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Yadav PD, Sardana V, Deshpande GR, Shinde PV, Thangaraj JWV, George LS, Sapkal GN, Patil DY, Sahay RR, Shete AM, Joshi M, Murhekar M, Godbole S, Gupta N, Prakash S, Rathore M, Ujjainiya R, Singh AP, Mishra A, Dash D, Chaudhary K, Sengupta S. Neutralizing antibody responses to SARS-CoV-2 Omicron variants: Post six months following two-dose & three-dose vaccination of ChAdOx1 nCoV-19 or BBV152. Indian J Med Res 2024; 159:223-231. [PMID: 38517215 PMCID: PMC11050759 DOI: 10.4103/ijmr.ijmr_948_23] [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: 05/18/2023] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND OBJECTIVES The Omicron sub-lineages are known to have higher infectivity, immune escape and lower virulence. During December 2022 - January 2023 and March - April 2023, India witnessed increased SARS-CoV-2 infections, mostly due to newer Omicron sub-lineages. With this unprecedented rise in cases, we assessed the neutralization potential of individuals vaccinated with ChAdOx1 nCoV (Covishield) and BBV152 (Covaxin) against emerging Omicron sub-lineages. METHODS Neutralizing antibody responses were measured in the sera collected from individuals six months post-two doses (n=88) of Covishield (n=44) or Covaxin (n=44) and post-three doses (n=102) of Covishield (n=46) or Covaxin (n=56) booster dose against prototype B.1 strain, lineages of Omicron; XBB.1, BQ.1, BA.5.2 and BF.7. RESULTS The sera of individuals collected six months after the two-dose and the three-dose demonstrated neutralizing activity against all variants. The neutralizing antibody (NAbs) level was highest against the prototype B.1 strain, followed by BA5.2 (5-6 fold lower), BF.7 (11-12 fold lower), BQ.1 (12 fold lower) and XBB.1 (18-22 fold lower). INTERPRETATION CONCLUSIONS Persistence of NAb responses was comparable in individuals with two- and three-dose groups post six months of vaccination. Among the Omicron sub-variants, XBB.1 showed marked neutralization escape, thus pointing towards an eventual immune escape, which may cause more infections. Further, the correlation of study data with complete clinical profile of the participants along with observations for cell-mediated immunity may provide a clear picture for the sustained protection due to three-dose vaccination as well as hybrid immunity against the newer variants.
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Affiliation(s)
| | - Viren Sardana
- Big Data and Informatics Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | | | | | | | - Leyanna S. George
- Division of Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | | | | | - Rima R. Sahay
- Maximum Containment Laboratory, Pune, Maharashtra, India
| | - Anita M. Shete
- Maximum Containment Laboratory, Pune, Maharashtra, India
| | - Madhavi Joshi
- Department of Science & Technology, Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Manoj Murhekar
- Department of Epidemiology & Biostatistics, ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - Sheela Godbole
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Nivedita Gupta
- Division of Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Satyartha Prakash
- Big Data and Informatics Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Mamta Rathore
- Cardiometabolic Disease Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Rajat Ujjainiya
- Cardiometabolic Disease Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Ajay Pratap Singh
- Cardiometabolic Disease Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Aastha Mishra
- Cardiometabolic Disease Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Debasis Dash
- Cardiometabolic Disease Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Kumardeep Chaudhary
- Big Data and Informatics Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Shantanu Sengupta
- Big Data and Informatics Unit, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, India
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Aggarwal M, Garg NM, Agrawal A, Sardana V. Lung Function Reference Equations for Indian Ethnic Groups Based on a Handheld Forced Oscillation Device for Age 9-19 Years. Indian J Pediatr 2023; 90:61-68. [PMID: 35713768 DOI: 10.1007/s12098-022-04176-2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 01/25/2022] [Indexed: 01/10/2023]
Abstract
OBJECTIVE To develop regression equations to predict forced oscillation technique (FOT) parameters in Indian children and adolescents. METHODS Lung function was assessed in a multigeographic cohort of residential school children using a portable FOT-based device (PulmoScan) and spirometry. FOT measurements were performed in 1497 study participants, aged 9-19 y, from 8 Indian districts. Bland-Altman analysis was performed for additional 32 adult subjects to compare the results of PulmoScan to a standard IOS device in an outpatient setting. Reference equations were developed for Rrs and Xrs from the data of healthy subjects with normal spirometry using multivariate regression model for Indo-European, Dravidian, and mixed ethnic groups. RESULTS X5 (bias = 0.02) showed a better agreement than resistance parameters (R5 bias = 0.75, R20 bias = -0.22) in IOS/PulmoScan comparison. Anthropometric variables (age, height, and weight) were positively correlated with reactance (X5) and negatively with resistance parameters (R5, R10, R15, and R20), with most associations being stronger in boys. Final regression model considered ethnicity as a key determinant along with anthropometry. CONCLUSION Multiethnic reference equations were developed for Indian children aged 9-19 y based on a novel handheld FOT device.
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Affiliation(s)
- Mohit Aggarwal
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Neerja Mittal Garg
- CSIR-Central Scientific Instruments Organization, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Anurag Agrawal
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
| | - Viren Sardana
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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Guin D, Yadav S, Singh P, Singh P, Thakran S, Kukal S, Kanojia N, Paul PR, Pattnaik B, Sardana V, Grover S, Hasija Y, Saso L, Agrawal A, Kukreti R. Human genetic factors associated with pneumonia risk, a cue for COVID-19 susceptibility. Infection, Genetics and Evolution 2022; 102:105299. [PMID: 35545162 PMCID: PMC9080029 DOI: 10.1016/j.meegid.2022.105299] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/30/2022] [Accepted: 05/02/2022] [Indexed: 01/08/2023]
Abstract
Pneumonia, an acute respiratory tract infection, is one of the major causes of mortality worldwide. Depending on the site of acquisition, pneumonia can be community acquired pneumonia (CAP) or nosocomial pneumonia (NP). The risk of pneumonia, is partially driven by host genetics. CYP1A1 is a widely studied pulmonary CYP family gene primarily expressed in peripheral airway epithelium. The CYP1A1 genetic variants, included in this study, alter the gene activity and are known to contribute in lung inflammation, which may cause pneumonia pathogenesis. In this study, we performed a meta-analysis to establish the possible contribution of CYP1A1 gene, and its three variants (rs2606345, rs1048943 and rs4646903) towards the genetic etiology of pneumonia risk. Using PRISMA guidelines, we systematically reviewed and meta-analysed case-control studies, evaluating risk of pneumonia in patients carrying the risk alleles of CYP1A1 variants. Heterogeneity across the studies was evaluated using I2 statistics. Based on heterogeneity, a random-effect (using maximum likelihood) or fixed-effect (using inverse variance) model was applied to estimate the effect size. Pooled odds ratio (OR) was calculated to estimate the overall effect of the risk allele association with pneumonia susceptibility. Egger's regression test and funnel plot were used to assess publication bias. Subgroup analysis was performed based on pneumonia type (CAP and NP), population, as well as age group. A total of ten articles were identified as eligible studies, which included 3049 cases and 2249 healthy controls. The meta-analysis findings revealed CYP1A1 variants, rs2606345 [T vs G; OR = 1.12 (0.75–1.50); p = 0.02; I2 = 84.89%], and rs1048943 [G vs T; OR = 1.19 (0.76–1.61); p = 0.02; I2 = 0.00%] as risk markers whereas rs4646903 showed no statistical significance for susceptibility to pneumonia. On subgroup analysis, both the genetic variants showed significant association with CAP but not with NP. We additionally performed a spatial analysis to identify the key factors possibly explaining the variability across countries in the prevalence of the coronavirus disease 2019 (COVID-19), a viral pneumonia. We observed a significant association between the risk allele of rs2606345 and rs1048943, with a higher COVID-19 prevalence worldwide, providing us important links in understanding the variability in COVID-19 prevalence.
