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Chakraborty S, Kopsco H, Evans C, Mateus-Pinilla N, Smith R. Assessing knowledge gaps and empowering Extension workers in Illinois with information on ticks and tickborne diseases through KAP surveys. Heliyon 2024; 10:e25789. [PMID: 38352775 PMCID: PMC10862665 DOI: 10.1016/j.heliyon.2024.e25789] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/19/2024] [Accepted: 02/02/2024] [Indexed: 02/16/2024] Open
Abstract
Tickborne diseases (TBDs) are increasingly prevalent in Illinois and the Upper Midwest region. People who work in occupations that require time outdoors in agricultural or natural settings, such as some Extension workers, are at risk of tick bites and TBDs. Additionally, Extension workers are often a primary source of information about ticks and TBDs in rural communities. However, there is limited information on the level of awareness about ticks and TBDs in the Extension community. The goals of this study were to sequentially i) determine the baseline awareness of Extension workers in Illinois about ticks and TBDs using a knowledge, attitudes, and practices (KAP) survey tool, ii) provide comprehensive training on ticks and TBDs to this demographic, and iii) measure the uptake of knowledge after the training intervention through a post-training survey. The study period was from June 2022 until May 2023. We received 233 pre-training and 93 paired post-training survey responses. Most survey respondents were Extension volunteers, identified as women, and were over 50 years old. Knowledge about ticks and TBDs varied. We identified several gaps in their current tick awareness, most importantly, in tick prevention measures, tick identification, and TBDs in general. TBD knowledge, attitude, and practice scores all significantly improved after training (p < 0.001), with a mean difference of 10.47, 1.49, and 2.64 points, respectively. Additionally, both Extension professionals (79.2 %) and Extension volunteers (66.7 %) were more likely to feel confident in engaging with their stakeholders on ticks and TBDs after participating in training. Poisson models revealed that higher attitude and practice scores and greater self-reported knowledge were the factors most significantly associated with higher TBD knowledge. We found that greater concern for ticks and TBD (attitudes) and adherence to science-based prevention and management methods (practices) were also associated with higher knowledge scores. To our knowledge, this is the first study in Illinois to capture Extension workers' awareness of ticks and TBDs. The results highlight Extension workers' interest in filling knowledge gaps through learning, and the importance of training Extension workers to disseminate reliable and updated information on ticks and TBDs to their constituents, a critical step in preventing TBDs.
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Affiliation(s)
- S. Chakraborty
- Program in Ecology, Evolution & Conservation Biology, University of Illinois, Urbana Champaign, 505 S Goodwin Avenue, Urbana, IL, 61801, USA
| | - H. Kopsco
- Department of Ecology, Evolution and Environmental Biology, Columbia University, 10th floor Schermerhorn Ext., 1200 Amsterdam Ave, New York, NY, 10027, USA
- Prairie Research Institute, Illinois Natural History Survey, University of Illinois, Urbana Champaign, 1816 S Oak, Champaign, IL, 61820, USA
| | - C. Evans
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana Champaign, 354 State Highway 145 N, Simpson, IL, 62985, USA
| | - N. Mateus-Pinilla
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana Champaign, 354 State Highway 145 N, Simpson, IL, 62985, USA
- Prairie Research Institute, Illinois Natural History Survey, University of Illinois, Urbana Champaign, 1816 S Oak, Champaign, IL, 61820, USA
| | - R.L. Smith
- Department of Pathobiology, University of Illinois, Urbana Champaign, 2001 S Lincoln Ave, Urbana, IL, 61802, USA
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Chakraborty J, Chakraborty S, Chakraborty S, Narayan MN. Entanglement of MAPK pathways with gene expression and its omnipresence in the etiology for cancer and neurodegenerative disorders. Biochim Biophys Acta Gene Regul Mech 2023; 1866:194988. [PMID: 37739217 DOI: 10.1016/j.bbagrm.2023.194988] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
Mitogen Activated Protein Kinase (MAPK) is one of the most well characterized cellular signaling pathways that controls fundamental cellular processes including proliferation, differentiation, and apoptosis. These cellular functions are consequences of transcription of regulatory genes that are influenced and regulated by the MAP-Kinase signaling cascade. MAP kinase components such as Receptor Tyrosine Kinases (RTKs) sense external cues or ligands and transmit these signals via multiple protein complexes such as RAS-RAF, MEK, and ERKs and eventually modulate the transcription factors inside the nucleus to induce transcription and other regulatory functions. Aberrant activation, dysregulation of this signaling pathway, and genetic alterations in any of these components results in the developmental disorders, cancer, and neurodegenerative disorders. Over the years, the MAPK pathway has been a prime pharmacological target, to treat complex human disorders that are genetically linked such as cancer, Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. The current review re-visits the mechanism of MAPK pathways in gene expression regulation. Further, a current update on the progress of the mechanistic understanding of MAPK components is discussed from a disease perspective.
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Affiliation(s)
- Joydeep Chakraborty
- Institute for Advancing Health through Agriculture, Texas A&M Agrilife, College Station, TX, USA
| | - Sayan Chakraborty
- Department of Anesthesiology, Weill Cornell School of Medicine, New York, USA
| | - Sohag Chakraborty
- Human Oncology & Pathogenesis Program (HOPP), Memorial Sloan Kettering Cancer Center, New York, USA
| | - Mahesh N Narayan
- Department of Chemistry and Biochemistry, University of Texas, El Paso, TX, USA.
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Chakraborty S, Khandelwal A, Agarwalla R, Jamir L, Bhattacharyya H. ARTIFICIAL INTELLIGENCE: CREATING NEW PARADIGMS IN THE MANAGEMENT OF NON-COMMUNICABLE DISEASES. Georgian Med News 2023:200-202. [PMID: 38236124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The role of Artificial Intelligence (AI) in medical science is growing immensely. Since AI contains features that can address both preventive and therapeutic aspects of non-communicable diseases (NCDs), it can potentially lessen the massive burden of morbidity and mortality associated with NCDs. AI can help in various ways in NCDs including predicting disease occurrence, monitoring, ensuring treatment and follow-up of patients. Low- and middle-income countries can harness the benefit of AI for the management of chronic diseases and effectively address challenges like manpower shortage, accessibility to health care, etc. However, AI needs to be used responsibly and rationally in NCDs for its maximum benefit.
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Affiliation(s)
- S Chakraborty
- 1Department of Community and Family Medicine, All India Institute of Medical Sciences (AIIMS), Guwahati, Assam, India
| | - A Khandelwal
- 2Department of Anaesthesiology, Critical Care and Pain Medicine, All India Institute of Medical Sciences (AIIMS), Guwahati, Assam, India
| | - R Agarwalla
- 1Department of Community and Family Medicine, All India Institute of Medical Sciences (AIIMS), Guwahati, Assam, India
| | - L Jamir
- 1Department of Community and Family Medicine, All India Institute of Medical Sciences (AIIMS), Guwahati, Assam, India
| | - H Bhattacharyya
- 1Department of Community and Family Medicine, All India Institute of Medical Sciences (AIIMS), Guwahati, Assam, India
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Mukherjee S, Ghosh S, Bawali S, Chatterjee R, Saha A, Sengupta A, Keswani T, Sarkar S, Ghosh P, Chakraborty S, Khamaru P, Bhattacharyya A. Administration of soluble gp130Fc disrupts M-1 macrophage polarization, dendritic cell activation, MDSC expansion and Th-17 induction during experimental cerebral malaria. Int Immunopharmacol 2023; 123:110671. [PMID: 37494839 DOI: 10.1016/j.intimp.2023.110671] [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: 05/12/2023] [Revised: 07/05/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023]
Abstract
Regulatory effect of IL-6 on various immune cells plays a crucial role during experimental cerebral malaria pathogenesis. IL-6 neutralization can restore distorted ratios of myeloid dendritic cells and plasmacytoid dendritic cells as well as the balance between Th-17 and T-regulatory cells. IL-6 can also influence immune cells through classical and trans IL-6 signalling pathways. As trans IL-6 signalling is reportedly involved during malaria pathogenesis, we focused on studying the effects of trans IL-6 signalling blockade on various immune cell populations and how they regulate ECM progression. Results show that administration of sgp130Fc recombinant chimera protein lowers the parasitemia, increases the survivability of Plasmodium berghei ANKA infected mice, and restores the distorted ratios of M1/M2 macrophage, mDC/pDC, and Th-17/Treg. IL-6 trans signalling blockade has been found to affect both expansion of myeloid derived suppressor cells (MDSCs) and expression of inflammatory markers on them during Plasmodium berghei ANKA infection indicating that trans IL-6 signalling might regulate various immune cells and their function during ECM. In this work for the first time, we delineate the effect of sgp130Fc administration on influencing the immunological changes within the host secondary lymphoid organ during ECM induced by Plasmodium berghei ANKA infection.
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Affiliation(s)
- Saikat Mukherjee
- Immunology Laboratory, Department of Zoology, University of Calcutta. 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
| | - Soubhik Ghosh
- Immunology Laboratory, Department of Zoology, University of Calcutta. 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
| | - Sriparna Bawali
- Immunology Laboratory, Department of Zoology, University of Calcutta. 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
| | - Rimbik Chatterjee
- Immunology Laboratory, Department of Zoology, University of Calcutta. 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
| | - Atreyee Saha
- Immunology Laboratory, Department of Zoology, University of Calcutta. 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
| | - Anirban Sengupta
- Department of Biomedical and Clinical Sciences, Linköping University, 58185 Linköping, Sweden
| | - Tarun Keswani
- Center for Immunological and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA 149 13th Street Charlestown, MA 02129, USA
| | - Samrat Sarkar
- Immunology Laboratory, Department of Zoology, University of Calcutta. 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
| | - Pronabesh Ghosh
- Immunology Laboratory, Department of Zoology, University of Calcutta. 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
| | - Sayan Chakraborty
- Immunology Laboratory, Department of Zoology, University of Calcutta. 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
| | - Poulomi Khamaru
- Immunology Laboratory, Department of Zoology, University of Calcutta. 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India
| | - Arindam Bhattacharyya
- Immunology Laboratory, Department of Zoology, University of Calcutta. 35, Ballygunge Circular Road, Kolkata-700019, West Bengal, India.
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Roy AM, Iyer R, Chakraborty S. The extracellular matrix in hepatocellular carcinoma: Mechanisms and therapeutic vulnerability. Cell Rep Med 2023; 4:101170. [PMID: 37652015 PMCID: PMC10518608 DOI: 10.1016/j.xcrm.2023.101170] [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: 12/20/2022] [Revised: 04/04/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023]
Abstract
The tumor microenvironment (TME) is influenced by a "disorganized" extracellular matrix (ECM) that sensitizes cancer cells toward mechanical stress, signaling, and structural alterations. In hepatocellular carcinoma (HCC), lack of knowledge about key ECM proteins driving the TME refractory to targeted therapies poses a barrier to the identification of new therapeutic targets. Herein, we discuss the contributions of various ECM components that impact hepatocytes and their surrounding support network during tumorigenesis. In addition, the underpinnings by which ECM proteins transduce mechanical signals to the liver TME are detailed. Finally, in view of the bidirectional feedback between the ECM, transformed hepatocytes, and immune cells, we highlight the potential role of the ECM disorganization process in shaping responses to immune checkpoint inhibitors and targeted therapies. Our comprehensive characterization of these ECM components may provide a roadmap for innovative therapeutic approaches to restrain HCC.
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Affiliation(s)
- Arya Mariam Roy
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Renuka Iyer
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
| | - Sayan Chakraborty
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; Program of Developmental Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263.
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Li F, Ling X, Chakraborty S, Fountzilas C, Wang J, Jamroze A, Liu X, Kalinski P, Tang DG. Role of the DEAD-box RNA helicase DDX5 (p68) in cancer DNA repair, immune suppression, cancer metabolic control, virus infection promotion, and human microbiome (microbiota) negative influence. J Exp Clin Cancer Res 2023; 42:213. [PMID: 37596619 PMCID: PMC10439624 DOI: 10.1186/s13046-023-02787-x] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/01/2023] [Indexed: 08/20/2023] Open
Abstract
There is increasing evidence indicating the significant role of DDX5 (also called p68), acting as a master regulator and a potential biomarker and target, in tumorigenesis, proliferation, metastasis and treatment resistance for cancer therapy. However, DDX5 has also been reported to act as an oncosuppressor. These seemingly contradictory observations can be reconciled by DDX5's role in DNA repair. This is because cancer cell apoptosis and malignant transformation can represent the two possible outcomes of a single process regulated by DDX5, reflecting different intensity of DNA damage. Thus, targeting DDX5 could potentially shift cancer cells from a growth-arrested state (necessary for DNA repair) to apoptosis and cell killing. In addition to the increasingly recognized role of DDX5 in global genome stability surveillance and DNA damage repair, DDX5 has been implicated in multiple oncogenic signaling pathways. DDX5 appears to utilize distinct signaling cascades via interactions with unique proteins in different types of tissues/cells to elicit opposing roles (e.g., smooth muscle cells versus cancer cells). Such unique features make DDX5 an intriguing therapeutic target for the treatment of human cancers, with limited low toxicity to normal tissues. In this review, we discuss the multifaceted functions of DDX5 in DNA repair in cancer, immune suppression, oncogenic metabolic rewiring, virus infection promotion, and negative impact on the human microbiome (microbiota). We also provide new data showing that FL118, a molecular glue DDX5 degrader, selectively works against current treatment-resistant prostate cancer organoids/cells. Altogether, current studies demonstrate that DDX5 may represent a unique oncotarget for effectively conquering cancer with minimal toxicity to normal tissues.
