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7. Genomic Surveillance and Phylodynamic Analyses Reveal the Emergence of Novel Mutations and Co-mutation Patterns Within SARS-CoV-2 Variants Prevalent in India.

Author

Biswas, Nupur, Mallick, Priyanka, Maity, Sujay Krishna, Bhowmik, Debaleena, Mitra, Arpita Ghosh, Saha, Soumen, Roy, Aviral, Chakrabarti, Partha, Paul, Sandip, and Chakrabarti, Saikat

Subjects
SARS-CoV-2, WHOLE genome sequencing, COVID-19, VIRAL mutation, GENETIC mutation, EXOMES
Abstract

Identification of the genomic diversity and the phylodynamic profiles of prevalent variants is critical to understand the evolution and spread of SARS-CoV-2 variants. We performed whole-genome sequencing of 54 SARS-CoV-2 variants collected from COVID-19 patients in Kolkata, West Bengal during August–October 2020. Phylogeographic and phylodynamic analyses were performed using these 54 and other sequences from India and abroad that are available in the GISAID database. We estimated the clade dynamics of the Indian variants and compared the clade-specific mutations and the co-mutation patterns across states and union territories of India over the time course. Frequent mutations and co-mutations observed within the major clades across time periods do not show much overlap, indicating the emergence of newer mutations in the viral population prevailing in the country. Furthermore, we explored the possible association of specific mutations and co-mutations with the infection outcomes manifested in Indian patients. [ABSTRACT FROM AUTHOR]

Published
2024
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8. Counterion Effects on Nano-confined Metal-Drug-DNA Complexes

Author

Biswas, Nupur, Chakraborty, Sreeja, Datta, Alokmay, Sarkar, Munna, Mukhopadhyay, Mrinmay K., Bera, Mrinal K., and Seto, Hideki

Subjects
Condensed Matter - Soft Condensed Matter, Condensed Matter - Mesoscale and Nanoscale Physics, Physics - Biological Physics
Abstract

We have explored morphology of DNA molecules bound with Cu-complexes of piroxicam molecules, a non-steroidal anti-inflammatory drug (NSAID), under one-dimensional confinement of thin films and have studied the effect of counterions present in a buffer. X-ray reflectivity at and away from the Cu K absorption edge and atomic force microscopy studies reveal that confinement segregates the drug molecules preferentially in a top layer of the DNA film, and counterions enhance this segregation.

Published
2014
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9. Effects of Counterions on Nano-confined DNA Thin Films

Author

Biswas, Nupur, Chakraborty, Sreeja, Datta, Alokmay, Sarkar, Munna, Mukhopadhyay, Mrinmay K., Bera, Mrinal K., and Seto, Hideki

Subjects
Condensed Matter - Soft Condensed Matter
Abstract

DNA molecules spin-coated on amorphous quartz substrates are shown to form stable films. Electron density profiles (EDPs) along the film depth show that film prepared from aqueous solution of DNA exhibits layering of the molecules in three stacks parallel to the substrate whereas film prepared from counterion added solution does not have layering but have smaller thickness and enhanced surface roughness, although both films have 'liquid-like' height-height correlations. We explain these results by a model of film of a 'liquid' comprising of rod-like molecules where the counterion concentration in the liquid determines the rod length.

Published
2014

10. 'Coffee-ring' patterns of polymer droplets: chain entanglement effect

Author

Biswas, Nupur and Datta, Alokmay

Subjects
Condensed Matter - Soft Condensed Matter
Abstract

Dried droplets of polymer solutions of different molecular weights and concentrations leave various types of 'coffee-ring' patterns. These patterns are consequence of contact line motion. We have observed for very low molecular weight the droplet periphery part contains spheroidal structures whereas central part contains continuous layer. For higher molecular weight contact line exhibits 'stick-slip' motion. Whereas for very high molecular weight contact line delays enough to start motion and finally moves uninterruptedly leaving a continuous layer of polymer. We have explained this phenomena in terms of chain entanglement which is resultant of molecular weight and solution concentration. Depending on the entanglement chains can exhibit 'granular' and 'collective' behavior even when monomer numbers remain same within the droplets.

Published
2014

20. Genomic Surveillance and Phylodynamic Analyses Reveal the Emergence of Novel Mutations and Co-mutation Patterns Within SARS-CoV-2 Variants Prevalent in India

Author

Biswas, Nupur, primary, Mallick, Priyanka, additional, Maity, Sujay Krishna, additional, Bhowmik, Debaleena, additional, Mitra, Arpita Ghosh, additional, Saha, Soumen, additional, Roy, Aviral, additional, Chakrabarti, Partha, additional, Paul, Sandip, additional, and Chakrabarti, Saikat, additional

Published
2021
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21. Genomic surveillance and phylodynamic analyses reveal emergence of novel mutation and co-mutation patterns within SARS-CoV2 variants prevalent in India

Author

Biswas, Nupur, primary, Mallick, Priyanka, additional, Maity, Sujay Krishna, additional, Bhowmik, Debaleena, additional, Mitra, Arpita Ghosh, additional, Saha, Soumen, additional, Roy, Aviral, additional, Chakrabarti, Partha, additional, Paul, Sandip, additional, and Chakrabarti, Saikat, additional

Published
2021
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24. Corrigendum: Genomic surveillance and phylodynamic analyses reveal the emergence of novel mutations and co-mutation patterns within SARS-CoV-2 variants prevalent in India.