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Gidde PS, Prasad SS, Singh AP, Bhatheja N, Prakash S, Singh P, Saboo A, Takhar R, Gupta S, Saurav S, M V R, Singh A, Sardana V, Mahajan H, Kalyanpur A, Mandal AS, Mahajan V, Agrawal A, Agrawal A, Venugopal VK, Singh S, Dash D. Validation of expert system enhanced deep learning algorithm for automated screening for COVID-Pneumonia on chest X-rays. Sci Rep 2021; 11:23210. [PMID: 34853342 PMCID: PMC8636645 DOI: 10.1038/s41598-021-02003-w] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/01/2021] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV2 pandemic exposed the limitations of artificial intelligence based medical imaging systems. Earlier in the pandemic, the absence of sufficient training data prevented effective deep learning (DL) solutions for the diagnosis of COVID-19 based on X-Ray data. Here, addressing the lacunae in existing literature and algorithms with the paucity of initial training data; we describe CovBaseAI, an explainable tool using an ensemble of three DL models and an expert decision system (EDS) for COVID-Pneumonia diagnosis, trained entirely on pre-COVID-19 datasets. The performance and explainability of CovBaseAI was primarily validated on two independent datasets. Firstly, 1401 randomly selected CxR from an Indian quarantine center to assess effectiveness in excluding radiological COVID-Pneumonia requiring higher care. Second, curated dataset; 434 RT-PCR positive cases and 471 non-COVID/Normal historical scans, to assess performance in advanced medical settings. CovBaseAI had an accuracy of 87% with a negative predictive value of 98% in the quarantine-center data. However, sensitivity was 0.66-0.90 taking RT-PCR/radiologist opinion as ground truth. This work provides new insights on the usage of EDS with DL methods and the ability of algorithms to confidently predict COVID-Pneumonia while reinforcing the established learning; that benchmarking based on RT-PCR may not serve as reliable ground truth in radiological diagnosis. Such tools can pave the path for multi-modal high throughput detection of COVID-Pneumonia in screening and referral.
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Affiliation(s)
| | - Shyam Sunder Prasad
- CSIR-Central Electronics Engineering Research Institute, Pilani, Rajasthan, 333031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ajay Pratap Singh
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Nitin Bhatheja
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Satyartha Prakash
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Prateek Singh
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Aakash Saboo
- Centre for Advanced Research in Imaging, Neurosciences Genomics (CARING), New Delhi, India
| | - Rohit Takhar
- Centre for Advanced Research in Imaging, Neurosciences Genomics (CARING), New Delhi, India
| | - Salil Gupta
- Centre for Advanced Research in Imaging, Neurosciences Genomics (CARING), New Delhi, India
| | - Sumeet Saurav
- CSIR-Central Electronics Engineering Research Institute, Pilani, Rajasthan, 333031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Raghunandanan M V
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | | | - Viren Sardana
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Harsh Mahajan
- Centre for Advanced Research in Imaging, Neurosciences Genomics (CARING), New Delhi, India
| | - Arjun Kalyanpur
- Teleradiology Solutions, 7G, Opposite Graphite India, Whitefield, Bangalore, Karnataka, 560048, India
| | - Atanendu Shekhar Mandal
- CSIR-Central Electronics Engineering Research Institute, Pilani, Rajasthan, 333031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vidur Mahajan
- Centre for Advanced Research in Imaging, Neurosciences Genomics (CARING), New Delhi, India
| | - Anurag Agrawal
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anjali Agrawal
- Teleradiology Solutions, 12B Sriram Road, Civil Lines, Delhi, 110054, India.
| | | | - Sanjay Singh
- CSIR-Central Electronics Engineering Research Institute, Pilani, Rajasthan, 333031, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Debasis Dash
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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5
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Dhar MS, Marwal R, VS R, Ponnusamy K, Jolly B, Bhoyar RC, Sardana V, Naushin S, Rophina M, Mellan TA, Mishra S, Whittaker C, Fatihi S, Datta M, Singh P, Sharma U, Ujjainiya R, Bhatheja N, Divakar MK, Singh MK, Imran M, Senthivel V, Maurya R, Jha N, Mehta P, A V, Sharma P, VR A, Chaudhary U, Soni N, Thukral L, Flaxman S, Bhatt S, Pandey R, Dash D, Faruq M, Lall H, Gogia H, Madan P, Kulkarni S, Chauhan H, Sengupta S, Kabra S, Gupta RK, Singh SK, Agrawal A, Rakshit P. Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India. Science 2021; 374:995-999. [PMID: 34648303 PMCID: PMC7612010 DOI: 10.1126/science.abj9932] [Citation(s) in RCA: 160] [Impact Index Per Article: 53.3] [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: 06/15/2021] [Accepted: 10/06/2021] [Indexed: 01/16/2023]
Abstract
Delhi, the national capital of India, experienced multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks in 2020 and reached population seropositivity of >50% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant, B.1.617.2 (Delta), replaced B.1.1.7 (Alpha). A Bayesian model explains the growth advantage of Delta through a combination of increased transmissibility and reduced sensitivity to immune responses generated against earlier variants (median estimates: 1.5-fold greater transmissibility and 20% reduction in sensitivity). Seropositivity of an employee and family cohort increased from 42% to 87.5% between March and July 2021, with 27% reinfections, as judged by increased antibody concentration after a previous decline. The likely high transmissibility and partial evasion of immunity by the Delta variant contributed to an overwhelming surge in Delhi.
