.
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Affiliation(s)
- Shichen Zhang
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Lanlan Zhang
- State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Lu Wang
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Hongqiu Wang
- Systems Hub, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, China
| | - Jiaxin Wu
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Haoyang Cai
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Chunheng Mo
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Jian Yang
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
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Naser SS, Singh D, Preetam S, Kishore S, Kumar L, Nandi A, Simnani FZ, Choudhury A, Sinha A, Mishra YK, Suar M, Panda PK, Malik S, Verma SK. Posterity of nanoscience as lipid nanosystems for Alzheimer's disease regression. Mater Today Bio 2023; 21:100701. [PMID: 37415846 PMCID: PMC10320624 DOI: 10.1016/j.mtbio.2023.100701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 07/08/2023] Open
Abstract
Alzheimer's disease (AD) is a type of dementia that affects a vast number of people around the world, causing a great deal of misery and death. Evidence reveals a relationship between the presence of soluble Aβ peptide aggregates and the severity of dementia in Alzheimer's patients. The BBB (Blood Brain Barrier) is a key problem in Alzheimer's disease because it prevents therapeutics from reaching the desired places. To address the issue, lipid nanosystems have been employed to deliver therapeutic chemicals for anti-AD therapy in a precise and targeted manner. The applicability and clinical significance of lipid nanosystems to deliver therapeutic chemicals (Galantamine, Nicotinamide, Quercetin, Resveratrol, Curcumin, HUPA, Rapamycin, and Ibuprofen) for anti-AD therapy will be discussed in this review. Furthermore, the clinical implications of the aforementioned therapeutic compounds for anti-AD treatment have been examined. Thus, this review will pave the way for researchers to fashion therodiagnostics approaches based on nanomedicine to overcome the problems of delivering therapeutic molecules across the blood brain barrier (BBB).
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Affiliation(s)
- Shaikh Sheeran Naser
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar 751024, Odisha, India
| | - Dibyangshee Singh
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar 751024, Odisha, India
| | - Subham Preetam
- Institute of Advanced Materials, IAAM, Gammalkilsvägen 18, 59053 Ulrika, Sweden
| | - Shristi Kishore
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, Jharkhand 834001, India
| | - Lamha Kumar
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India
| | - Aditya Nandi
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar 751024, Odisha, India
| | - Faizan Zarreen Simnani
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar 751024, Odisha, India
| | - Anmol Choudhury
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar 751024, Odisha, India
| | - Adrija Sinha
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar 751024, Odisha, India
| | - Yogendra Kumar Mishra
- Mads Clausen Institute, NanoSYD, University of Southern Denmark, Alison 2, 6400 Sønderborg, Denmark
| | - Mrutyunjay Suar
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar 751024, Odisha, India
| | - Pritam Kumar Panda
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120 Uppsala, Sweden
| | - Sumira Malik
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India
| | - Suresh K. Verma
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar 751024, Odisha, India
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