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Affiliation(s)
- Fengzhi Li
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA.
- Program of Developmental Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.
| | - Xiang Ling
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
- Canget BioTekpharma LLC, Buffalo, NY, 14203, USA
| | - Sayan Chakraborty
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
- Program of Developmental Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Christos Fountzilas
- Program of Developmental Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Jianmin Wang
- Department of Bioinformatics & Biostatistics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Anmbreen Jamroze
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
| | - Xiaozhuo Liu
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
| | - Pawel Kalinski
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Program of Tumor Immunology & Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Dean G Tang
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
- Program of Developmental Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
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Namgial T, Singh AK, Singh NP, Francis A, Chattopadhyay D, Voloudakis A, Chakraborty S. Correction to: Differential expression of genes during recovery of Nicotiana tabacum from tomato leaf curl Gujarat virus infection. Planta 2023; 258:51. [PMID: 37490148 PMCID: PMC10368538 DOI: 10.1007/s00425-023-04206-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Affiliation(s)
- T Namgial
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, 11855, Greece
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - A K Singh
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - N P Singh
- Laboratory of Plant Molecular Biology, National Institute of Plant Genome Research, New Delhi, 110067, India
| | - A Francis
- Laboratory of Plant Molecular Biology, National Institute of Plant Genome Research, New Delhi, 110067, India
| | - D Chattopadhyay
- Laboratory of Plant Molecular Biology, National Institute of Plant Genome Research, New Delhi, 110067, India
| | - A Voloudakis
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, 11855, Greece.
| | - S Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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Namgial T, Singh AK, Singh NP, Francis A, Chattopadhyay D, Voloudakis A, Chakraborty S. Differential expression of genes during recovery of Nicotiana tabacum from tomato leaf curl Gujarat virus infection. Planta 2023; 258:37. [PMID: 37405593 PMCID: PMC10322791 DOI: 10.1007/s00425-023-04182-4] [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] [Grants] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/10/2023] [Indexed: 07/06/2023]
Abstract
MAIN CONCLUSION Nicotiana tabacum exhibits recovery response towards tomato leaf curl Gujarat virus. Transcriptome analysis revealed the differential expression of defense-related genes. Genes encoding for cysteine protease inhibitor, hormonal- and stress-related to DNA repair mechanism are found to be involved in the recovery process. Elucidating the role of host factors in response to viral infection is crucial in understanding the plant host-virus interaction. Begomovirus, a genus in the family Geminiviridae, is reported throughout the globe and is known to cause serious crop diseases. Tomato leaf curl Gujarat virus (ToLCGV) infection in Nicotiana tabacum resulted in initial symptom expression followed by a quick recovery in the systemic leaves. Transcriptome analysis using next-generation sequencing (NGS) revealed a large number of differentially expressed genes both in symptomatic as well as recovered leaves when compared to mock-inoculated plants. The virus infected N. tabacum results in alteration of various metabolic pathways, phytohormone signaling pathway, defense related protein, protease inhibitor, and DNA repair pathway. RT-qPCR results indicated that Germin-like protein subfamily T member 2 (NtGLPST), Cysteine protease inhibitor 1-like (NtCPI), Thaumatin-like protein (NtTLP), Kirola-like (NtKL), and Ethylene-responsive transcription factor ERF109-like (NtERTFL) were down-regulated in symptomatic leaves when compared to recovered leaves of ToLCGV-infected plants. In contrast, the Auxin-responsive protein SAUR71-like (NtARPSL) was found to be differentially down-regulated in recovered leaves when compared to symptomatic leaves and the mock-inoculated plants. Lastly, Histone 2X protein like (NtHH2L) gene was found to be down-regulated, whereas Uncharacterized (NtUNCD) was up-regulated in both symptomatic as well as recovered leaves compared to the mock-inoculated plants. Taken together, the present study suggests potential roles of the differentially expressed genes that might govern tobacco's susceptibility and/or recovery response towards ToLCGV infection.
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Affiliation(s)
- T Namgial
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, 11855, Greece
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - A K Singh
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - N P Singh
- Laboratory of Plant Molecular Biology, National Institute of Plant Genome Research, New Delhi, 110067, India
| | - A Francis
- Laboratory of Plant Molecular Biology, National Institute of Plant Genome Research, New Delhi, 110067, India
| | - D Chattopadhyay
- Laboratory of Plant Molecular Biology, National Institute of Plant Genome Research, New Delhi, 110067, India
| | - A Voloudakis
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, 11855, Greece.
| | - S Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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Mokhtari RB, Ashayeri N, Baghaie L, Sambi M, Satari K, Baluch N, Bosykh DA, Szewczuk MR, Chakraborty S. The Hippo Pathway Effectors YAP/TAZ-TEAD Oncoproteins as Emerging Therapeutic Targets in the Tumor Microenvironment. Cancers (Basel) 2023; 15:3468. [PMID: 37444578 DOI: 10.3390/cancers15133468] [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: 05/09/2023] [Revised: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Various cancer cell-associated intrinsic and extrinsic inputs act on YAP/TAZ proteins to mediate the hyperactivation of the TEAD transcription factor-based transcriptome. This YAP/TAZ-TEAD activity can override the growth-limiting Hippo tumor-suppressor pathway that maintains normal tissue homeostasis. Herein, we provide an integrated summary of the contrasting roles of YAP/TAZ during normal tissue homeostasis versus tumor initiation and progression. In addition to upstream factors that regulate YAP/TAZ in the TME, critical insights on the emerging functions of YAP/TAZ in immune suppression and abnormal vasculature development during tumorigenesis are illustrated. Lastly, we discuss the current methods that intervene with the YAP/TAZ-TEAD oncogenic signaling pathway and the emerging applications of combination therapies, gut microbiota, and epigenetic plasticity that could potentiate the efficacy of chemo/immunotherapy as improved cancer therapeutic strategies.
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Affiliation(s)
- Reza Bayat Mokhtari
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Neda Ashayeri
- Division of Hematology and Oncology, Department of Pediatrics, Ali-Asghar Children Hospital, Iran University of Medical Science, Tehran 1449614535, Iran
| | - Leili Baghaie
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Manpreet Sambi
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Kosar Satari
- Division of Hematology and Oncology, Department of Pediatrics, Ali-Asghar Children Hospital, Iran University of Medical Science, Tehran 1449614535, Iran
| | - Narges Baluch
- Department of Immunology and Allergy, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Dmitriy A Bosykh
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Myron R Szewczuk
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Sayan Chakraborty
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
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Pandey A, Bhushan R, Rohilla A, Chakraborty S, Singh RP, Ojha S, Mehta D, Kumar S, Chamoli SK. Fabrication of thin Molybdenum backed target using rolling method. Appl Radiat Isot 2023; 199:110860. [PMID: 37290268 DOI: 10.1016/j.apradiso.2023.110860] [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: 09/04/2022] [Revised: 02/15/2023] [Accepted: 04/08/2023] [Indexed: 06/10/2023]
Abstract
A successful attempt was made to fabricate a thin foil of natural Mo target on a thick Au backing with Indium in between to improve adhesion between the foils. Rolling at elevated temperature was considered to fabricate Mo foil while gold foil was fabricated employing conventional rolling technique. The heating of Mo foil under natural environment lead to the oxidation or carbonization on foil surface which was confirmed through Energy Dispersive X-ray Spectroscopy (EDS) measurements. Indium of thickness ∼86μg/cm2 was evaporated on Mo foil to improve adhesion between Mo and Au foils. The characterization of fabricated thin Mo foil was done using the Energy Dispersive X-ray Spectroscopy (EDS) and the Scanning Electron microscope (SEM) techniques. Thickness measurement of the target (Mo-Au) was done using Energy Dispersive X-ray Fluorescence (EDXRF) technique, in the measurements the thickness of the Mo foil and of gold backing are found out to be 1.3 mg/cm2 and 9 mg/cm2 respectively.
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Affiliation(s)
- Anand Pandey
- Department of Physics & Astrophysics, University of Delhi, New Delhi, India
| | - Ravi Bhushan
- Department of Physics & Astrophysics, University of Delhi, New Delhi, India
| | - Aman Rohilla
- Institute of Space Sciences, Shandong University, Weihai 264209, People's Republic of China
| | - S Chakraborty
- Variable Energy Cyclotron Centre, Kolkata 700064, India
| | - R P Singh
- Inter University Accelerator Centre, Aruna Asaf Ali Marg, New Delhi, India
| | - Sunil Ojha
- Inter University Accelerator Centre, Aruna Asaf Ali Marg, New Delhi, India
| | - D Mehta
- Department of Physics, Punjab University, Chandigarh, India
| | - Sanjeev Kumar
- Goswami Ganesh Dutta Sanatan Dharma College, Sector 32 Chandigarh, India
| | - S K Chamoli
- Department of Physics & Astrophysics, University of Delhi, New Delhi, India.
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Chatterjee S, Das A, Paul D, Chakraborty S, Choudhury P. Utilization of fleshing waste of leather processing for the growth of zygomycetes: A new substrate for economical production of bio-polymer chitosan. J Environ Manage 2023; 343:118141. [PMID: 37245305 DOI: 10.1016/j.jenvman.2023.118141] [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] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/16/2023] [Accepted: 05/08/2023] [Indexed: 05/30/2023]
Abstract
A simple scalable method has been developed to obtain protein hydrolysate from fleshing waste generated during leather processing. UV-Vis, FTIR and Solid State C13 NMR analyses identified that prepared protein hydrolysate is basically collagen hydrolysate. DLS and MALDI-TOF-MS spectra indicated that the prepared protein hydrolysate is mostly comprised of di- and tri-peptides and less poly-dispersed than the standard commercial product. A combination of 0.3% Yeast extract, 1% Protein Hydrolysate (PHz) and 2% Glucose is found to be the most efficient nutrient composition for the fermentative growth of three well-known chitosan producing zygomycetes group of fungi. Mucor sp. showed highest yield of biomass (2.74 g/L) as well as chitosan (335 mg/L). Biomass and chitosan yield for Rhizopus oryzae were found 1.53 g/L; 239 mg/L. Same for Absidia coerulea were 2.05 g/L and 212 mg/L, respectively. This work shows promising prospect of utilization of fleshing waste of leather processing for the low-cost production of industrially important biopolymer chitosan.
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Affiliation(s)
- Sandipan Chatterjee
- Regional Center Kolkata, CSIR-Central Leather Research Institute 3/1C, Matheswar Tala Road, Kolkata, 700046, India.
| | - Ashmita Das
- Regional Center Kolkata, CSIR-Central Leather Research Institute 3/1C, Matheswar Tala Road, Kolkata, 700046, India
| | - Debasmita Paul
- Regional Center Kolkata, CSIR-Central Leather Research Institute 3/1C, Matheswar Tala Road, Kolkata, 700046, India
| | - Sayan Chakraborty
- Regional Center Kolkata, CSIR-Central Leather Research Institute 3/1C, Matheswar Tala Road, Kolkata, 700046, India
| | - Poushali Choudhury
- Regional Center Kolkata, CSIR-Central Leather Research Institute 3/1C, Matheswar Tala Road, Kolkata, 700046, India
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12
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Kumari S, Chakraborty S, Ahmad M, Kumar V, Tailor PB, Biswal BK. Identification of probable inhibitors for the DNA polymerase of the Monkeypox virus through the virtual screening approach. Int J Biol Macromol 2023; 229:515-528. [PMID: 36584781 PMCID: PMC9794403 DOI: 10.1016/j.ijbiomac.2022.12.252] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 10/06/2022] [Revised: 12/09/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022]
Abstract
Given the paucity of antiviral treatments for monkeypox disease, caused by the Monkeypox virus (MPXV), there is a pressing need for the development/identification of new drugs to treat the infection. MPXV possesses a linear dsDNA genome that is replicated by a DNA replication complex of which DNA polymerase (DPol) forms an important component. Owing to the importance of DPol in the viral life cycle, identifying/designing small molecules abolishing its function could yield new antivirals. In this study, we first used the AlphaFold artificial intelligence program to model the 3D structure of the MPXV DPol; like the fold of DPol from other organisms, the MPXV DPol structure has the characteristic exonuclease, thumb, palm, and fingers sub-domains arrangement. Subsequently, we have identified several inhibitors through virtual screening of ZINC and antiviral libraries. Molecules with phenyl scaffold along with alanine-based and tetrazole-based molecules showed the best docking score of -8 to -10 kcal/mol. These molecules bind in the palm and fingers sub-domains interface region, which partially overlaps with the DNA binding path. The delineation of DPol/inhibitor interactions showed that majorly active site residues ASP549, ASP753, TYR550, ASN551, SER552, and ASN665 interact with the inhibitors. These compounds exhibit good Absorption, Distribution, Metabolism and Excretion properties.