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Affiliation(s)
| | - Robin Marwal
- National Centre for Disease Control, Delhi, India
| | | | | | - Bani Jolly
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Rahul C. Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Viren Sardana
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Salwa Naushin
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Mercy Rophina
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Thomas A. Mellan
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Swapnil Mishra
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Charles Whittaker
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Saman Fatihi
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Meena Datta
- National Centre for Disease Control, Delhi, India
| | | | - Uma Sharma
- National Centre for Disease Control, Delhi, India
| | - Rajat Ujjainiya
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Nitin Bhatheja
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Mohit Kumar Divakar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Mohamed Imran
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Vigneshwar Senthivel
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Ranjeet Maurya
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Neha Jha
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Priyanka Mehta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Vivekanand A
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Pooja Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Arvinden VR
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Namita Soni
- National Centre for Disease Control, Delhi, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Seth Flaxman
- Department of Mathematics, Imperial College London, London, UK
| | - Samir Bhatt
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Debasis Dash
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Mohammed Faruq
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Hemlata Lall
- National Centre for Disease Control, Delhi, India
| | - Hema Gogia
- National Centre for Disease Control, Delhi, India
| | - Preeti Madan
- National Centre for Disease Control, Delhi, India
| | | | | | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - The Indian SARS-CoV-2 Genomics Consortium (INSACOG)‡
- National Centre for Disease Control, Delhi, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
- Department of Mathematics, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | - Ravindra K. Gupta
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | | | - Anurag Agrawal
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
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6
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Dhar MS, Marwal R, Vs R, Ponnusamy K, Jolly B, Bhoyar RC, Sardana V, Naushin S, Rophina M, Mellan TA, Mishra S, Whittaker C, Fatihi S, Datta M, Singh P, Sharma U, Ujjainiya R, Bhatheja N, Divakar MK, Singh MK, Imran M, Senthivel V, Maurya R, Jha N, Mehta P, A V, Sharma P, Vr A, Chaudhary U, Soni N, Thukral L, Flaxman S, Bhatt S, Pandey R, Dash D, Faruq M, Lall H, Gogia H, Madan P, Kulkarni S, Chauhan H, Sengupta S, Kabra S, Gupta RK, Singh SK, Agrawal A, Rakshit P, Nandicoori V, Tallapaka KB, Sowpati DT, Thangaraj K, Bashyam MD, Dalal A, Sivasubbu S, Scaria V, Parida A, Raghav SK, Prasad P, Sarin A, Mayor S, Ramakrishnan U, Palakodeti D, Seshasayee ASN, Bhat M, Shouche Y, Pillai A, Dikid T, Das S, Maitra A, Chinnaswamy S, Biswas NK, Desai AS, Pattabiraman C, Manjunatha MV, Mani RS, Arunachal Udupi G, Abraham P, Atul PV, Cherian SS. Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India. Science 2021; 374:995-999. [PMID: 34648303 DOI: 10.1101/2021.06.02.21258076] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Delhi, the national capital of India, experienced multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks in 2020 and reached population seropositivity of >50% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant, B.1.617.2 (Delta), replaced B.1.1.7 (Alpha). A Bayesian model explains the growth advantage of Delta through a combination of increased transmissibility and reduced sensitivity to immune responses generated against earlier variants (median estimates: 1.5-fold greater transmissibility and 20% reduction in sensitivity). Seropositivity of an employee and family cohort increased from 42% to 87.5% between March and July 2021, with 27% reinfections, as judged by increased antibody concentration after a previous decline. The likely high transmissibility and partial evasion of immunity by the Delta variant contributed to an overwhelming surge in Delhi.
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Affiliation(s)
| | - Robin Marwal
- National Centre for Disease Control, Delhi, India
| | | | | | - Bani Jolly
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Rahul C Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Viren Sardana
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Salwa Naushin
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Mercy Rophina
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Thomas A Mellan
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Swapnil Mishra
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Charles Whittaker
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Saman Fatihi
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Meena Datta
- National Centre for Disease Control, Delhi, India
| | | | - Uma Sharma
- National Centre for Disease Control, Delhi, India
| | - Rajat Ujjainiya
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Nitin Bhatheja
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Mohit Kumar Divakar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Mohamed Imran
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Vigneshwar Senthivel
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Ranjeet Maurya
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Neha Jha
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Priyanka Mehta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Vivekanand A
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Pooja Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Arvinden Vr
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Namita Soni
- National Centre for Disease Control, Delhi, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Seth Flaxman
- Department of Mathematics, Imperial College London, London, UK
| | - Samir Bhatt
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Debasis Dash
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Mohammed Faruq
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Hemlata Lall
- National Centre for Disease Control, Delhi, India
| | - Hema Gogia
- National Centre for Disease Control, Delhi, India
| | - Preeti Madan
- National Centre for Disease Control, Delhi, India
| | | | | | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Ravindra K Gupta
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | | | - Anurag Agrawal
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
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7
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Naushin S, Sardana V, Ujjainiya R, Bhatheja N, Kutum R, Bhaskar AK, Pradhan S, Prakash S, Khan R, Rawat BS, Tallapaka KB, Anumalla M, Chandak GR, Lahiri A, Kar S, Mulay SR, Mugale MN, Srivastava M, Khan S, Srivastava A, Tomar B, Veerapandian M, Venkatachalam G, Vijayakumar SR, Agarwal A, Gupta D, Halami PM, Peddha MS, Sundaram GM, Veeranna RP, Pal A, Agarwal VK, Maurya AK, Singh RK, Raman AK, Anandasadagopan SK, Karuppanan P, Venkatesan S, Sardana HK, Kothari A, Jain R, Thakur A, Parihar DS, Saifi A, Kaur J, Kumar V, Mishra A, Gogeri I, Rayasam G, Singh P, Chakraborty R, Chaturvedi G, Karunakar P, Yadav R, Singhmar S, Singh D, Sarkar S, Bhattacharya P, Acharya S, Singh V, Verma S, Soni D, Seth S, Vashisht S, Thakran S, Fatima F, Singh AP, Sharma A, Sharma B, Subramanian M, Padwad YS, Hallan V, Patial V, Singh D, Tripude NV, Chakrabarti P, Maity SK, Ganguly D, Sarkar J, Ramakrishna S, Kumar BN, Kumar KA, Gandhi SG, Jamwal PS, Chouhan R, Jamwal VL, Kapoor N, Ghosh D, Thakkar G, Subudhi U, Sen P, Chaudhury SR, Kumar R, Gupta P, Tuli A, Sharma D, Ringe RP, D A, Kulkarni M, Shanmugam D, Dharne MS, Dastager SG, Joshi R, Patil AP, Mahajan SN, Khan AH, Wagh V, Yadav RK, Khilari A, Bhadange M, Chaurasiya AH, Kulsange SE, Khairnar K, Paranjape S, Kalita J, Sastry NG, Phukan T, Manna P, Romi W, Bharali P, Ozah D, Sahu RK, Babu EVSSK, Sukumaran R, Nair AR, Valappil PK, Puthiyamadam A, Velayudhanpillai A, Chodankar K, Damare S, Madhavi Y, Aggarwal VV, Dahiya S, Agrawal A, Dash D, Sengupta S. Insights from a Pan India Sero-Epidemiological survey (Phenome-India Cohort) for SARS-CoV2. eLife 2021; 10:e66537. [PMID: 33876727 PMCID: PMC8118652 DOI: 10.7554/elife.66537] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/09/2021] [Indexed: 12/14/2022] Open
Abstract
To understand the spread of SARS-CoV2, in August and September 2020, the Council of Scientific and Industrial Research (India) conducted a serosurvey across its constituent laboratories and centers across India. Of 10,427 volunteers, 1058 (10.14%) tested positive for SARS-CoV2 anti-nucleocapsid (anti-NC) antibodies, 95% of which had surrogate neutralization activity. Three-fourth of these recalled no symptoms. Repeat serology tests at 3 (n = 607) and 6 (n = 175) months showed stable anti-NC antibodies but declining neutralization activity. Local seropositivity was higher in densely populated cities and was inversely correlated with a 30-day change in regional test positivity rates (TPRs). Regional seropositivity above 10% was associated with declining TPR. Personal factors associated with higher odds of seropositivity were high-exposure work (odds ratio, 95% confidence interval, p value: 2.23, 1.92-2.59, <0.0001), use of public transport (1.79, 1.43-2.24, <0.0001), not smoking (1.52, 1.16-1.99, 0.0257), non-vegetarian diet (1.67, 1.41-1.99, <0.0001), and B blood group (1.36, 1.15-1.61, 0.001).