Author

Biswas, Nupur, Mallick, Priyanka, Maity, Sujay Krishna, Bhowmik, Debaleena, Mitra, Arpita Ghosh, Saha, Soumen, Roy, Aviral, Chakrabarti, Partha, Paul, Sandip, and Chakrabarti, Saikat

Subjects
SARS-CoV-2, GENETIC mutation, EXOMES
Abstract

This document is a corrigendum for an article titled "Genomic surveillance and phylodynamic analyses reveal the emergence of novel mutations and co-mutation patterns within SARS-CoV-2 variants prevalent in India." The corrigendum addresses an error in affiliation 2, which should have been listed as "Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India" instead of "Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India." The authors apologize for the error and clarify that it does not affect the scientific conclusions of the article. The corrigendum also includes a note from the publisher stating that the views expressed in the article are solely those of the authors and do not necessarily represent the views of their affiliated organizations or the publisher. [Extracted from the article]

Published
2024
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32. Contributors

Author

Ahamed, Ashif, Alam, Syed Sahajada Mahafujul, Ali, Safdar, Alluri, Anjani, Amjad, Elham, Ashili, Shashaanka, Bardini, Roberta, Bhatt, Shaifali, Binokay, Leman, Biswas, Nupur, Bizzaro, Jeffrey W., Choubey, Jyotsna, Choudhari, Jyoti Kant, Chouhan, Usha, Das, Arpan Jyoti, Dhas, Yogita, Elengoe, Asita, Garg, Prekshi, Grizzi, Fabio, Gupta, Abhinav, Gutti, Ravi Kumar, Hassan, Md Samim, Hedayat, Kamyar M., Hegazi, Mohamed A.A.A., Hoque, Mehboob, Jamil, Zarnain, Jones, Lawrence D., Karakülah, Gökhan, Karthik, Raja Pavan, Kesari, Santosh, Kishor, P.B. Kavi, Kurmi, Sonu, Manoj, Gautham, Marcum, James, Mishra, Sanjana, Mishra, Amit, Nair, Pramod P., Naqvi, Wayez, Nasrin, Taslima, Natte, Sai Bharath, Oktay, Yavuz, Parasher, Aanya, Pragya, Shashwati, Prusty, Dhaneswar, Sahariah, Biju Prava, Samanta, Arijit, Shaik Mohideen, Habeeb, Singh, Ananya, Singh, Tiratha Raj, Sneha, K.H., Sokouti, Babak, Srivastava, Varshita, Srivastava, Neha, Srivastava, Prachi, Sudeesh, Adhithya, Sundararajan, Vijayaraghava Seshadri, Suravajhala, Prashanth N., Taverna, Gianluigi, Valadi, Jayaraman K., and Vishwakarma, Anshu

Published
2025
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34. Risk reduction in anesthesia and sedation—An analysis of process improvement towards zero adverse events.

Author

Mitra, Manasij, Basu, Maitraye, Shailendra, Kumar, and Biswas, Nupur

Subjects
ANESTHESIA, PATIENT-centered care, PATIENT safety, TEACHING hospitals, PRIMARY care, HEALTH risk assessment, ANESTHESIA complications
Abstract

Introduction: Anesthesia is a complex domain that is highly technical and skill based. Primary Care Physicians often have to do the initial evaluation of surgical patients they encounter during their daily practice before referring them to the surgical team. Thus, the Primary Care Physician's preliminary knowledge in anesthesia processes, risks involved and interventions that can be done to minimize these risks can improve patient-centered care and ultimately patient safety. Materials and Methods: The study was conceptualized and conducted in the Department of Anesthesiology from January 2018 to December 2018 in a 600 bed Multispecialty teaching hospital in Bihar, India. The study aimed towards Anesthesia Care related Risk Identification and Reduction and encompassed process improvements. Results: Risk Severity Analysis of the Critical Steps of Anesthesia Care was done. The average Hazard Score reduced from 21.59 during January 2018 to March 2018 to 8.23 during April 2018 to June 2018 subsequently to 3.53 during July 2018 to September 2018 and finally to 2.12 during October 2018 to December 2018. Thus, there was an overall reduction of 90.18% in the Hazard Score from April'18 to June'18 quarter to October 2018 to December 2018 quarter. Conclusion: Adverse Anesthesia/Sedation Events reported during the period from January 2019 to December 2019 was "Zero". A systematic approach towards Risk Reduction not only lead to reduction in Hazard Score and Process Improvement but also made the Anesthesia Care Safe which is evident in the consistency of reporting "Zero" Adverse Anesthesia/Sedation Events for the last one year. [ABSTRACT FROM AUTHOR]

Published
2020
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49. Integrin Modulating Factor: A 30-kD Protein that Modulates the Expression and Function of α5β1 Integrin Receptor.

Author

Ray, Subrata, Chattopadhyay, Nibedita, Sanyal, Utpal, Biswas, Nupur, and Chatterjee, Amitava

Subjects
CELL membranes, INTEGRINS, LIGANDS (Biochemistry), CELL culture
Abstract

Reports the identification of a 30-kilo Dalton protein produced in a SiHa cell culture medium that can modulate the expression and function of the α5β1 integrin receptor in HeLaS3 cells. Methodology; Results; Discussion.

Published
2001

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