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Affiliation(s)
- Swati Kumari
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sayan Chakraborty
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Mohammed Ahmad
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Varun Kumar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | | | - Bichitra K Biswal
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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13
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Boila LD, Ghosh S, Bandyopadhyay SK, Jin L, Murison A, Zeng AGX, Shaikh W, Bhowmik S, Muddineni SSNA, Biswas M, Sinha S, Chatterjee SS, Mbong N, Gan OI, Bose A, Chakraborty S, Arruda A, Kennedy JA, Mitchell A, Lechman ER, Banerjee D, Milyavsky M, Minden MD, Dick JE, Sengupta A. KDM6 demethylases integrate DNA repair gene regulation and loss of KDM6A sensitizes human acute myeloid leukemia to PARP and BCL2 inhibition. Leukemia 2023; 37:751-764. [PMID: 36720973 DOI: 10.1038/s41375-023-01833-z] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 02/01/2023]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous, aggressive malignancy with dismal prognosis and with limited availability of targeted therapies. Epigenetic deregulation contributes to AML pathogenesis. KDM6 proteins are histone-3-lysine-27-demethylases that play context-dependent roles in AML. We inform that KDM6-demethylase function critically regulates DNA-damage-repair-(DDR) gene expression in AML. Mechanistically, KDM6 expression is regulated by genotoxic stress, with deficiency of KDM6A-(UTX) and KDM6B-(JMJD3) impairing DDR transcriptional activation and compromising repair potential. Acquired KDM6A loss-of-function mutations are implicated in chemoresistance, although a significant percentage of relapsed-AML has upregulated KDM6A. Olaparib treatment reduced engraftment of KDM6A-mutant-AML-patient-derived xenografts, highlighting synthetic lethality using Poly-(ADP-ribose)-polymerase-(PARP)-inhibition. Crucially, a higher KDM6A expression is correlated with venetoclax tolerance. Loss of KDM6A increased mitochondrial activity, BCL2 expression, and sensitized AML cells to venetoclax. Additionally, BCL2A1 associates with venetoclax resistance, and KDM6A loss was accompanied with a downregulated BCL2A1. Corroborating these results, dual targeting of PARP and BCL2 was superior to PARP or BCL2 inhibitor monotherapy in inducing AML apoptosis, and primary AML cells carrying KDM6A-domain mutations were even more sensitive to the combination. Together, our study illustrates a mechanistic rationale in support of a novel combination therapy for AML based on subtype-heterogeneity, and establishes KDM6A as a molecular regulator for determining therapeutic efficacy.
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Affiliation(s)
- Liberalis Debraj Boila
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Subhadeep Ghosh
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Subham K Bandyopadhyay
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Liqing Jin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Andy G X Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Wasim Shaikh
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Satyaki Bhowmik
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | | | - Mayukh Biswas
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Irving Cancer Research Center, Columbia University Medical Center, New York, NY, 10032, USA
| | - Sayantani Sinha
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Shankha Subhra Chatterjee
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Nathan Mbong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Anwesha Bose
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Sayan Chakraborty
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India
| | - Andrea Arruda
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - James A Kennedy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.,Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, ON, M5G 2C4, Canada.,Department of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Amanda Mitchell
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Eric R Lechman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Debasis Banerjee
- Park Clinic, Gorky Terrace and Ramakrishna Mission Seva Pratisthan, Kolkata, 700017, West Bengal, India
| | - Michael Milyavsky
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada.,Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, ON, M5G 2C4, Canada.,Department of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Amitava Sengupta
- Stem Cell & Leukemia Lab, CSIR-Indian Institute of Chemical Biology, IICB-Translational Research Unit of Excellence, Salt Lake, Kolkata, 700091, West Bengal, India. .,Academy of Scientific & Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India. .,CSIR-IICB-Cancer Biology & Inflammatory Disorder Division, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India.
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14
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Baker J, Chakraborty S, Buccoliero R, Thakur S. Wilson's disease - a tricky diagnosis on the acute take. Acute Med 2023; 22:96-100. [PMID: 37306135 DOI: 10.52964/amja.0941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Wilson's disease is a rare genetic disorder that affects copper metabolism in the body, leading to excess copper accumulation in various organs, including the liver and brain. It often presents to both primary and secondary care, with a combination of liver disease and neurological or psychiatric symptoms, but the presentation can be highly variable. Early recognition and treatment of Wilson's disease is important to prevent critical hepatic and neurological complications. In this case report, we describe the presentation of an 18-year-old male university student with a combination of dysphagia, tremors, and slurred speech, which progressed over several months. Through a series of investigations, the patient was diagnosed with Wilson's disease and received appropriate treatment. This report highlights the importance of considering Wilson's disease in patients with a wide range of symptoms and the need for a pragmatic approach to diagnosis, including routine and additional testing as necessary.
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Affiliation(s)
- J Baker
- Harrogate and District NHS Foundation Trust
| | | | | | - S Thakur
- Harrogate and District NHS Foundation Trust
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15
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Chakraborty S, Mann IR, Watt CEJ, Rae IJ, Olifer L, Ozeke LG, Sandhu JK, Mauk BH, Spence H. Intense chorus waves are the cause of flux-limiting in the heart of the outer radiation belt. Sci Rep 2022; 12:21717. [PMID: 36522393 PMCID: PMC9755534 DOI: 10.1038/s41598-022-26189-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Chorus waves play a key role in outer Van Allen electron belt dynamics through cyclotron resonance. Here, we use Van Allen Probes data to reveal a new and distinct population of intense chorus waves excited in the heart of the radiation belt during the main phase of geomagnetic storms. The power of the waves is typically ~ 2-3 orders of magnitude greater than pre-storm levels, and are generated when fluxes of ~ 10-100 keV electrons approach or exceed the Kennel-Petschek limit. These intense chorus waves rapidly scatter electrons into the loss cone, capping the electron flux to a value close to the limit predicted by Kennel and Petschek over 50 years ago. Our results are crucial for understanding the limits to radiation belt fluxes, with accurate models likely requiring the inclusion of this chorus wave-driven flux-limiting process, that is independent of the acceleration mechanism or source responsible for enhancing the flux.
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Affiliation(s)
- S. Chakraborty
- grid.42629.3b0000000121965555Department of Mathematics, Physics and Electrical Engineering, Northumbria University, Newcastle upon Tyne, UK
| | - I. R. Mann
- grid.42629.3b0000000121965555Department of Mathematics, Physics and Electrical Engineering, Northumbria University, Newcastle upon Tyne, UK ,grid.17089.370000 0001 2190 316XDepartment of Physics, University of Alberta, Edmonton, AB Canada
| | - C. E. J. Watt
- grid.42629.3b0000000121965555Department of Mathematics, Physics and Electrical Engineering, Northumbria University, Newcastle upon Tyne, UK
| | - I. J. Rae
- grid.42629.3b0000000121965555Department of Mathematics, Physics and Electrical Engineering, Northumbria University, Newcastle upon Tyne, UK
| | - L. Olifer
- grid.17089.370000 0001 2190 316XDepartment of Physics, University of Alberta, Edmonton, AB Canada
| | - L. G. Ozeke
- grid.17089.370000 0001 2190 316XDepartment of Physics, University of Alberta, Edmonton, AB Canada
| | - J. K. Sandhu
- grid.42629.3b0000000121965555Department of Mathematics, Physics and Electrical Engineering, Northumbria University, Newcastle upon Tyne, UK
| | - B. H. Mauk
- grid.21107.350000 0001 2171 9311Applied Physics Laboratory, Johns Hopkins University, Laurel, MD USA
| | - H. Spence
- grid.167436.10000 0001 2192 7145Institute for the Study of Earth, Oceans, and Space, University of New Hampshire, Durham, NH USA
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16
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Dorjee L, Chakraborty S, Bhatia A, Manu CB, Medhi R. Migrated and Impacted Foreign Body of Retropharyngeal Space: A Case Report. Indian J Otolaryngol Head Neck Surg 2022; 74:5664-5667. [PMID: 36742513 PMCID: PMC9895500 DOI: 10.1007/s12070-021-02928-8] [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: 12/21/2020] [Accepted: 10/14/2021] [Indexed: 02/07/2023] Open
Abstract
Foreign body upper aerodigestive tract is a common presentation but foreign body migrating into retropharyngeal space is not only uncommon, but its management also differs and is challenging too. Here we present a case of a foreign body migrating into the retropharyngeal space which was removed intraorally. A 28- year old male patient presented with complaints of pain while swallowing following consumption of sausage and pork two days earlier to the onset of symptoms. X-Ray Neck AP and lateral view were done which revealed a thin metallic foreign body at the level of the T4 vertebra. Upper gastrointestinal endoscopy and rigid esophagoscopy were done in which a foreign body was not visualized in the esophageal lumen. NCCT neck was done which gave precise location and was removed intraorally with the patient in Rose position. A repeat x-ray was done on the 5th day which revealed no foreign body, the patient was discharged on the 7th day. Although the upper aerodigestive tract foreign body is common, foreign body migrating to the posterior pharyngeal wall or into the retropharyngeal space is not common and it is difficult to remove a migrated foreign body many cases requiring open procedures, thoracoscopy, thoracotomy.
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Affiliation(s)
- L. Dorjee
- Dept. of Otorhinolaryngology, NEIGRIHMS, Shillong, Meghalaya 793018 India
| | - S. Chakraborty
- Dept. of Otorhinolaryngology, NEIGRIHMS, Shillong, India
| | - A. Bhatia
- Dept. of Otorhinolaryngology, NEIGRIHMS, Shillong, India
| | - C. B. Manu
- Dept. of Otorhinolaryngology, NEIGRIHMS, Shillong, India
| | - R. Medhi
- Dept. of Otorhinolaryngology, NEIGRIHMS, Shillong, India
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17
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Khamaru P, Chakraborty S, Bhattacharyya A. AMPK activator AICAR in combination with anti-mouse IL10 mAb restores the functionality of intra-tumoral Tfh cells in the 4T1 mouse model. Cell Immunol 2022; 382:104639. [PMID: 36375313 DOI: 10.1016/j.cellimm.2022.104639] [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: 05/03/2022] [Revised: 10/12/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022]
Abstract
4T1 cell-mediated TNBC breast cell carcinoma is a highly malignant mice tumor model which resembles an advanced stage of breast cancer in humans. Tumor progression occurs depending on the intra-tumoral balance of pro- and anti- tumorigenic immune cells. Enhancement of T-cell-mediated anti-tumor immunity will be advantageous for inhibiting tumor progression and improving the efficacy of cancer therapy. This study is focused on alleviating suppressed anti-tumor immune response by improving CD4+ T follicular helper cell (Tfh) response in 4T1 mice. We employed anti-IL10 mAb along with metabolic drugs 2-deoxy-D-glucose (2DG) which inhibits the glycolytic pathway and Cpt1a inhibitor Etomoxir which inhibits FAO. AMPK activator AICAR with or without anti-IL10 mAb was also used to ameliorate metabolic stress and exhaustion faced by immune cells. Our results demonstrate that synergistic treatment with 2DG/Etomoxir + anti-IL10 mAb induced Tfh cell, memory B, and GC B cell response more potently compared to treatment with 2DG or Etomoxir treatment alone as observed in several LNs and tumor tissue of 4T1 mouse. However, AICAR + anti-IL10 mAb increased the frequency of intratumoral Tfh cells, simultaneously downregulated Tfr cells; and improved humoral response by stimulating upregulation of memory B, GC B, and plasmablasts in tumor-draining, axillary, and mesenteric LNs of 4T1 mouse.
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Affiliation(s)
- Poulomi Khamaru
- Immunology Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, West Bengal, India
| | - Sayan Chakraborty
- Immunology Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, West Bengal, India
| | - Arindam Bhattacharyya
- Immunology Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, West Bengal, India.
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18
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Hajra A, Patel N, Bandyopadhyay D, Chakraborty S, Goel A, Gupta R, Amgai B, Malik A. Incidence of in-hospital all-cause mortality, resource utilization and complications in patients with adult congenital heart disease undergoing TAVR-a national inpatient sample study. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.1595] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
The prevalence of congenital heart disease (CHD) in adults in the United States is approximately 1.4 million. (1) With the advancement in diagnostic modalities and advanced treatments, including minimally invasive techniques, the life expectancy of individuals with CHD has greatly improved. (2) As these patients enter the 8th decade of their lives, the risk of calcification and aortic stenosis increases like the population without CHD. Current evidence supports transcatheter aortic valve replacement (TAVR) over surgical aortic valve replacement in individuals with moderate to high surgical risk. (3) Adults with acyanotic CHD (ACHD) with a higher risk for surgical complications are candidates for consideration of TAVR. There are sparse data about the cardiovascular outcome in these patients.
Purpose
With this National inpatient sample (NIS) study, the authors have shown the incidence of in-hospital all-cause mortality, resource utilization, and complications in adult patients with ACHD undergoing TAVR.
Methods
NIS 2016–2018 were utilized to conduct the study. Analyses were performed using STATA, version 16.0. Using appropriate ICD-10-PCS codes, authors identified adult patients with ACHD undergoing TAVR. The primary outcome of the study is to identify the impact of ACHD on all-cause in-hospital mortality and complications. Secondary outcomes of interest were resource utilization.