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Neelapu BC, Kharbanda OP, Sardana V, Gupta A, Vasamsetti S, Balachandran R, Sardana HK. Automatic localization of three-dimensional cephalometric landmarks on CBCT images by extracting symmetry features of the skull. Dentomaxillofac Radiol 2018; 47:20170054. [PMID: 28845693 DOI: 10.1259/dmfr.20170054] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
To propose an algorithm for automatic localization of 3D cephalometric landmarks on CBCT data, those are useful for both cephalometric and upper airway volumetric analysis. 20 landmarks were targeted for automatic detection, of which 12 landmarks exist on the mid-sagittal plane. Automatic detection of mid-sagittal plane from the volume is a challenging task. Mid-sagittal plane is detected by extraction of statistical parameters of the symmetrical features of the skull. The mid-sagittal plane is partitioned into four quadrants based on the boundary definitions extracted from the human anatomy. Template matching algorithm is applied on the mid-sagittal plane to identify the region of interest ROI, further the edge features are extracted, to form contours in the individual regions. The landmarks are automatically localized by using the extracted knowledge of anatomical definitions of the landmarks. The overall mean error for detection of 20 landmarks was 1.88 mm with a standard deviation of 1.10 mm. The cephalometric land marks on CBCT data were detected automatically with in the mean error less than 2 mm.
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Affiliation(s)
- Bala Chakravarthy Neelapu
- 1 Academy of Scientific & Innovative Research (AcSIR) , Chennai , India.,3 CSIR- Central Scientific Instruments Organisation , Chandigarh , India
| | - Om Prakash Kharbanda
- 2 Division of Orthodontics and Dentofacial Deformities, Centre for Dental Education and Research, All India Institute of Medical Sciences , New Delhi , India
| | - Viren Sardana
- 1 Academy of Scientific & Innovative Research (AcSIR) , Chennai , India.,3 CSIR- Central Scientific Instruments Organisation , Chandigarh , India
| | - Abhishek Gupta
- 4 Department of Computer Science & Engineering, Shri Mata Vaishno Devi University , Kakryal, Katra, Jammu and Kashmir , India
| | - Srikanth Vasamsetti
- 1 Academy of Scientific & Innovative Research (AcSIR) , Chennai , India.,3 CSIR- Central Scientific Instruments Organisation , Chandigarh , India
| | - Rajiv Balachandran
- 2 Division of Orthodontics and Dentofacial Deformities, Centre for Dental Education and Research, All India Institute of Medical Sciences , New Delhi , India
| | - Harish Kumar Sardana
- 1 Academy of Scientific & Innovative Research (AcSIR) , Chennai , India.,3 CSIR- Central Scientific Instruments Organisation , Chandigarh , India
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9
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Neelapu BC, Kharbanda OP, Sardana HK, Gupta A, Vasamsetti S, Balachandran R, Rana SS, Sardana V. The reliability of different methods of manual volumetric segmentation of pharyngeal and sinonasal subregions. Oral Surg Oral Med Oral Pathol Oral Radiol 2017; 124:577-587. [DOI: 10.1016/j.oooo.2017.08.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 08/21/2017] [Accepted: 08/27/2017] [Indexed: 11/25/2022]
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10
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Gupta A, Kharbanda OP, Balachandran R, Sardana V, Kalra S, Chaurasia S, Sardana HK. Authors' response. Am J Orthod Dentofacial Orthop 2017; 151:1018-1019. [PMID: 28554439 DOI: 10.1016/j.ajodo.2017.03.005] [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] [Received: 03/08/2017] [Revised: 03/08/2017] [Accepted: 03/10/2017] [Indexed: 10/19/2022]
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11
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Neelapu BC, Kharbanda OP, Sardana HK, Balachandran R, Sardana V, Kapoor P, Gupta A, Vasamsetti S. Craniofacial and upper airway morphology in adult obstructive sleep apnea patients: A systematic review and meta-analysis of cephalometric studies. Sleep Med Rev 2016; 31:79-90. [PMID: 27039222 DOI: 10.1016/j.smrv.2016.01.007] [Citation(s) in RCA: 191] [Impact Index Per Article: 23.9] [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: 06/29/2015] [Revised: 01/15/2016] [Accepted: 01/24/2016] [Indexed: 12/14/2022]
Abstract
Obstructive sleep apnea (OSA) is one of the common sleep breathing disorders in adults, characterised by frequent episodes of upper airway collapse during sleep. Craniofacial disharmony is an important risk factor for OSA. Overnight polysomnography (PSG) study is considered to be the most reliable confirmatory investigation for OSA diagnosis, whereas the precise localization of site of obstruction to the airflow cannot be detected. Identifying the cause of OSA in a particular ethnic population/individual subject helps to understand the etiological factors and effective management of OSA. The objective of the meta-analysis is to elucidate altered craniofacial anatomy on lateral cephalograms in adult subjects with established OSA. Significant weighted mean difference with insignificant heterogeneity was found for the following parameters: anterior lower facial height (ALFH: 2.48 mm), position of hyoid bone (Go-H: 5.45 mm, S-H: 6.89 mm, GoGn-H: 11.84°, GoGn-H: 7.22 mm, N-S-H: 2.14°), and pharyngeal airway space (PNS-Phw: -1.55 mm, pharyngeal space: -495.74 mm2 and oro-pharyngeal area: -151.15 mm2). Significant weighted mean difference with significant heterogeneity was found for the following parameters: cranial base (SN: -2.25 mm, S-N-Ba: -1.45°), position and length of mandible (SNB: -1.49° and Go-Me: -5.66 mm) respectively, maxillary length (ANS-PNS: -1.76 mm), tongue area (T: 366.51 mm2), soft palate area (UV: 125.02 mm2), and upper airway length (UAL: 5.39 mm). This meta-analysis supports the relationship between craniofacial disharmony and obstructive sleep apnea. There is a strong evidence for reduced pharyngeal airway space, inferiorly placed hyoid bone and increased anterior facial heights in adult OSA patients compared to control subjects. The cephalometric analysis provides insight into anatomical basis of the etiology of OSA that can influence making a choice of appropriate therapy.
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Affiliation(s)
- Bala Chakravarthy Neelapu
- Academy of Scientific & Innovative Research (AcSIR), India; CSIR-Central Scientific Instruments Organisation, Chandigarh, 160030, India
| | - Om Prakash Kharbanda
- Division of Orthodontics and Dentofacial Deformities, Centre for Dental Education and Research, All India Institute of Medical Sciences, New Delhi, 110029, India.
| | - Harish Kumar Sardana
- Academy of Scientific & Innovative Research (AcSIR), India; CSIR-Central Scientific Instruments Organisation, Chandigarh, 160030, India
| | - Rajiv Balachandran
- Division of Orthodontics and Dentofacial Deformities, Centre for Dental Education and Research, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Viren Sardana
- Academy of Scientific & Innovative Research (AcSIR), India; CSIR-Central Scientific Instruments Organisation, Chandigarh, 160030, India
| | - Priyanka Kapoor
- Faculty of Dentistry, Jamia Millia Islamia, New Delhi, 110025, India
| | - Abhishek Gupta
- Academy of Scientific & Innovative Research (AcSIR), India; CSIR-Central Scientific Instruments Organisation, Chandigarh, 160030, India
| | - Srikanth Vasamsetti
- Academy of Scientific & Innovative Research (AcSIR), India; CSIR-Central Scientific Instruments Organisation, Chandigarh, 160030, India
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Gupta A, Kharbanda OP, Sardana V, Balachandran R, Sardana HK. Accuracy of 3D cephalometric measurements based on an automatic knowledge-based landmark detection algorithm. Int J Comput Assist Radiol Surg 2015; 11:1297-309. [PMID: 26704370 DOI: 10.1007/s11548-015-1334-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 11/23/2015] [Indexed: 12/31/2022]
Abstract
PURPOSE To evaluate the accuracy of three-dimensional cephalometric measurements obtained through an automatic landmark detection algorithm compared to those obtained through manual identification. METHODS The study demonstrates a comparison of 51 cephalometric measurements (28 linear, 16 angles and 7 ratios) on 30 CBCT (cone beam computed tomography) images. The analysis was performed to compare measurements based on 21 cephalometric landmarks detected automatically and those identified manually by three observers. RESULTS Inter-observer ICC for each landmark was found to be excellent ([Formula: see text]) among three observers. The unpaired t-test revealed that there was no statistically significant difference in the measurements based on automatically detected and manually identified landmarks. The difference between the manual and automatic observation for each measurement was reported as an error. The highest mean error in the linear and angular measurements was found to be 2.63 mm ([Formula: see text] distance) and [Formula: see text] ([Formula: see text]-Me angle), respectively. The highest mean error in the group of distance ratios was 0.03 (for N-Me/N-ANS and [Formula: see text]). CONCLUSION Cephalometric measurements computed from automatic detection of landmarks on 3D CBCT image were as accurate as those computed from manual identification.
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Affiliation(s)
- Abhishek Gupta
- Academy of Scientific & Innovative Research (AcSIR), New Delhi, India.,CSIR-Central Scientific Instruments Organisation, Chandigarh, 160030, India
| | - Om Prakash Kharbanda
- Centre for Dental Education and Research, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Viren Sardana
- CSIR-Central Scientific Instruments Organisation, Chandigarh, 160030, India
| | - Rajiv Balachandran
- Centre for Dental Education and Research, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Harish Kumar Sardana
- Academy of Scientific & Innovative Research (AcSIR), New Delhi, India. .,CSIR-Central Scientific Instruments Organisation, Chandigarh, 160030, India.
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13
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Vasamsetti S, Sardana V, Kumar P, Kharbanda OP, Sardana HK. Automatic Landmark Identification in Lateral Cephalometric Images Using Optimized Template Matching. J Med Imaging Hlth Inform 2015. [DOI: 10.1166/jmihi.2015.1426] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Qureshi S, Pandey A, Sirohi TR, Verma SR, Sardana V, Agrawal C, Asthana AK, Madan M. Mixed pulmonary infection in an immunocompromised patient: a rare case report. Indian J Med Microbiol 2014; 32:79-81. [PMID: 24399397 DOI: 10.4103/0255-0857.124330] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Patients who are immunocompromised are predisposed to a variety of common and uncommon pulmonary infections. We report a case of mixed pulmonary infection by drug resistant tuberculosis with a nocardiosis in a 49-year-old man who was a known case of chronic obstructive pulmonary disease, on prolonged corticosteroid use with diabetes mellitus. Chronic use of corticosteroids is a predisposing factor for opportunistic infections, such as nocardiosis or tuberculosis. Since such a mixed infection is rare, maybe a combined approach to therapy early in the course of disease would be effective in such cases.
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Affiliation(s)
| | - A Pandey
- Department of Microbiology, Subharti Medical College, Swami Vivekanand Subharti University, Meerut, Uttar Pradesh, India
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Agrawal A, Bhattacharya J, Baranwal N, Bhatla S, Dube S, Sardana V, Gaur DR, Balazova D, Brahmachari SK. Integrating health care delivery and data collection in rural India using a rapidly deployable ehealth center. PLoS Med 2013; 10:e1001468. [PMID: 23825182 PMCID: PMC3692411 DOI: 10.1371/journal.pmed.1001468] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Anurag Agrawal and colleagues describe their experience of setting up a readily deployable cargo container-based health center in rural India. Please see later in the article for the Editors' Summary
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Affiliation(s)
- Anurag Agrawal
- Council of Scientific and Industrial Research (CSIR), Institute of Genomics and Integrative Biology, India.
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16
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Arya N, Sardana V, Saxena M, Rangarajan A, Katti DS. Recapitulating tumour microenvironment in chitosan-gelatin three-dimensional scaffolds: an improved in vitro tumour model. J R Soc Interface 2012; 9:3288-302. [PMID: 22977099 DOI: 10.1098/rsif.2012.0564] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Owing to the reduced co-relationship between conventional flat Petri dish culture (two-dimensional) and the tumour microenvironment, there has been a shift towards three-dimensional culture systems that show an improved analogy to the same. In this work, an extracellular matrix (ECM)-mimicking three-dimensional scaffold based on chitosan and gelatin was fabricated and explored for its potential as a tumour model for lung cancer. It was demonstrated that the chitosan-gelatin (CG) scaffolds supported the formation of tumoroids that were similar to tumours grown in vivo for factors involved in tumour-cell-ECM interaction, invasion and metastasis, and response to anti-cancer drugs. On the other hand, the two-dimensional Petri dish surfaces did not demonstrate gene-expression profiles similar to tumours grown in vivo. Further, the three-dimensional CG scaffolds supported the formation of tumoroids, using other types of cancer cells such as breast, cervix and bone, indicating a possible wider potential for in vitro tumoroid generation. Overall, the results demonstrated that CG scaffolds can be an improved in vitro tool to study cancer progression and drug screening for solid tumours.
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Affiliation(s)
- Neha Arya
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, Uttar Pradesh, India
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17
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Sardana V, Balappanavar AY, Patil GB, Kulkarni N, Sagari SG, Gupta KD. Impact of a modified carbonated beverage on human dental plaque and salivary pH: an in vivo study. J Indian Soc Pedod Prev Dent 2012; 30:7-12. [PMID: 22565511 DOI: 10.4103/0970-4388.95563] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [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: 11/04/2022] Open
Abstract
BACKGROUND To assess the plaque and salivary pH changes at different time intervals in vivo after consumption of a carbonated beverage modified with sodium fluoride and calcium phosphate. MATERIALS AND METHODS Twenty-four subjects aged 18-25 years were recruited and randomly assigned to three groups (group A, original drink Sprite; group B, Sprite with sodium fluoride; group C, Sprite with calcium phosphate). Collection of pooled plaque and unstimulated saliva was done before and after the drinks were consumed by the subjects at 5-, 10-, 20- and 30-minute intervals. RESULTS The pH rise was higher with group C for plaque and group B for saliva. CONCLUSIONS Modification of the test carbonated beverage with calcium phosphate and fluoride may exert some protective potential, especially in high caries risk candidates.
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Affiliation(s)
- V Sardana
- Public Health Dentistry, Teerthanker Mahaveer Dental College and Research Center, Moradabad, Uttar Pradesh, India
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18
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Inglese L, Fantoni C, Sardana V. Can IVUS-virtual histology improve outcomes of percutaneous carotid treatment? J Cardiovasc Surg (Torino) 2009; 50:735-744. [PMID: 19935604] [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] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Several previous studies focusing on comparison between outcomes of carotid artery stenting (CAS) and carotid endoarterectomy (CEA) have put forward conflicting results about the non-inferiority of CAS compared to CEA. Likely outcomes after CAS have been greatly limited by incomplete knowledge of atherosclerotic carotid pathology and probably inappropriate patient selection criteria. In the current practice, only the degree of lumen obstruction is indication to an invasive treatment (CEA or CAS) in symptomatic or asymptomatic patients, but it has been recently demonstrated that histology of carotid plaques also plays a major role. Indeed, plaque morphology and composition seem to influence more importantly outcomes of CAS than those of CEA. Angiography is a poor diagnostic tool to detect the severity and composition of atherosclerotic lesions. Virtual histology (VH) is a new technology incorporated in the latest intravascular ultrasound (IVUS) equipment that allows a validated histological characterization of plaques by performing a spectral, objective and highly-reproducible analysis of the radiofrequency and amplitude data of the ultrasound waves that cross different tissues. This manuscript reports authors' experience with the use of IVUS-VH during CAS. This new technology, by characterizing morphology, extension and histology of carotid plaque, seems to provide important information for confirming percentage of carotid stenosis and judging its embolic potential, tailoring the procedure and guiding the choice of stent and finally for checking stent apposition and complete covering of vulnerable plaques. According to authors' opinion IVUS-VH has the potential to optimize patients' and lesions' selection criteria for CAS in order to improve its outcomes.