Results
134,170 patients were identified who had TAVR done between 2016–2018. Patients aged ≤18 years were excluded (N=25). Out of 134,170 patients that underwent TAVR, 1,170 (0.87%) were noted to have ACHD. Using the greedy algorithm, 1,115 matched pairs were generated. The ACHD group had a higher burden of co-morbidities including atrial fibrillation (46.2% vs. 38.8%, p=0.016), pulmonary hypertension (27.4% vs. 17.5%, p<0.001), metabolic syndrome (1.3% vs. 0.3%, p=0.005), peripheral vascular disease (29.5% vs. 24.1%, p=0.049), alcohol use disorder (3.0% vs. 1.3%, p=0.018), coagulation disorder (22.7% vs. 12.8%, p<0.001), drug abuse (1.3% vs. 0.4%, p=0.043), liver disease (7.3% vs. 3.1%, p<0.001) and electrolyte disturbances (20.5% vs. 14.9%, p=0.017). We also noted a possible trend towards higher complication odds (cardiac complications such as the need for pericardial drain or cardiac implantable electronic device and cardiac arrest) in patients with ACHD undergoing TAVR without statistical significance based on multivariate analysis. On propensity matching, no difference was found in the incidence of overall cardiac complications between patients with ACHD and patients without ACHD, except STEMI (OR 4.16, 95% CI, 1.08–16.00, p=0.038).
Conclusion(s)
The study points towards the possible safety of pursuing TAVR in ACHD patients provided adequate technical support and operator competency.
Funding Acknowledgement
Type of funding sources: None.
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Affiliation(s)
- A Hajra
- Albert Einstein College of Medicine, Internal Medicine , Bronx , United States of America
| | - N Patel
- University of Kansas Hospital, Cardiology , Kansas City , United States of America
| | - D Bandyopadhyay
- New York Medical College, Cardiology , Valhalla , United States of America
| | - S Chakraborty
- Miami Valley Hospital, Internal Medicine , Columbus , United States of America
| | - A Goel
- New York Medical College, Cardiology , Valhalla , United States of America
| | - R Gupta
- Lehigh Valley Hospital, Cardiology , Allentown , United States of America
| | - B Amgai
- The Wright Center for Graduate Medical Education, Internal Medicine , Scranton , United States of America
| | - A Malik
- New York Medical College, Cardiology , Valhalla , United States of America
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19
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Goel A, Malik A, Bandyopadhyay D, Chakraborty S, Gupta R, Hajra A, Abbott JD, Ahmad H. Same-day discharge following transcatheter aortic valve replacement: a propensity-matched analysis from national readmission database. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.1582] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
The length of hospital stay following transcatheter aortic valve replacement (TAVR) has decreased in recent years, and next-day discharge strategy is being increasingly adopted in some centers. Whether it is safe to further expedite discharge post-TAVR in selected patients by allowing discharge on the same day as the procedure remains unknown. In addition to potentially decreasing hospitalization costs, it could also limit the inpatient footprint and strain on healthcare resources.
Purpose
The purpose of our study was to compare the 30-day readmission rate in patients receiving TAVR who were discharged the same day (same-day discharge or SDD group) with those who were discharged on a different day (different-day discharge or DDD group). Additionally, we aimed to identify risk factors for readmission after TAVR.
Methods
We used the United States Nationwide Readmission Database to identify all adults who underwent elective TAVR in the years 2015–2019. The primary outcome of this study was all-cause 30-day readmission rate. The secondary outcomes were total hospital costs for the index admission, and risk factors for 30-day readmission. Propensity score matching was conducted to compare the SDD and DDD groups. Independent risk factors of 30-day readmission were identified using multivariate Cox proportional hazards regression analysis of the unmatched cohort.
Results
Of the 196,618 patients who received TAVR (mean age 79.5±8.4 years, 45.0% females), 245 (0.12%) patients were discharged on the same day they received TAVR (SDD group), and the remaining 196,373 were discharged on a different day (DDD group). In the DDD group, the median length of hospital stay was 2 days (interquartile range 1–4 days). A 1:3 propensity score analysis generated a matched cohort including 245 and 889 patients in the SDD and DDD groups, respectively. The 30-day readmission rate was similar between the SDD and DDD groups (11.0% versus 10.8%, hazard ratio [HR] 1.01, 95% confidence interval [CI] 0.59–1.71, p=0.989). Hospitalization costs were significantly lower in the SDD group than the DDD group ($37,811±18,029 versus $49,130±27,007, p<0.001) (see Picture 1). Age, female gender, history of diabetes, chronic kidney disease, chronic pulmonary disease, oxygen use, prior stroke, peripheral vascular disease, anemia, liver disease, and cancer were found to be independent risk factors for 30-day readmission after TAVR (see Picture 2).
Conclusion
In this large nationwide database analysis, patients receiving uncomplicated TAVR who were discharged on the same day as the procedure had a similar all-cause 30-day readmission rate and significantly lower hospital costs compared to those discharged on a different day. These results indicate that same-day discharge after TAVR may be a safe and feasible option in carefully selected patients.
Funding Acknowledgement
Type of funding sources: None.
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Affiliation(s)
- A Goel
- Westchester Medical Center , Valhalla , United States of America
| | - A Malik
- Westchester Medical Center , Valhalla , United States of America
| | - D Bandyopadhyay
- Westchester Medical Center , Valhalla , United States of America
| | - S Chakraborty
- Miami Valley Hospital , Columbus , United States of America
| | - R Gupta
- Lehigh Valley Hospital , Allentown , United States of America
| | - A Hajra
- Jacobi Medical Center/Albert Einstein College of Medicine , New York , United States of America
| | - J D Abbott
- Brown University , Providence , United States of America
| | - H Ahmad
- Westchester Medical Center , Valhalla , United States of America
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Agarwala V, MV C, Daga A, Basu M, Ganguly M, Kumar S, Mandal K, Chakraborty S, Sunani D, Choudhary N, Basu K, Das S, Mallik S. 1578P Scalp cooling system for prevention of chemotherapy induced alopecia: A single center one-year prospective observational study. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1671] [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: 11/01/2022] Open
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21
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Chakraborty S, Jain A, Sarmah SP. An integrated mathematical model based on grey optimal ranking for supplier selection considering pandemic situation. OPSEARCH 2022. [PMCID: PMC9400579 DOI: 10.1007/s12597-022-00601-4] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Optimal selection and allocation of suppliers are crucial decisions for an organization and it becomes more critical when the firm faces disruptive events. The recent outbreak of COVID-19 has led to massive supply disruptions in a supply chain. This paper aims to address the supplier selection and allocation problem of manufacturing firms under pandemic environment. In this study, a novel Mixed Integer Linear Programming (MILP) model integrated with grey optimal ranking of suppliers considering factors related to pandemic situation is proposed. The methodology is implemented in two subsequent stages. In the first stage, Grey Relational Analysis is adopted to determine the grey possibility scoring, and in the second stage, a supplier selection model is proposed to integrate the grey scoring to a MILP model to determine optimal allocation of suppliers. The paper presents a numerical study to demonstrate the proposed model and sensitivity analysis is conducted to deduce key managerial insights regarding the factors affecting the allocation under pandemic situation. Further, the illustration demonstrates how the proposed method integrates the expert ranking based approach and the cost minimization approach. The study is generic in nature and provides useful directions for practitioners involved in supplier selection in manufacturing organizations.
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Affiliation(s)
- Sayan Chakraborty
- Department of Operations and IT, ICFAI Business School Hyderabad, ICFAI Foundation for Higher Education, Hyderabad, India
| | - Akshat Jain
- Department of Industrial and Systems Engineering, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - S. P. Sarmah
- Department of Industrial and Systems Engineering, Indian Institute of Technology Kharagpur, Kharagpur, India
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22
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Chakraborty S, Bhattacharya S. Remote working in India during the COVID-19 crisis. CM 2022. [DOI: 10.18137/cardiometry.2022.23.369380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
India has been reeling from the effects of the COVID-19 pandemic and has enforced a nationwide lockdown to ensure the spread is contained, and the situation is under control. This has paved the way for corporate across the length and breadth of the country to embrace remote working as the only feasible option to continue their business. Earlier, it used to be the IT sector employees and a handful of employees from other industries who had the privilege of working remotely. Now, with remote working becoming the norm, we aim to capture how it has affected people’s working style and if interactions with family at home during work hours affect their work. We also aim to find out whether performance takes a hit due to the absence of co-workers.A questionnaire was filled up by employees working from home that sought out details about their working style, daily routine, interactions with other people (family member or colleague), and their thoughts on the remote working lifestyle. The major factors were measured on a five-point Likert scale.People work for a longer time when working from home, due to distractions caused by interactions with family members or other people and also the absence of colleagues causes problems to be solved at a slower pace. Women work longer hours when compared to men, additionally due to household chores. The absence of colleagues coupled with distractions at home cause people to prefer working from the office rather than from home. This study would help identify what sort of impact remote working has on an employee’s performance and how it can affect the working style.The paper analyses the effect of remote working and the presence of family at home on an employee’s performance.
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23
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Chakraborty H, Kayal T, Lianthuamluaia L, Sarkar UK, Das AK, Chakraborty S, Sahoo BK, Mondal K, Mandal S, Das BK. Use of geographical information systems (GIS) in assessing ecological profile, fish community structure and production of a large reservoir of Himachal Pradesh. Environ Monit Assess 2022; 194:643. [PMID: 35930070 DOI: 10.1007/s10661-022-10292-5] [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: 01/21/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
The present study demonstrates the spatial analysis and mapping of fish and different measures of environmental parameters and fish diversity of Pong reservoir, Himachal Pradesh, using Kriging spatial interpolation methods for geographical information system mapping. Seasonal data on environmental parameters, potential fish habitat and fish diversity was collected from lentic (dam), lentic (reservoir), transitional and lotic zone of the reservoir.. Important environmental parameters like water temperature, dissolved oxygen, electrical conductivity, water depth and transparency showed variations across the different zones of the reservoir. The sediment of the reservoir was sandy clay loam in nature as per texture analysis. Fish species richness, Shannon index and evenness index showed a similarity of the lotic and lentic (reservoir) zones of the reservoir. Six potential fish breeding grounds were identified in the reservoir indicating high conservation significance. The analysis of data showed a declining trend in fish production from 456.9 tonnes during the decade 1976-1987 to 347.91 tonnes during 2009-2020. The factors like anthropogenic climate change, predation of a stocked fish juvenile by water birds, undersized fish stocking and unscientific management are the probable reasons for the decreasing fish production. The spatial variation pattern of the water spread area, environmental parameters, fish catch and potential fish breeding grounds depicted in the GIS platform can be used as an important information base by the policy makers for fisheries management. The stocking of large size fish as a stocking material and adequate protection of the potential fish breeding grounds are the key advisories for the sustainable enhancement of fisheries as well as conservation.
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Affiliation(s)
- H Chakraborty
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - T Kayal
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - L Lianthuamluaia
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - U K Sarkar
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - A K Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - S Chakraborty
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - B K Sahoo
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - K Mondal
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - S Mandal
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - B K Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, India.
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24
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Rathore P, Chakraborty S, Gupta M, Sarmah SP. Towards a sustainable organic waste supply chain: A comparison of centralized and decentralized systems. J Environ Manage 2022; 315:115141. [PMID: 35525041 DOI: 10.1016/j.jenvman.2022.115141] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 12/15/2021] [Revised: 04/12/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
Proper disposal of Municipal Solid (MSW) waste is an important issue as it causes land, air, and water pollution. Organic MSW provides a habitat environment to insects and often it spreads dangerous diseases. Major reasons identified behind this as the non-separation of MSW at the source and lack of facilities (bins) in the appropriate place for collection of wastes. The present study has proposed an integrated three-stage model to provide a solution to the problem of (i) allocation of the bin for waste collection, (ii) allocation and comparison of centralized and decentralized composting plants, and finally, (iii) vehicle routing for waste collection. The proposed generic model is applied to an Indian city, Bilaspur located in the state of Chhattisgarh. From the results, it is observed that the first stage model provides an optimal number of bins required and allocation of it at minimum cost. Taking it as input for the second stage model, it identifies the best locations for centralized and decentralized composting plants. The result also reveals that decentralized composting plants are more economical than centralized plants. Finally, the third stage of the model identifies the vehicle routing for the waste collection considering both centralized and decentralized plants to minimize the cost. Further, sensitivity analysis is carried out on collection rate and participation percentage parameters to draw additional insights for better management of MSW.
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Affiliation(s)
- Pradeep Rathore
- School of Business, Woxsen University, Hyderabad, 502345, India.
| | - Sayan Chakraborty
- ICFAI Business School Hyderabad, ICFAI Foundation for Higher Education, Hyderabad, 501203, India.
| | - Mihir Gupta
- Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
| | - S P Sarmah
- Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
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25
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Chakraborty S, Khamaru P, Bhattacharyya A. Regulation of immune cell metabolism in health and disease: Special focus on T and B cell subsets. Cell Biol Int 2022; 46:1729-1746. [PMID: 35900141 DOI: 10.1002/cbin.11867] [Citation(s) in RCA: 4] [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: 10/30/2021] [Revised: 04/03/2022] [Accepted: 07/05/2022] [Indexed: 12/15/2022]
Abstract
Metabolism is a dynamic process and keeps changing from time to time according to the demand of a particular cell to meet its bio-energetic requirement. Different immune cells rely on distinct metabolic programs which allow the cell to balance its requirements for energy, molecular biosynthesis, and effector activity. In the aspect of infection and cancer immunology, effector T and B cells get exhausted and help tumor cells to evade immunosurveillance. On the other hand, T cells become hyperresponsive in the scenario of autoimmune diseases. In this article, we have explored the uniqueness and distinct metabolic features of key CD4+ T and B helper cell subsets, CD4+ T, B regulatory cell subsets and CD8+ T cells regarding health and disease. Th1 cells rely on glycolysis and glutaminolysis; inhibition of these metabolic pathways promotes Th1 cells in Treg population. However, Th2 cells are also dependent on glycolysis but an abundance of lactate within TME shifts their metabolic dependency to fatty acid metabolism. Th17 cells depend on HIF-1α mediated glycolysis, ablation of HIF-1α reduces Th17 cells but enhance Treg population. In contrast to effector T cells which are largely dependent on glycolysis for their differentiation and function, Treg cells mainly rely on FAO for their function. Therefore, it is of utmost importance to understand the metabolic fates of immune cells and how it facilitates their differentiation and function for different disease models. Targeting metabolic pathways to restore the functionality of immune cells in diseased conditions can lead to potent therapeutic measures.
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Affiliation(s)
- Sayan Chakraborty
- Immunology Laboratory, Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
| | - Poulomi Khamaru
- Immunology Laboratory, Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
| | - Arindam Bhattacharyya
- Immunology Laboratory, Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
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26
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Chakraborty S, Qian L, Baker JBH, Ruohoniemi JM, Kuyeng K, Mclnerney JM. Driving Influences of the Doppler Flash Observed by SuperDARN HF Radars in Response to Solar Flares. J Geophys Res Space Phys 2022; 127:e2022JA030342. [PMID: 35864909 PMCID: PMC9286435 DOI: 10.1029/2022ja030342] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Sudden enhancement in high-frequency absorption is a well-known impact of solar flare-driven Short-Wave Fadeout (SWF). Less understood, is a perturbation of the radio wave frequency as it traverses the ionosphere in the early stages of SWF, also known as the Doppler flash. Investigations have suggested two possible sources that might contribute to it's manifestation: first, enhancements of plasma density in the D-and lower E-regions; second, the lowering of the F-region reflection point. Our recent work investigated a solar flare event using first principles modeling and Super Dual Auroral Radar Network (SuperDARN) HF radar observations and found that change in the F-region refractive index is the primary driver of the Doppler flash. This study analyzes multiple solar flare events observed across different SuperDARN HF radars to determine how flare characteristics, properties of the traveling radio wave, and geophysical conditions impact the Doppler flash. In addition, we use incoherent scatter radar data and first-principles modeling to investigate physical mechanisms that drive the lowering of the F-region reflection points. We found, (a) on average, the change in E- and F-region refractive index is the primary driver of the Doppler flash, (b) solar zenith angle, ray's elevation angle, operating frequency, and location of the solar flare on the solar disk can alter the ionospheric regions of maximum contribution to the Doppler flash, (c) increased ionospheric Hall and Pedersen conductance causes a reduction of the daytime eastward electric field, and consequently reduces the vertical ion-drift in the lower and middle latitude ionosphere, which results in lowering of the F-region ray reflection point.
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Affiliation(s)
- S. Chakraborty
- Bradley Department of Electrical and Computer EngineeringVirginia TechBlacksburgVAUSA
| | - L. Qian
- National Center for Atmospheric ResearchBoulderCOUSA
| | - J. B. H. Baker
- Bradley Department of Electrical and Computer EngineeringVirginia TechBlacksburgVAUSA
| | - J. M. Ruohoniemi
- Bradley Department of Electrical and Computer EngineeringVirginia TechBlacksburgVAUSA
| | - K. Kuyeng
- Radio Observatorio de JicamarcaInstituto Geofisico del PeruLimaPeru
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27
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Huq FN, Momenuzzaman NAM, Chowdhury AW, Hoque MM, Khan KN, Begum F, Shafique AM, Anis R, Rahman MA, Nahar S, Chakraborty S, Ahmad T, Khan TA, Ullah R, Rahman MM. Effect of telephone-monitored home-based cardiac rehabilitation exercise on functional capacity and quality of life in heart failure patients in a lower-middle-income country. Eur J Prev Cardiol 2022. [DOI: 10.1093/eurjpc/zwac056.248] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Funding Acknowledgements
Type of funding sources: None.
Introduction
Chronic heart failure (CHF) prevails as one of the major cardiovascular diseases in lower-middle-income countries (LMICs) like Bangladesh. Home-Based Cardiac Rehabilitation (HBCR) is a cost-effective method of secondary prevention of chronic heart failure which, if provided, might not only improve the health status of the patients but might also reduce the financial and hospitalization burden on the health care system of these countries. The study aims to assess the scope and benefits of HBCR in such low resource settings.
Purpose
The study evaluates the effect of telephone-monitored HBCR exercise programme in improving the functional capacity and quality of life (QoL) in patients of CHF with reduced ejection fraction due to ischemic heart disease (IHD).
Method
This self-controlled interventional study was conducted from August 2019 to July 2020 at a heart failure clinic, a tertiary healthcare centre in Bangladesh. A total of 115 patients of CHF with ejection fraction <40% and in NYHA class II and III were included in the study according to selection criteria. The functional capacity of the patients was evaluated by NYHA classification and 6-minute walk test. The quality of life of the patients was evaluated by Minnesota Living with Heart Failure Questionnaire (MLHFQ). All patients were advised to perform HBCR exercise as per recommended guideline and were telephone-monitored 2-weekly. After the 3-months study period, the participants were divided into compliant and partial compliant groups based on their adherence to the guideline. Repeat evaluation of patients' condition was carried out. Results were then compared within the groups and data was analyzed through appropriate statistical methods.
Results
Significant improvement of NYHA class (p<0.05), and 6-minute walk test distance (6MWTD) (1102.01±215.90 feet vs 1243.30±217.86 feet; p<0.001) were noticed after the rehabilitation programme. Improvement of total MLHFQ score was also observed (35.53±14 vs 28.22±12.84; p<0.001) at 3-months follow up. The functional capacity and quality of life of the patients in both the compliant and partially compliant groups showed significant improvement after the rehabilitation programme (p<0.001); though no difference was found in the indicators when compared between compliant vs partially compliant groups after rehabilitation except for 6MWTD (1302.86±219.61 feet vs 1230.71±212.284 feet, p<0.001).
Conclusion
From the results, it can be concluded that any amount of routine exercise tends to improve quality of life and symptoms in patients of chronic heart failure with reduced ejection fraction. However, to achieve the best effect in functional capacity and overall health status, the addition of a structured exercise programme like HBCR can be beneficial for proper rehabilitation in low resource settings. Further validation of the results is recommended through randomized control trials in larger study groups.
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Affiliation(s)
- FN Huq
- United Hospital Ltd, Cardiology, Dhaka, Bangladesh
| | | | - AW Chowdhury
- Dhaka Medical College Hospital, Cardiology, Dhaka, Bangladesh
| | - MM Hoque
- Bangabandhu Sheikh Mujib Medical University (BSMMU), Biochemistry, Dhaka, Bangladesh
| | - KN Khan
- United Hospital Ltd, Cardiology, Dhaka, Bangladesh
| | - F Begum
- United Hospital Ltd, Cardiology, Dhaka, Bangladesh
| | - AM Shafique
- United Hospital Ltd, Cardiology, Dhaka, Bangladesh
| | - R Anis
- United Hospital Ltd, Cardiology, Dhaka, Bangladesh
| | - MA Rahman
- Sorkari Karmachari Hospital, Cardiology, Dhaka, Bangladesh
| | - S Nahar
- United Hospital Ltd, Cardiology, Dhaka, Bangladesh
| | | | - T Ahmad
- United Hospital Ltd, Cardiology, Dhaka, Bangladesh
| | - TA Khan
- United Hospital Ltd, Cardiology, Dhaka, Bangladesh
| | - R Ullah
- United Hospital Ltd, Cardiology, Dhaka, Bangladesh
| | - MM Rahman
- Keraniganj Upazila Health Complex, Dhaka, Bangladesh
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28
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Chakraborty S. Monitoring COVID-19 Cases and Vaccination in Indian States and Union Territories Using Unsupervised Machine Learning Algorithm. Ann Data Sci 2022; 10:967-989. [PMID: 38625290 PMCID: PMC9065662 DOI: 10.1007/s40745-022-00404-w] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 10/20/2021] [Accepted: 10/30/2021] [Indexed: 11/01/2022]
Abstract
The worldwide spread of the novel coronavirus originating from Wuhan, China led to an ongoing pandemic as COVID-19. The disease being a contagion transmitted rapidly in India through the people having travel histories to the affected countries, and their contacts that tested positive. Millions of people across all states and union territories (UT) were affected leading to serious respiratory illness and deaths. In the present study, two unsupervised clustering algorithms namely k-means clustering and hierarchical agglomerative clustering are applied on the COVID-19 dataset in order to group the Indian states/UTs based on the pandemic effect and the vaccination program from the period of March, 2020 to early June, 2021. The aim of the study is to observe the plight of each state and UT of India combating the novel coronavirus infection and to monitor their vaccination status. The research study will be helpful to the government and to the frontline workers coping to restrict the transmission of the virus in India. Also, the results of the study will provide a source of information for future research regarding the COVID-19 pandemic in India.
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Affiliation(s)
- S. Chakraborty
- Department of Mathematical and Computational Sciences, National Institute of Technology Karnataka, Mangalore, 575025 India
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29
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Biswas S, Mukherjee A, Chakraborty S, Chaturvedi A, Samanta B, Khanra D, Ray S, Sharma RK. Impact of plasma glucose and duration of type 2 diabetes mellitus on SYNTAX Score II in patients suffering from non ST-elevation myocardial infarction. Kardiologiia 2022; 62:40-48. [PMID: 35414360 DOI: 10.18087/cardio.2022.3.n1799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
Aim The objective was to assess the correlation of fasting plasma glucose (FPG), HbA1c, and the duration of type 2 diabetes mellitus (T2DM) with SYNTAX score (SS) II in patients with non-ST elevation myocardial infarction (NSTEMI).Material and methods FPG and HbA1C were measured in 398 patients presenting with NSTEMI at admission. SS II was calculated using an online calculator. Patients were stratified according to SS II (≤21.5, 21.5-30.6, and ≥30.6), defined as SS II low, mid, and high, respectively.Results 37.7 % of subjects were diabetic. Correlations of FPG (R=0.402, R2=0.162, p<0.001) and HbA1c (R=0.359, R2=0.129, p<0.001) with SS II were weak in the overall population. Duration of T2DM showed very strong correlation with SS II (R=0.827, R2=0.347). For the prediction of high SS II in the study population, FPG≥98.5 mg / dl demonstrated a sensitivity of 58 % and a specificity of 60 %, and HbA1c ≥6.05 demonstrated a sensitivity of 63 % and a specificity of 69 %. Duration of T2DM (adjusted odds ratio (OR): 1.182; 95 % confidence interval (CI): 1.185-2.773) and FPG (OR: 0.987; 95 % CI: 0.976-0.9959) were significantly associated with high SS II after controlling for other risk factors. Duration of T2DM (Beta=0.439) contributed strongly to variance of SS II, whereas HbA1c (Beta=0.063) contributed weakly.Conclusion Duration of T2DM is a very important risk factor for severity of coronary artery disease.
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Affiliation(s)
- S Biswas
- Nilratan Sircar Medical College and Hospital
| | - A Mukherjee
- Nilratan Sircar Medical College and Hospital
| | | | | | - B Samanta
- Nilratan Sircar Medical College and Hospital
| | - D Khanra
- Heart and Lung Centre, Royal Wolverhampton NHS Trust
| | - S Ray
- Jagannath Gupta Institute of Medical Sciences and Hospitals
| | - R K Sharma
- Nilratan Sircar Medical College and Hospital
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30
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Dai L, Chakraborty S, Wu G, Ye J, Lau YH, Ramanarayan H, Wu DT. Molecular simulation of linear octacosane via a CG10 coarse grain scheme. Phys Chem Chem Phys 2022; 24:5351-5359. [PMID: 35169819 DOI: 10.1039/d1cp05143a] [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] [Indexed: 11/21/2022]
Abstract
Following our previous work on the united-atom simulation on octacosane (C28H58) (Dai et al., Phys. Chem. Chem. Phys., 2021, 23, 21262-21271), we developed a coarse grain scheme (CG10), which is able to reproduce the pivotal phase characteristics of octacosane with highly improved computational efficiency. The CG10 octacosane chain was composed of 10 consecutive beads, maintaining the fundamental zigzag chain morphology. When the potential functions were set up and the coefficients were parameterized, our CG10 models yielded solid phase diagrams and transitions during an annealing process. We also detected the melting point by various means: direct observation, bond order, density tracking, and an enthalpy plot. Furthermore, our CG10 successfully reproduced the liquid density with only 2% underestimation, indicating its applicability across the solid and liquid phases. Therefore, with the ability to reproduce critical structure and property characteristics, our CG10 scheme provides an effective means of numerically modelling octacosane with highly improved computational efficiency.