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Affiliation(s)
- L Inglese
- Department of Interventional Cardiovascular Radiology, IRCCS, San Donato Policlinic, San Donato Milanese, Milan, Italy.
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Srivastava AK, Sardana V, Prasad K, Behari M. Diagnostic dilemma in flaccid paralysis following anti-rabies vaccine. Neurol India 2004; 52:132-3. [PMID: 15069272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
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20
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Srivastava AK, Khanna N, Sardana V, Gaekwad S, Prasad K, Behari M. Cerebral venous thrombosis in ulcerative colitis. Neurol India 2002; 50:215-7. [PMID: 12134195] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Cerebral venous thrombosis is a rare complication of ulcerative colitis. We report a case of 29 year old male who developed superior sagittal, left lateral and sigmoid sinus thrombosis secondary to ulcerative colitis. He was successfully treated with low molecular weight heparin and steroids.
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Affiliation(s)
- A K Srivastava
- Department of Neurology, Neurosciences Center, All India Institute of Medical Sciences, New Delhi, 110029, India
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21
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Singh S, Sardana V, Prasad K, Behari M. Physician assisted suicide--the perspective of a neurologist. J Assoc Physicians India 2001; 49:823-8. [PMID: 11837473] [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] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Modern medicine has resulted in a better control and treatment of many diseases. This has provided a better life for patients with treatable disorders, but at the same times has prolonged the suffering of the patients with diseases that are not treatable. This is of particular importance for the patients with neurological diseases, as some of these conditions have a relentlessly progressive course and cause significant distress to the patient. Recent times have seen an expansion of the scope of the various "rights of the patient" and according to some, this includes the "right to die". As a result of this concept of regarding the autonomy of the patient, the phenomenon of physician assisted suicide has emerged and is a topic of intense debate amongst the physicians, social workers and politicians all over the world. The present article puts forth the current concepts and brings out the exact definitions of the terms like physician-assisted suicide, voluntary active euthanasia and voluntary passive euthanasia. It presents the statements made by the various societies and organisations regarding the PAS. It also brings forth the point of view of the authors about this aspect of medicine. The authors share the view of the various scientific organisations, and opine that though the idea of physician assisted suicide may be morally justifiable in certain circumstances, it should not be made legal.
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Affiliation(s)
- S Singh
- Department of Neurology, Neuroscience's Centre, All India Institute of Medical Sciences
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Abstract
OBJECTIVES The clinical data on cases of Juvenile Myoclonic Epilepsy (JME) were analysed. Response to initial small dosages (lower than usual) of sodium valproate and further lower maintenance dosages in patients who were seizure free for 2 years on drug were assessed. MATERIAL AND METHODS Seventy-six patients who were diagnosed to have Juvenile Myoclonic Epilepsy on definite criteria were studied. All patients were put on sodium valproate in dosages (lower than usual) for initial control and further lower maintenance dosage and response evaluated. RESULTS The clinical profile was found to be similar as in other parts of India. There was a female preponderance and average delay of 4.9 years in final diagnosis. Forty-eight (63.1%) patients showed good control on 15 mg/kg/day dosages of sodium valproate. After a seizure free interval of 2 years, 58% of patients could be maintained on small dosages ranging from 3-5 mg/kg/day to 6-8 mg/kg/day. CONCLUSION The majority of JME patients responded well not only to sodium valproate in dosages lower than usually prescribed but required very small dosages for maintenance after a seizure free period of 2 years.
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Affiliation(s)
- A Panagariya
- Department of Neurology, SMS Medical College, Jaipur, Rajasthan, India
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Carroll SS, Sardana V, Yang Z, Jacobs AR, Mizenko C, Hall D, Hill L, Zugay-Murphy J, Kuo LC. Only a small fraction of purified hepatitis C RNA-dependent RNA polymerase is catalytically competent: implications for viral replication and in vitro assays. Biochemistry 2000; 39:8243-9. [PMID: 10889032 DOI: 10.1021/bi991992s] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzymatic activity of a C-terminally truncated form of the RNA-dependent RNA polymerase, termed NS5B(Delta21), of the hepatitis C virus (strain BK) has been investigated using both homopolymeric and heteropolymeric RNA templates. Incorporation of nucleotides into a heteropolymeric RNA template as catalyzed by NS5B(Delta21) is characterized by biphasic reaction time courses. At high concentrations of nucleoside triphosphate in reactions allowing a preincubation of NS5B(Delta21) and RNA template, an initial rapid phase of the reaction is followed by a slower linear phase. The amplitude of the first phase of the reaction varies directly with the concentration of the enzyme in the reaction. It is shown here that full-length copies of the template are produced during the first phase of the reaction. Our results reveal that NS5B(Delta21) is processive but only a small fraction, less than 1%, of the purified enzyme present participates productively in the reaction. Most importantly, the turnover number for the hepatitis C NS5B(Delta21) is comparable to those observed for other polymerases such as the HIV-1 reverse transcriptase. The combined results reconcile in part the apparent discrepancy of the low, observed specific activity of the purified enzyme and the rapid generation of HCV in vivo.
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Affiliation(s)
- S S Carroll
- Department of Antiviral Research, Merck Research Labs, West Point, Pennsylvania, 19486, USA
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24
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Chen Z, Yan Y, Munshi S, Li Y, Zugay-Murphy J, Xu B, Witmer M, Felock P, Wolfe A, Sardana V, Emini EA, Hazuda D, Kuo LC. X-ray structure of simian immunodeficiency virus integrase containing the core and C-terminal domain (residues 50-293)--an initial glance of the viral DNA binding platform. J Mol Biol 2000; 296:521-33. [PMID: 10669606 DOI: 10.1006/jmbi.1999.3451] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The crystal structure of simian immunodeficiency virus (SIV) integrase that contains in a single polypeptide the core and the C-terminal deoxyoligonucleotide binding domain has been determined at 3 A resolution with an R-value of 0.203 in the space group P2(1)2(1)2(1). Four integrase core domains and one C-terminal domain are found to be well defined in the asymmetric unit. The segment extending from residues 114 to 121 assumes the same position as seen in the integrase core domain of avian sarcoma virus as well as human immunodeficiency virus type-1 (HIV-1) crystallized in the absence of sodium cacodylate. The flexible loop in the active site, composed of residues 141-151, remains incompletely defined, but the location of the essential Glu152 residue is unambiguous. The residues from 210-218 that link the core and C-terminal domains can be traced as an extension from the core with a short gap at residues 214-215. The C(alpha) folding of the C-terminal domain is similar to the solution structure of this domain from HIV-1 integrase. However, the dimeric form seen in the NMR structure cannot exist as related by the non-crystallographic symmetry in the SIV integrase crystal. The two flexible loops of the C-terminal domain, residues 228-236 and residues 244-249, are much better fixed in the crystal structure than in the NMR structure with the former in the immediate vicinity of the flexible loop of the core domain. The interface between the two domains encompasses a solvent-exclusion area of 1500 A(2). Residues from both domains purportedly involved in DNA binding are narrowly distributed on the same face of the molecule. They include Asp64, Asp116, Glu152 and Lys159 from the core and Arg231, Leu234, Arg262, Arg263 and Lys264 from the C-terminal domain. A model for DNA binding is proposed to bridge the two domains by tethering the 228-236 loop of the C-terminal domain and the flexible loop of the core.
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Affiliation(s)
- Z Chen
- Department of Antiviral Research, Merck Research Laboratories, West Point, PA, 19486-0004, USA
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Panagariya A, Sureka RK, Sharma B, Sardana V. Neurological complications following honey bee sting. J Assoc Physicians India 1998; 46:984. [PMID: 11229239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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26
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Yan Y, Li Y, Munshi S, Sardana V, Cole JL, Sardana M, Steinkuehler C, Tomei L, De Francesco R, Kuo LC, Chen Z. Complex of NS3 protease and NS4A peptide of BK strain hepatitis C virus: a 2.2 A resolution structure in a hexagonal crystal form. Protein Sci 1998; 7:837-47. [PMID: 9568891 PMCID: PMC2143993 DOI: 10.1002/pro.5560070402] [Citation(s) in RCA: 216] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The crystal structure of the NS3 protease of the hepatitis C virus (BK strain) has been determined in the space group P6(3)22 to a resolution of 2.2 A. This protease is bound with a 14-mer peptide representing the central region of the NS4A protein. There are two molecules of the NS3(1-180)-NS4A(21'-34') complex per asymmetric unit. Each displays a familiar chymotrypsin-like fold that includes two beta-barrel domains and four short alpha-helices. The catalytic triad (Ser-139, His-57, and Asp-81) is located in the crevice between the beta-barrel domains. The NS4A peptide forms an almost completely enclosed peptide surface association with the protease. In contrast to the reported H strain complex of NS3 protease-NS4A peptide in a trigonal crystal form (Kim JL et al., 1996, Cell 87:343-355), the N-terminus of the NS3 protease is well-ordered in both molecules in the asymmetric unit of our hexagonal crystal form. The folding of the N-terminal region of the NS3 protease is due to the formation of a three-helix bundle as a result of crystal packing. When compared with the unbound structure (Love RA et al., 1996, Cell 87:331-342), the binding of the NS4A peptide leads to the ordering of the N-terminal 28 residues of the NS3 protease into a beta-strand and an alpha-helix and also causes local rearrangements important for a catalytically favorable conformation at the active site. Our analysis provides experimental support for the proposal that binding of an NS4A-mimicking peptide, which increases catalytic rates, is necessary but not sufficient for formation of a well-ordered, compact and, hence, highly active protease molecule.
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Affiliation(s)
- Y Yan
- Department of Antiviral Research, Merck Research Laboratories, West Point, Pennsylvania 19486, USA
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27
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Abstract
A 55-year-old woman with a history of bipolar affective disorder developed hyperpyrexia, rigidity and depressed consciousness (neuroleptic malignant syndrome) after commencing neuroleptic therapy. On regaining consciousness, she was mute and had signs suggesting pancerebellar involvement. Hyperpyrexia, which is a cardinal feature of neuroleptic malignant syndrome, may have caused cerebellar damage. Neuroleptic malignant syndrome needs both early recognition and prompt treatment to obviate devastating complications.
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Affiliation(s)
- V Lal
- Department of Neurology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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28
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Sardana V, Sardana M. Purification of viral polymerases: general considerations. Methods Enzymol 1996; 275:3-16. [PMID: 9026645 PMCID: PMC7133202 DOI: 10.1016/s0076-6879(96)75003-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- V Sardana
- Department of Antiviral Research, Merck Research Laboratories, West Point, Pennsylvania 19486, USA
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29
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Breslow E, Sardana V, Deeb R, Barbar E, Peyton DH. NMR behavior of the aromatic protons of bovine neurophysin-I and its peptide complexes: implications for solution structure and for function. Biochemistry 1995; 34:2137-47. [PMID: 7857924 DOI: 10.1021/bi00007a006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The NMR behavior of the aromatic protons of bovine neurophysin-I and its complexes was interpreted with reference to the 2.8 A crystal structure of the dipeptide complex of bovine neurophysin-II and to mechanisms underlying the thermodynamic linkage between neurophysin dimerization and peptide binding. Large binding-induced shifts in the ring proton signals of Tyr-2 of ligand peptides (approximately 0.5 ppm upfield and approximately 0.35 ppm downfield at 25 degrees C for the 3,5- and 2,6-ring protons, respectively) were demonstrated. Consistent with the crystal structure, and in disagreement with conclusions by other investigators, evidence is presented indicating the absence of dipolar contact between Tyr-2 ring protons and protein Phe ring protons. The large binding-induced shifts are attributed to a strong influence of proximal neurophysin carbonyl and disulfide groups on the bound Tyr-2 ring, of potential importance in binding specificity. Resolution of the behavior of neurophysin Phe residues -22 and -35 and of their proton NOE contacts provided insights into the conformational changes associated with peptide binding and with dimerization. Within the amino domain of the protein, as evidenced by the behavior of interface residue Phe-35 and its NOE contacts, binding-induced changes in the subunit interface appeared to involve principally the junction between this interface region and the 3,10-helix that connects it to the binding site in the liganded state. By contrast, as judged by the NOE contacts of His-80, the corresponding interface participant of the carboxyl domain, peptide binding induced a marked decrease in side-chain mobility within the carboxyl domain segment of the interface. Interactions of Phe-22 with protons assigned to Ala-68, neither of which is an interface participant, were demonstrated to be markedly altered both by dimerization in the unliganded state and by peptide binding to the dimer. Since Phe-22 is adjacent to the peptide-binding site, the results collectively support a model in which conformational differences between unliganded monomer and dimer are important contributors to the preferential binding of peptide to the dimer and indicate that the amino and carboxyl domain segments of the interface, which are homologous, are affected differently by peptide binding.
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Affiliation(s)
- E Breslow
- Department of Biochemistry, Cornell University Medical College, New York, New York 10021
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30
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Padma MV, Sardana V, Behari M, Ahuja GK. Antiphospholipid syndrome--a case report. J Assoc Physicians India 1994; 42:826-7. [PMID: 7876057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- M V Padma
- Department of Neurology, All India Institute of Medicine Sciences, New Delhi
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31
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Sardana V, Saxena R, Choudhary VP. Pseudotumour and factor X deficiency--a rare presentation. J Assoc Physicians India 1994; 42:822-3. [PMID: 7876055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- V Sardana
- Dept. of Haematology, AIIMS, New Delhi
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Tsarbopoulos A, Pramanik BN, Labdon JE, Reichert P, Gitlin G, Patel S, Sardana V, Nagabhushan TL, Trotta PP. Isolation and characterization of a resistant core peptide of recombinant human granulocyte-macrophage colony-stimulating factor (GM-CSF); confirmation of the GM-CSF amino acid sequence by mass spectrometry. Protein Sci 1993; 2:1948-58. [PMID: 8268804 PMCID: PMC2142278 DOI: 10.1002/pro.5560021116] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A trypsin-resistant core peptide of recombinant human granulocyte-macrophage colony-stimulating factor (rhGM-CSF) was isolated and analyzed by high-energy Cs+ liquid secondary-ion (LSI) mass spectrometric analysis. This analysis provided successful detection of the high-mass disulfide-linked core peptide as well as information confirming the existence of disulfide pairing. Similarly, LSI mass spectrometric analysis of the peptide fragments isolated chromatographically from a Staphylococcus aureus V8 protease digest of rhGM-CSF provided rapid confirmation of the cDNA-derived sequence and determination of the existing disulfide bonds between cysteine residues 54-96 and 88-121. Electrospray ionization mass spectrometry was employed to measure the molecular weight of the intact protein and to determine the number of the disulfide bonds in the protein molecule by comparative analysis of the protein before and after reduction with beta-mercaptoethanol.