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Affiliation(s)
- L Dai
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore.
| | - S Chakraborty
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore.
| | - G Wu
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore.
| | - J Ye
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore.
| | - Y H Lau
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore.
| | - H Ramanarayan
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore.
| | - D T Wu
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore.
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31
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Datta SS, Ghose S, Ghosh M, Jain A, Mandal S, Chakraborty S, Caduff C. Journeys: understanding access, affordability and disruptions to cancer care in India. Ecancermedicalscience 2022; 16:1342. [PMID: 35242223 PMCID: PMC8831108 DOI: 10.3332/ecancer.2022.1342] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Indexed: 11/21/2022] Open
Abstract
Background Much of the global cancer burden is in low- and middle-income countries (LMICs). Along with the high incidence of cancer, most LMICs have unevenly distributed health care resources. This study is a qualitative exploration of the journey of patients accessing cancer care in India and their caregivers. Methods The study followed a cross-sectional qualitative design. Participants were recruited by stratified purposive sampling, and all common cancers in India as reported by the GLOBOCAN database were included in the study. Consenting patients and their caregivers were interviewed using in-depth interview techniques. The data was analysed using principles of qualitative content analysis. Results Cancer patients (n = 100) and their caregivers (n = 48) were interviewed for the study. The six themes that emerged were related to a) the journey of patients to access care, b) the psychological journey of patients, c) stigma of cancer patients, d) decision-making and adherence to treatment, e) economic costs of cancer care and its impact and f) modifiers to accessing cancer care. Conclusions Planning and policymaking in the future of cancer care delivery need to consider the views expressed by the cancer patients and their caregivers as regards to access, adherence and disruptions to cancer care in India. Future policies will hopefully address some of the difficulties faced by patients.
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Affiliation(s)
- Soumitra Shankar Datta
- Department of Palliative Care & Psycho-oncology, Tata Medical Center, Major Arterial Road, New Town, Rajarhat, Kolkata 700160, India
- MRC Clinical Trials Unit, Institute of Clinical Trials and Methodology, University College London, 90 High Holborn, London WC1V 6LJ, UK
- https://orcid.org/0000-0003-1674-5093
| | - Soumita Ghose
- Department of Administration and Policy, Tata Medical Center, Major Arterial Road, New Town, Rajarhat, Kolkata 700160, India
| | - Manisha Ghosh
- Department of Palliative Care & Psycho-oncology, Tata Medical Center, Major Arterial Road, New Town, Rajarhat, Kolkata 700160, India
| | - Amruta Jain
- Department of Palliative Care & Psycho-oncology, Tata Medical Center, Major Arterial Road, New Town, Rajarhat, Kolkata 700160, India
| | - Sumedha Mandal
- Department of Palliative Care & Psycho-oncology, Tata Medical Center, Major Arterial Road, New Town, Rajarhat, Kolkata 700160, India
| | - Sayan Chakraborty
- Department of Palliative Care & Psycho-oncology, Tata Medical Center, Major Arterial Road, New Town, Rajarhat, Kolkata 700160, India
| | - Carlo Caduff
- Department of Global Health & Social Medicine, King’s College London, Bush House, 40 Aldwych, London WC2B 4BG, UK
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Bhattacharya B, Ranjan P, Prakash S, Damle NA, Chakraborty S, Sikdar S. Antibiotic scintigraphy in tuberculosis: A new horizon? Indian J Tuberc 2022; 69:20-26. [PMID: 35074146 DOI: 10.1016/j.ijtb.2021.03.012] [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: 12/08/2020] [Accepted: 03/19/2021] [Indexed: 06/14/2023]
Abstract
Tuberculosis (TB) continues to be a major cause of death worldwide that can be effectively treated with timely diagnosis and treatment. With the advent of nuclear imaging techniques like 18Fluorine Fluoro-2-Deoxy-D-Glucose Positron Emission Tomography (18F-FDG) PET/CT, the diagnosis of tuberculosis, particularly its extrapulmonary forms, has received great impetus in cases where microbiological confirmation cannot be achieved. Although detection of mycobacteria either by staining, culture or nucleic acid amplification techniques still form the gold standard of diagnosis, newer diagnostic techniques are always welcome in the field which can expedite clinical management. Use of radiolabeled antibiotics is one such evolving sphere which needs further research. Moving ahead from radiolabeled leukocytes, antibiotics are being increasingly focused upon to act as a vehicle to locate infectious lesions. Antibiotics like ciprofloxacin have been labeled with diagnostic radionuclides such as Technetium-99m (Tc-99m) and used to image many infectious diseases with encouraging results in TB. However, the nonspecific attributes of ciprofloxacin have hindered its growth to assist the diagnosis of TB. A novel approach would be to utilize ethambutol, a specific antitubercular agent, which has been found to be safe and effective in the diagnosis of TB in the available published studies. Ethambutol is known to be taken up specifically by tubercular lesions. This forms the basis of using Tc-99m labelled ethambutol for imaging TB lesions. An added advantage would be its ability to differentiate tubercular from malignant and fungal lung lesions that are the usual differentials in patients suspected of having TB. Most of the studies involving ethambutol have been done in skeletal TB and its validation in other forms of TB is still awaited. Recently the role of PET-CT has also been explored in human studies using 11C Rifampicin to study the antibiotic uptake in tubercular lesions. This review summarizes the available evidence regarding diagnosis of TB by radiolabeled antibiotic imaging to emphasize the need for accelerated research in the fight against TB.
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Affiliation(s)
- Bisakh Bhattacharya
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Piyush Ranjan
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India.
| | - Sneha Prakash
- Department of Nuclear Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Nishikant Avinash Damle
- Department of Nuclear Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Sayan Chakraborty
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Sunit Sikdar
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India
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Chakraborty S, Pradhan R, Dey N, González Crespo R, R.S. Tavares JM. Effect of optimization framework on rigid and non-rigid multimodal image registration. ScienceAsia 2022. [DOI: 10.2306/scienceasia1513-1874.2022.s001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Maniyar RR, Chakraborty S, Jarboe T, Suriano R, Wallack M, Geliebter J, Tiwari RK. Interacting Genetic Lesions of Melanoma in the Tumor Microenvironment: Defining a Viable Therapy. Adv Exp Med Biol 2021; 1350:123-143. [PMID: 34888847 DOI: 10.1007/978-3-030-83282-7_6] [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] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Melanoma is the most aggressive form of skin cancer with an estimated 106,110 newly diagnosed cases in the United States of America in 2021 leading to an approximated 7180 melanoma-induced deaths. Cancer typically arises from an accumulation of somatic mutations and can be associated with mutagenic or carcinogenic exposure. A key characteristic of melanoma is the extensive somatic mutation rate of 16.8 mutations/Mb, which is largely attributed to UV exposure. Bearing the highest mutational load, many of them occur in key driver pathways, most commonly the BRAFV600E in the mitogen-activated protein kinase (MAPK) pathway. This driver mutation is targeted clinically with FDA-approved therapies using small molecule inhibitors of oncogenic BRAFV600E and MEK, which has greatly expanded therapeutic intervention following a melanoma diagnosis. Up until 2011, therapeutic options for metastatic melanoma were limited, and treatment typically fell under the spectrum of surgery, radiotherapy, and chemotherapy.Attributed to the extensive mutation rate, as well as having the highest number of neoepitopes, melanoma is deemed to be extremely immunogenic. However, despite this highly immunogenic nature, melanoma is notorious for inducing an immunosuppressive microenvironment which can be relieved by checkpoint inhibitor therapy. The two molecules currently approved clinically are ipilimumab and nivolumab, which target the molecules CTLA-4 and PD-1, respectively.A plethora of immunomodulatory molecules exist, many with redundant functions. Additionally, these molecules are expressed not only by immune cells but also by tumor cells within the tumor microenvironment. Tumor profiling of these cell surface checkpoint molecules is necessary to optimize a clinical response. The presence of immunomodulatory molecules in melanoma, using data from The Cancer Genome Atlas and validation of expression in two model systems, human melanoma tissues and patient-derived melanoma cells, revealed that the expression levels of B and T lymphocyte attenuator (BTLA), TIM1, and CD226, concurrently with the BRAFV600E mutation status, significantly dictated overall survival in melanoma patients. These molecules, along with herpesvirus entry mediator (HVEM) and CD160, two molecules that are a part of the HVEM/BTLA/CD160 axis, had a higher expression in human melanoma tissues when compared to normal skin melanocytes and have unique roles to play in T cell activation. New links are being uncovered between the expression of immunomodulatory molecules and the BRAFV600E genetic lesion in melanoma. Small molecule inhibitors of the MAPK pathway regulate the surface expression of this multifaceted molecule, making BTLA a promising target for immuno-oncology to be targeted in combination with small molecule inhibitors, potentially alleviating T regulatory cell activation and improving patient prognosis.
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Affiliation(s)
- R R Maniyar
- Human Oncology and Pathogenesis Program, Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Chakraborty
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - T Jarboe
- Departments of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY, USA
| | - R Suriano
- Division of Natural Sciences, College of Mount Saint Vincent, Bronx, NY, USA
| | - M Wallack
- Department Surgery, Metropolitan Hospital, New York, NY, USA
| | - J Geliebter
- Departments of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY, USA
| | - R K Tiwari
- Departments of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY, USA.
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Chakraborty S, Nadar RA, Tiwari A. Designing a drone assisted sample collection and testing system during epidemic outbreaks. JGOSS 2021. [DOI: 10.1108/jgoss-02-2021-0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Purpose
A major component in managing pandemic outbreaks involves testing the suspected individuals and isolating them to avoid transmission in the community. This requires setting up testing centres for diagnosis of the infected individuals, which usually involves movement of either patient from their residence to the testing centre or personnel visiting the patient, thus aggregating the risk of transmission to localities and testing centres. The purpose of this paper is to investigate and minimize such movements by developing a drone assisted sample collection and diagnostic system.
Design/methodology/approach
Effective control of an epidemic outbreak calls for a rapid response and involves testing suspected individuals and isolating them to avoid transmission in the community. This paper presents the problem in a two-phase manner by locating sample collection centres while assigning neighbourhoods to these collection centres and thereafter, assigning collection centres to nearest testing centres. To solve the mathematical model, this study develops a mixed-integer linear programming model and propose an integrated genetic algorithm with a local search-based approach (GA-LS) to solve the problem.
Findings
Proposed approach is demonstrated as a case problem in an Indian urban city named Kolkata. Computational results show that the integrated GA-LS approach is capable of producing good quality solutions within a short span of time, which aids to the practicality in the circumstance of a pandemic.
Social implications
The COVID-19 pandemic has shown that the large-scale outbreak of a transmissible disease may require a restriction of movement to take control of the exponential transmission. This paper proposes a system for the location of clinical sample collection centres in such a way that drones can be used for the transportation of samples from the neighbourhood to the testing centres.
Originality/value
Epidemic outbreaks have been a reason behind a major number of deaths across the world. The present study addresses the critical issue of identifying locations of temporary sample collection centres for drone assisted testing in major cities, which is by its nature unique and has not been considered by any other previous literature. The findings of this study will be of particular interest to the policy-makers to build a more robust epidemic resistance.
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Naik S, Haldar SN, Soneja M, Mundadan NG, Garg P, Mittal A, Desai D, Trilangi PK, Chakraborty S, Begam NN, Bhattacharya B, Maher G, Mahishi N, Rajanna C, Kumar SS, Arunan B, Kirtana J, Gupta A, Patidar D, Kodan P, Sethi P, Ray A, Jorwal P, Kumar A, Nischal N, Sinha S, Biswas A, Wig N. Post COVID-19 sequelae: A prospective observational study from Northern India. Drug Discov Ther 2021; 15:254-260. [PMID: 34719599 DOI: 10.5582/ddt.2021.01093] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Post COVID-19 sequelae are a constellation of symptoms often reported after recovering from COVID-19. There is a need to better understand the clinical spectrum and long-term course of this clinical entity. The aim of this study is to describe the clinical features and risk factors of post COVID-19 sequelae in the North Indian population. This prospective observational study was conducted at a tertiary healthcare centre in Northern India between October 2020 and February 2021. Patients aged >18 years with laboratory-confirmed COVID-19 were recruited after at least two weeks of diagnosis, and details were captured. A total of 1234 patients were recruited and followed up for a median duration of 91 days (IQR: 45-181 days). Among them, 495 (40.1%) had persistent symptoms post-discharge or recovery. In 223 (18.1%) patients, the symptoms resolved within four weeks; 150 (12.1%) patients had symptoms till 12 weeks, and 122 (9.9%) patients had symptoms beyond 12 weeks of diagnosis/symptom-onset of COVID-19. Most common symptoms included myalgia (10.9%), fatigue (5.5%), shortness of breath (6.1%), cough (2.1%), insomnia (1.4%), mood disturbances (0.48%) and anxiety (0.6%). Patients who were hospitalized were more likely to report fatigue as a feature of long COVID. Hypothyroidism (OR: 4.13, 95% CI: 2.2-7.6, p-value < 0.001) and hypoxia (SpO2 ≤ 93%) (OR: 1.7, 95% CI: 1.1-2.4, p-value 0.012) were identified as risk factors for long COVID sequelae. In conclusion, long COVID symptoms were common (22%), and 9.9% had the post COVID-19 syndrome. Myalgias, fatigue and dyspnoea were common symptoms. Patients with hypothyroidism and hypoxia during acute illness were at higher risk of long COVID.
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Affiliation(s)
- Shivdas Naik
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | | | - Manish Soneja
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | | | - Prerna Garg
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Ankit Mittal
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Devashish Desai
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | | | - Sayan Chakraborty
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Nazneen Nahar Begam
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Bisakh Bhattacharya
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Ganesh Maher
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Niranjan Mahishi
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Chaithra Rajanna
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Swasthi S Kumar
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Bharathi Arunan
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - J Kirtana
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Ankesh Gupta
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Diksha Patidar
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Parul Kodan
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Prayas Sethi
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Animesh Ray
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Pankaj Jorwal
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Arvind Kumar
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Neeraj Nischal
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Sanjeev Sinha
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Ashutosh Biswas
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Naveet Wig
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
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Patel N, Amgai B, Chakraborty S, Hajra A, Ashish K, Patel Z, Aryal B, Aronow W, Singh A. Effect of thrombocytopenia in patients with infective endocarditis: an insight from the National Inpatient Sample database. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.1726] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Introduction
Infective endocarditis (IE) is one of the feared diseases in septic patients, and incidences are rising due to the intravenous drug abuse epidemic. Sepsis causes an escalation of the platelet destructions leading to thrombocytopenia (1). Few independent hospital-based studies have proposed increase mortality with thrombocytopenia in patients with IE (2–5). We aim to evaluate the significance of thrombocytopenia in IE subjects from the national inpatient sample (NIS) database.
Method
We analyzed the NIS database from Jan-2016 to Dec-2018 using Stata 16.0. NIS is the largest publicly available all-payer inpatient care database in the United States, containing data on more than seven million hospital stays per year. We identified patients with IE with or without thrombocytopenia using ICD-10 codes. The primary outcome of interest was in-hospital mortality comparison. We adjusted potential confounders (age, sex, diabetes, hypertension, etc.) with multivariate logistic regression analysis. Further analysis was done after balancing the population co-morbidity using a Greedy propensity match for accuracy.
Results
A total of 174,495 subjects were included in this study with a diagnosis of IE. Among these individuals, 33,285 patients had a concurrent diagnosis of thrombocytopenia. The mean ages were 53±19.5 years for the thrombocytopenia group and 55±19.8 years for others. Females were equally represented in both cohorts. There were 4,945 (14.86%) vs 2,835 (2.01%) mortalities reported in with and without thrombocytopenia group respectively. After propensity matching, there was a pronounced increase in mortality [Odds ratio (OR): 1.93 (1.72 – 2.15), p-value: <0.001] in the group with thrombocytopenia comparing to others. Complications such as Major bleeding requiring blood transfusion [OR: 1.45 (1.35–1.57)], acute myocardial infarction [OR: 1.56 (1.35–1.70)], complete heart block [OR: 1.44 (1.16–1.53)], cardiac arrest [OR: 1.44 (1.25–1.72)], acute respiratory failure [OR: 1.51 (1.39–1.73)] and pressor support requirement [(OR: 1.73 (1.57–2.01)] were notably higher in the cohort of thrombocytopenia with statistically significant p-value (<0.001). The difference in length of stay between both cohorts after propensity match wasn't statistically significant.
Conclusion
In conclusion, IE patients with thrombocytopenia have higher incidences of in-patient mortality and poor outcomes than cohort without thrombocytopenia. Some of the adverse consequences could be temporally explained by complications related to underlying thrombocytopenia. Further investigations are needed to delineate the outcome in this group of subjects.
Funding Acknowledgement
Type of funding sources: None.
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Affiliation(s)
- N Patel
- Interfaith Medical Center, Internal Medicine, New York, United States of America
| | - B Amgai
- Geisinger Community Medical Center, Internal Medicine, Scranton, United States of America
| | - S Chakraborty
- Miami Valley Hospital, Ohio, United States of America
| | - A Hajra
- Jacobi Medical Center, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - K Ashish
- Crozer-Chester Medical Center, Internal Medicine, Upland, United States of America
| | - Z Patel
- AMC MET medical college, Ahmedabad, India
| | - B Aryal
- Interfaith Medical Center, Internal Medicine, New York, United States of America
| | - W Aronow
- Westchester Medical Center, Director of Cardiology Research, Valhalla, United States of America
| | - A Singh
- Geisinger Community Medical Center, Internal Medicine, Scranton, United States of America
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Patel N, Amgai B, Chakraborty S, Hajra A, Binit A, Patel Z, Ashish K, Reddy M, Aronow W, Khalid M. Impact of atrial fibrillation in patients with colorectal cancer: a national inpatient sample database analysis. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.0595] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Atrial fibrillation (AF) is the most common cardiac arrhythmia affecting approximately 1–2% overall population (1). Its causal relationship with colorectal cancer (CRC) is much for debate. According to one hypothesis, the presence of autoantibodies directed against ionic channels or acetylcholine receptors can predispose to the development of atrial fibrillation (2–3). Thus, AF may be regarded as an inflammatory complication in patients with colon cancer. Our study objective was to determine if AF impacts the outcome of patients with CRC.
Method
We analyzed the National Inpatient Sample (NIS) database from Oct-2015 to Dec 2018 using Stata 16.0. The NIS databases are released under the Healthcare Cost and Utilization Project, which includes inpatient admissions from the United States' participating hospitals. Total population with CRC were identified using their respective ICD-10 diagnostic codes then divided based on AF. To determine atrial fibrillation association with mortality and complications, we used multivariate logistic regression analysis using weights to generate nationally representative results. Later, a propensity-matched population analysis was done for the accuracy of the results.
Result
We found 245,305 patients admitted with CRC between Oct 2015 to Dec-2018 in the USA, out of which 28,170 (11.5%) were having AF. The mean age for the patients with AF was 77±10 compare to 65±14 years in those without AF. Patients with AF were associated with higher comorbidities and had a high population percentage with Carlson category three or above. There were 1,456 (5.2%) mortalities in the AF group compared to 5,689 (2.6%) in the other. The higher odds of mortality in patients with AF was present in multivariate logistic regression analysis in both non-propensity matched [1.71 (1.45–2.02), P-value: <0.000] and propensity-matched [1.44 (1.18–1.75), P-value: <0.001] cohorts. Patients with AF were hospitalized longer (9.20±7.8 vs. 6.85±7.0 days), leading to a high admission costs (US$ 25,875±22,875 vs. 20,087±19,314). Odds of complications such as need for blood transfusions [1.61 (1.05–1.29), P-value: 0.005], hemorrhage requiring blood transfusion [1.17 (1.05–1.29), P-value: 0.003], lower-GI bleed [1.31 (1.21–1.43), P-value: <0.001], sepsis [1.45 (1.30–1.62), P-value: <0.001], respiratory failure [1.39 (1.15–1.67), P-value: 0.001] etc. were also higher in group of patients with CRC and AF.
Conclusion
In our retrospective, propensity-matched national inpatient sample analyses of patients admitted with colorectal cancer, atrial fibrillation is associated with higher morbidity and mortality. AF was associated with a high burden of complications with prolonged hospital stay leading to increased health care expenditures.
Funding Acknowledgement
Type of funding sources: None.
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Affiliation(s)
- N Patel
- Interfaith Medical Center, Internal Medicine, New York, United States of America
| | - B Amgai
- Geisinger Community Medical Center, Internal Medicine, Scranton, United States of America
| | - S Chakraborty
- Miami Valley Hospital, Ohio, United States of America
| | - A Hajra
- Jacobi Medical Center, Albert Einstein College of Medicine, New York, United States of America
| | - A Binit
- Interfaith Medical Center, Internal Medicine, New York, United States of America
| | - Z Patel
- AMC MET medical college, Ahmedabad, India
| | - K Ashish
- Crozer-Chester Medical Center, Internal Medicine, Upland, United States of America
| | - M Reddy
- University of Kansas Medical Center, Division Chief, Cardiac Electrophysiology, Kansas City, United States of America
| | - W Aronow
- Westchester Medical Center, Director of Cardiology Research, Valhalla, United States of America
| | - M Khalid
- Maimonides Medical Center, New York, United States of America
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Patel N, Amgai B, Chakraborty S, Hajra A, Aryal B, Patel Z, Ashish K, Reddy M, Aronow W, Khalid M. Gender based outcome of IABP implantation in patients with acute coronary syndrome and cardiogenic shock: a national inpatient sample database analysis. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.1536] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Intra-Aortic Balloon counter-pulsation is frequently used as a circulatory support device in patients requiring hemodynamic support - in cardiogenic shock and in patients at risk of hemodynamic decompensation during a high-risk coronary intervention. Impact of IABP in this patient population has been variable. Certain studies have shown a beneficial effect of IABP on selected populations having acute coronary syndrome with cardiogenic shock (1–3). Our objective was to compare the outcomes based on gender in the ACS population with cardiogenic shock and IABP placement.
Methods
We analyzed the National Inpatient Sample database from Oct-2015 to Dec-2017 released under Healthcare Cost utilization Project in the USA using Stata 16.0. The population was identified using respective ICD-10 codes. We excluded the population with sudden cardiac arrest, pulmonary embolism, and patients with anatomical post-MI complications. Multivariate logistic regression analysis was done to determine the difference in outcomes based on gender using clinically relevant variables. Later, propensity-matched cohort analysis was performed based on the regression variables.
Results
Of 36, 990 patients who met our inclusion criteria 25,670 (69%) were male and 11,320 (31%) were female. The average age for male and female populations was 66±11 and 69±12 years. Femnales were more likely to have higher Charlson co-morbidity index three or above. We found higher mortality in the female population [3,146 (27.79%)] compared to male [5,884 (22.92%)] in univariate analyses. Propensity-matched multivariate regression analysis showed no difference [OR: 1.06 (0.91–1.22) with P-value: 0.482] in mortality after adjusting for clinically relevant variables. Subgroup analysis in STEMI and NSTEMI populations did not show a difference. The average hospital stay was similar in both cohorts, with the male having a higher cost per stay. We found no difference in most of the complications included in our study except for higher coronary artery dissection [OR: 2.98 (1.73–5.13), P-value: <0.001] and lower rates of AKI [OR: 0.72 (0.63–0.83), P-value: <0.001], AKI requiring hemodialysis [OR: 0.74 (0.56–0.97), P-value:0.031] and ventricular tachycardia [OR: 0.73 (0.64–0.84), P-value: <0.001] in the female population.
Conclusion
The inpatient population of ACS with Cardiogenic shock and IABP insertion showed no significant difference in mortality between males and females which was valid for subgroup analysis of NSTEMI and STEMI groups. Complications such as coronary artery dissection were higher, whereas AKI, AKI requiring hemodialysis, and ventricular tachycardias, were lower in females than males.
Funding Acknowledgement
Type of funding sources: None.
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Affiliation(s)
- N Patel
- Interfaith Medical Center, Internal Medicine, New York, United States of America
| | - B Amgai
- Geisinger Community Medical Center, Internal Medicine, Scranton, United States of America
| | - S Chakraborty
- Miami Valley Hospital, Ohio, United States of America
| | - A Hajra
- Jacobi Medical Center, Albert Einstein College of Medicine, New York, United States of America
| | - B Aryal
- Interfaith Medical Center, Internal Medicine, New York, United States of America
| | - Z Patel
- AMC MET medical college, Ahmedabad, India
| | - K Ashish
- Crozer-Chester Medical Center, Internal Medicine, Upland, United States of America
| | - M Reddy
- University of Kansas Medical Center, Division Chief, Cardiac Electrophysiology, Kansas City, United States of America
| | - W Aronow
- Westchester Medical Center, Director of Cardiology Research, Valhalla, United States of America
| | - M Khalid
- Maimonides Medical Center, New York, United States of America
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Kwek JW, Chakraborty S, Kuan KC, Yeo WC, Yin H, Liu CK, Guo L, Zidar J, Li C, Lim FCH. Interactions between poloxamer, PEOx-PPOy-PEOx, and non-ionic surfactant, sucrose monolaurate: A study on potential allergenic effect using model phospholipid membrane. Colloids Surf B Biointerfaces 2021; 209:112153. [PMID: 34673306 DOI: 10.1016/j.colsurfb.2021.112153] [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: 05/25/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 11/18/2022]
Abstract
Sugar-based surfactants are involved in skin related allergy cases in the past decade. Skin irritation starts with the interaction of the surfactant with the skin lipids leading to lipid emulsification and eventual barrier damage. Polymers or co-surfactants can be used to mitigate the allergenic effect but the mechanism of formulation mildness on skin remains unclear. We have used the quartz crystal microbalance (QCM) together with dissipative particle dynamics (DPD) simulation, small angle x-ray scattering (SAXS) as well as cell viability tests to decipher the interactions between poloxamers and sucrose monolaurate (SML), and how these interactions could prevent the disruption of a model supported phospholipid bilayer (SLB). Poloxamer addition to the SML solution can delay or totally prevent the disruption of the SLB depending on poloxamer type and concentration. Poloxamer P407 (Pluronic® F127) delays the onset of disruption while poloxamer P188 (Pluronic® F68) does not preserve the bilayer integrity even at high concentration of up to 15% w/w. Preservation of the SLB is likely due to the differences in the aggregates formation between SML-F127 and SML-F68 mixtures with corresponding retarded motion of SML micelles through the SML-F127 polymer matrix that improved cell viability.
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Affiliation(s)
- Jin W Kwek
- Institute of Chemical and Engineering Sciences, A⁎STAR, 1 Pesek Road, Jurong Island, 627833, Singapore.
| | - S Chakraborty
- Institute of High Performance Computing, A⁎STAR, 1 Fusionopolis Way, #16-16 Connexis, 138632, Singapore
| | - Kai C Kuan
- Institute of Chemical and Engineering Sciences, A⁎STAR, 1 Pesek Road, Jurong Island, 627833, Singapore
| | - Wen C Yeo
- Institute of Chemical and Engineering Sciences, A⁎STAR, 1 Pesek Road, Jurong Island, 627833, Singapore
| | - H Yin
- Department for Technology, Innovation and Enterprise, Singapore Polytechnic, 500 Dover Road, 139651, Singapore
| | - Connie K Liu
- Institute of Chemical and Engineering Sciences, A⁎STAR, 1 Pesek Road, Jurong Island, 627833, Singapore
| | - L Guo
- Institute of Chemical and Engineering Sciences, A⁎STAR, 1 Pesek Road, Jurong Island, 627833, Singapore
| | - J Zidar
- Institute of High Performance Computing, A⁎STAR, 1 Fusionopolis Way, #16-16 Connexis, 138632, Singapore
| | - C Li
- Department for Technology, Innovation and Enterprise, Singapore Polytechnic, 500 Dover Road, 139651, Singapore
| | - Freda C H Lim
- Institute of Chemical and Engineering Sciences, A⁎STAR, 1 Pesek Road, Jurong Island, 627833, Singapore; Institute of High Performance Computing, A⁎STAR, 1 Fusionopolis Way, #16-16 Connexis, 138632, Singapore.
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41
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Dai L, Rutkevych PP, Chakraborty S, Wu G, Ye J, Lau YH, Ramanarayan H, Wu DT. Molecular dynamics simulation of octacosane for phase diagrams and properties via the united-atom scheme. Phys Chem Chem Phys 2021; 23:21262-21271. [PMID: 34543374 DOI: 10.1039/d1cp02720d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We used the united-atom scheme to build three types of crystalline structures for octacosane (C28H58) and carried out molecular dynamics simulations to investigate their phase properties. By gradually heating the three polymorphs, we managed to reproduce the sequence of experimentally reported crystalline phases and rotator phases. By studying the system density, molecule morphology, chain tilt angle and cell anisotropy, we hypothesized three mechanisms behind the observed system deformations and phase transformations during the annealing process. Furthermore, our model successfully predicted the melting temperature and heat of fusion. We also reproduced the characteristics of the rotator phases and the liquid phase, validating the transferability of the united-atom scheme among the different condensed phases of octacosane. Our methodology represents an effective and efficient means of numerical study for octacosane and may be used for other members of the n-alkane family.
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Affiliation(s)
- L Dai
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore.
| | - P P Rutkevych
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research (A*STAR), Singapore
| | - S Chakraborty
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore.
| | - G Wu
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore.
| | - J Ye
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore.
| | - Y H Lau
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore.
| | - H Ramanarayan
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore.
| | - D T Wu
- Institute of High Performance Computing, Agency for Science, Technology and Research (A*STAR), Singapore.
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Dwivedy A, Mariadasse R, Ahmad M, Chakraborty S, Kar D, Tiwari S, Bhattacharyya S, Sonar S, Mani S, Tailor P, Majumdar T, Jeyakanthan J, Biswal BK. Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2. PLoS Comput Biol 2021; 17:e1009384. [PMID: 34516563 PMCID: PMC8478224 DOI: 10.1371/journal.pcbi.1009384] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 09/28/2021] [Accepted: 08/26/2021] [Indexed: 12/14/2022] Open
Abstract
Apart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, a well-known kinase inhibitor- Sorafenib showed a significant inhibition and dampened viral load in SARS-CoV-2 infected cells. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2. The on-going coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is significantly affecting the world health. Unfortunately, over 180 million cases of COVID-19 resulting in nearly 4 million deaths have been reported till June, 2021. In this study, using a combination of bioinformatics, biochemical and mass spectrometry methods, we show that the Nidovirus RdRp associated Nucleotidyl transferase (NiRAN) domain of the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 exhibits a kinase like activity. Additionally, we also show that few broad spectrum anti-cancer and anti-microbial drugs dampen this kinase like activity. Of note, Sorafenib, an FDA approved anti-cancer kinase inhibiting drug significantly reduces the SARS-CoV-2 load in cell lines. Our study suggests that NiRAN domain of the SARS-CoV-2 RdRp is indispensible for the successful viral life cycle and shows that abolishing this enzymatic function of RdRp by small molecule inhibitors may open novel avenues for COVID-19 therapeutics.
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Affiliation(s)
| | | | | | | | | | | | | | - Sudipta Sonar
- Translational Health Science and Technology Institute, Faridabad, India
| | - Shailendra Mani
- Translational Health Science and Technology Institute, Faridabad, India
| | | | - Tanmay Majumdar
- National Institute of Immunology, New Delhi, India
- * E-mail: (TM); (JJ); (BKB)
| | - Jeyaraman Jeyakanthan
- Department of Bioinformatics, Alagappa University, Tamil Nadu, India
- * E-mail: (TM); (JJ); (BKB)
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Dwivedy A, Mariadasse R, Ahmad M, Chakraborty S, Kar D, Tiwari S, Bhattacharyya S, Sonar S, Mani S, Tailor P, Majumdar T, Jeyakanthan J, Biswal BK. Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2. PLoS Comput Biol 2021. [DOI: https://doi.org/10.1371/journal.pcbi.1009384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Apart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, a well-known kinase inhibitor- Sorafenib showed a significant inhibition and dampened viral load in SARS-CoV-2 infected cells. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2.
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Menezes AFB, Mazucheli J, de Oliveira RP, Chakraborty S. Improved maximum likelihood estimation of the parameters of the Gamma-Uniform distribution with bias-corrections. COMMUN STAT-SIMUL C 2021. [DOI: 10.1080/03610918.2021.1951760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- A. F. B. Menezes
- Department of Statistics, Universidade Estadual de Maringá, DEs, Maringá, Paraná, Brazil
| | - J. Mazucheli
- Department of Statistics, Universidade Estadual de Maringá, DEs, Maringá, Paraná, Brazil
| | - R. P. de Oliveira
- Medical School, Universidade de São Paulo, Ribeirão Preto, Sao Paulo, Brazil
| | - S. Chakraborty
- Department of Statistics, Dibrugarh University, Dibrugarh, Assam, India
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Basu Achari R, Goyal L, Chakraborty S, Arunsingh M, Arun B, Das S, Bhattacharyya T, Mallick I, Chatterjee S, Chatterjee J, Dhara S, Ghosh N, Mukhopadhyay J. PO-1033 Molecular profile and early MRI changes after chemoradiation in high grade diffuse astrocytoma. Radiother Oncol 2021. [DOI: 10.1016/s0167-8140(21)07484-3] [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: 11/28/2022]
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Sengupta A, Sinha S, Chatterjee SS, Biswas M, Chakraborty S, Kumar S. 3123 – POLYBROMO SWI/SNF INTEGRATES CHROMATIN REMODELING & BMP/TGF-Β SIGNALING TO DETERMINE MESENCHYMAL STROMAL OSTEOLINEAGE COMMITMENT AND HEMATOPOIESIS. Exp Hematol 2021. [DOI: 10.1016/j.exphem.2021.12.340] [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: 11/24/2022]
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47
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Sasidharan R, Bhattacharyya T, H Lal V, Mallick I, ArunSingh M, Chakraborty S, Basu Achari R, Chatterjee S. PO-1233 Real world results of CTRT in Ca esophagus: Can SCOPE-1 results be replicated outside trial setting? Radiother Oncol 2021. [DOI: 10.1016/s0167-8140(21)07684-2] [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: 11/25/2022]
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48
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Chakraborty A, Chakraborty S, Sen S, Bhatacharya T, Khemka R. Modification of the sacral erector spinae plane block using an ultrasound-guided sacral foramen injection: dermatomal distribution and radiocontrast study. Anaesthesia 2021; 76:1538-1539. [PMID: 34309009 DOI: 10.1111/anae.15549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2021] [Indexed: 11/27/2022]
Affiliation(s)
| | | | - S Sen
- Tata Medical Center, Kolkata, India
| | | | - R Khemka
- Tata Medical Center, Kolkata, India
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49
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Ray S, Malekzadehmoghani M, S Ray S, Sen P, Chakraborty S. Molecular Genetics of Esophageal Cancer : Indian Perspective. Asian Pac J Cancer Biol 2021. [DOI: 10.31557/apjcb.2021.6.2.155-160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background: RIZ1 is one of the tumor-suppressor genes that is silenced in many human cancers. Change in RIZ1 expression has not been reported in ESCC patients. Therefore, the aim of this study was to investigate the role of RIZ1 in ESCC in the Indian population. Methods: Twelve esophageal squamous-cell carcinoma (ESCC) patients in stage IV and 12 healthy individuals were used in this study. Tissue sampling was taken from individuals and total RNA was isolated and then cDNA was synthesized using PCR. RIZ1 primers were then designed, and RIZ1 expression was quantified by qRT-PCR. Mapping of CpG islands in RIZ1 promoter was performed using bioinformatics tools. The promoter methylation status of this gene was studied using u methylation-specific PCR (MSP). T-student test was used to analyze the data.Results: Decreased RIZ1 expression was observed in ESCC compared with healthy controls. The results showed a relatively higher density of CpG dinucleotides in the RIZ1 promoter. No significant difference in promoter methylation was observed in blood and tissue samples.Conclusion: The study showed a significant down-regulation of RIZ-1 gene in the blood and tissue samples of ESCC patients that did not related to the altered promoter methylation.
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50
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Kalai S, Roychoudhury P, Dutta TK, Subudhi PK, Chakraborty S, Barman NN, Sen A. Multidrug resistant staphylococci isolated from pigs with exudative epidermitis in North eastern Region of India. Lett Appl Microbiol 2021; 72:535-541. [PMID: 33421175 DOI: 10.1111/lam.13448] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 07/06/2020] [Revised: 12/31/2020] [Accepted: 01/04/2021] [Indexed: 11/30/2022]
Abstract
Exudative epidermatitis or greasy pig disease (GPD) is a contagious disease of pig and endemic worldwide caused by toxigenic strains under genus Staphylococcus. The present study reported an outbreak of GPD in Champhai district of Mizoram adjoining to the southern border of Myanmar. A total of 60 samples were collected from 22 clinically affected animals and processed for isolation and identification of Staphylococcus spp. All the isolates were subjected to antimicrobial sensitivity assay, biofilm production assay and detection of virulence genes, biofilm genes and mec genes followed by cloning and sequencing for phylogenetic analysis. A total of 44 staphylococci belonged to four species (S. sciuri, S. aureus,S. lentus, and S. hyicus) were isolated. Majority of the isolates were multidrug resistant with maximum resistance against ampicillin, penicillin including vancomycin. None of the S. hyicus isolates was methicillin resistant (MRSH) but 66·67% isolates were MRSA. By PCR, mecA gene was detected in S. aureus (n = 2), S. sciuri (n = 4) and S. lentus (n = 3). Biofilm associated gene icaD was detected in S. aureus (n = 3), S. sciuri (n = 5), S. hyicus (n = 4) and S. lentus (n = 6). The exfoliative toxin genes (ehxB, shetA and tsst1) were detected in S. hyicus (n = 3) and S. aureus (n = 1) isolates. All the isolates were closely related with the isolates from pigs of China, Germany, Japan and USA. The pathogens might be transmitted through illegal migration of pigs from Myanmar to India.
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Affiliation(s)
- S Kalai
- Department of Veterinary Microbiology, CVSc&AH, Central Agricultural University, Aizawl, Mizoram, India
| | - P Roychoudhury
- Department of Veterinary Microbiology, CVSc&AH, Central Agricultural University, Aizawl, Mizoram, India
| | - T K Dutta
- Department of Veterinary Microbiology, CVSc&AH, Central Agricultural University, Aizawl, Mizoram, India
| | - P K Subudhi
- Department of Veterinary Microbiology, CVSc&AH, Central Agricultural University, Aizawl, Mizoram, India
| | - S Chakraborty
- Department of Veterinary Microbiology, CVSc&AH, Central Agricultural University, Aizawl, Mizoram, India
| | - N N Barman
- Department of Veterinary Microbiology, Assam Agricultural University, Guwahati, Assam, India
| | - A Sen
- Division of Animal Health, ICAR-RCNEH, Shillong, Meghalaya, India
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