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Affiliation(s)
- A Tsarbopoulos
- Shering-Plough Research Institute, Kenilworth, New Jersey 07033
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33
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Sardana M, Sardana V, Rodkey J, Wood T, Ng A, Vlasuk GP, Waxman L. Determination of disulfide bond pairs and stability in recombinant tick anticoagulant peptide. J Biol Chem 1991; 266:13560-3. [PMID: 1856193] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Tick anticoagulant peptide (TAP) is a potent and selective inhibitor of blood coagulation factor Xa (Waxman, L., Smith, D.E., Arcuri, K.E., and Vlasuk, G.P. (1990) Science 248, 593-596). The 60-amino acid sequence of TAP shows limited homology to Kunitz-type inhibitors, including cysteines at positions 5, 15, 33, 39, 55, and 59. For detailed biochemical and pharmacological studies, a recombinant version of TAP (rTAP) has been produced in yeast. To determine the arrangement of the disulfide bonds, rTAP was cleaved with trypsin and chymotrypsin and the purified peptides sequenced using a gas-phase sequenator. The positions of the disulfide bonds were assigned by identifying the cycle(s) at which di-phenylthiohydan-toin-cystine was released. The specific disulfide bridges, Cys-5 to Cys-59, Cys-15 to Cys-39, and Cys-33 to Cys-55, are analogous to those in the prototype Kunitz-type inhibitor, bovine pancreatic trypsin inhibitor (BPTI). While treatment of BPTI with dithiothreitol rapidly and specifically reduced one disulfide bond, the reduction of disulfide bonds in rTAP proceeded at a slower rate and appeared to be nonspecific, reaching a maximum of two disulfides reduced. Reduced rTAP derivatized with either iodoacetic acid or iodoacetamide lost 59% of its inhibitory activity. In contrast, BPTI alkylated with iodoacetic acid inhibited trypsin half as well as the iodoacetamide derivative. Although the arrangement of disulfides in the two inhibitors is the same, their susceptibility to reduction is markedly different.
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Affiliation(s)
- M Sardana
- Department of Biological Chemistry, Merck Sharp and Dohme Research Laboratories, West Point, Pennsylvania 19486
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Peyton D, Sardana V, Breslow E. Application of peptide-mediated ring current shifts to the study of neurophysin-peptide interactions: a partial model of the neurophysin-peptide complex. Biochemistry 1987; 26:1518-25. [PMID: 3593676 DOI: 10.1021/bi00380a004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Perdeuteriated peptides were synthesized that are capable of binding to the hormone binding site of neurophysin but that differ in the position of aromatic residues. The binding of these peptides to bovine neurophysin I and its des-1-8 derivative was studied by proton nuclear magnetic resonance spectroscopy in order to identify protein residues near the binding site through the observation of differential ring current effects on assignable protein resonances. Phenylalanine in position 3 of bound peptides was shown to induce significant ring current shifts in several resonances assignable to the 1-8 sequence, including those of Leu-3 and/or Leu-5, but was without effect on Tyr-49 ring protons. The magnitude of these shifts was dependent on the identity of peptide residue 1. By contrast, the sole demonstrable direct effect of an aromatic residue in position 1 was a downfield shift in Tyr-49 ring protons. Study of peptide binding to des-1-8-neurophysin demonstrated similar conformations of native and des-1-8 complexes except for the environment of Tyr-49, confirmed the peptide-induced ring current shift assignments in native neurophysin, and indicated an effect of binding on Thr-9. These observations are integrated with other results to provide a partial model of neurophysin-peptide complexes that places the ring of Tyr-49 at a distance 5-10 A from residue 1 of bound peptide and that places both the 1-8 sequence and the protein backbone region containing Tyr-49 proximal to each other and to peptide residue 3.(ABSTRACT TRUNCATED AT 250 WORDS)
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35
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Abstract
Photoaffinity labeling of the single neurophysin tyrosine, Tyr-49, with Met-Tyr-azido-Phe amide has been reported to inhibit both neurophysin self-association and peptide binding. Accordingly, we investigated the functional consequences of modification, principally by tetranitromethane, of Tyr-49. Tetranitromethane-mediated tyrosine-tyrosine cross-linking permitted synthesis of covalent neurophysin "dimers" and of peptide-protein conjugates, the latter potentially analogous to the photoaffinity-labeled product. The self-association and binding properties of the covalent dimers were found to be similar or enhanced relative to those of the native protein. In contrast to the photoaffinity-labeled product, covalent conjugates of Tyr-49 with the ligand peptides Met-Phe-Tyr amide, Phe-Tyr amide, and Tyr-Phe amide also generally exhibited normal or increased binding affinity for exogenous peptide; a subfraction of the Phe-Tyr amide adducts showed evidence of reduced affinity. Diiodination of Tyr-49 had no significant effect on binding. However, among the products of tetranitromethane treatment in the absence of peptide was a novel inactive non-cross-linked product, representing modification only of Tyr-49 but containing no demonstrable nitrophenol. As evidenced by circular dichroism and nuclear magnetic resonance (NMR), this product was not significantly unfolded and retained the ability to self-associate. These latter results provide the strongest evidence thus far of a role for Tyr-49 in peptide-hormone binding. The disparate effects of different Tyr-49 modifications are collectively interpreted and reconciled with NMR data and the properties of the photoaffinity-labeled protein to suggest potential mechanisms of Tyr-49 participation in binding and the probable orientation of Tyr-49 relative to peptide residue 3 in neurophysin complexes.
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Peyton D, Sardana V, Breslow E. Dimerization of native and proteolytically modified neurophysins as monitored by proton magnetic resonance spectroscopy: proximity of tyrosine-49 to the subunit interface. Biochemistry 1986; 25:6579-86. [PMID: 3790544 DOI: 10.1021/bi00369a036] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Neurophysin is a self-associating protein in which peptide-hormone binding and dimerization are thermodynamically linked. The structural basis of the linkage is unknown. We have studied the dimerization of bovine neurophysin I and two proteolytically modified derivatives by proton nuclear magnetic resonance spectroscopy in order to identify residues at the intersubunit contact regions and to evaluate the origin of the reported loss of dimerization associated with tryptic excision of residues 1-8. The concentration dependence at neural pH of the spectra of native neurophysin and des-90-92-neurophysin demonstrated a finite set of dimerization-sensitive resonances that included the ring protons of Tyr-49. Using these to monitor dimerization, we confirmed predictions of a large increase in the dimerization constant associated with carboxyl protonation. By the same criteria, dimerization of the des-1-8 protein, in disagreement with earlier reports, was found to be undiminished relative to that of the native protein. However, spectral changes in the Tyr-49 ring ortho proton region associated with dimerization of the des-1-8 protein differed significantly from those in the native protein and indicated an altered conformation of the des-1-8 dimer apparently restricted to the vicinity of Tyr-49. The results are shown to place Tyr-49 adjacent to both the intersubunit contact region and the 1-8 sequence in the native protein, loss of stabilizing interactions with 1-8 leading to altered interactions of Tyr-49 with the subunit interface. Because Tyr-49 is also close to the peptide-binding site, this arrangement spatially links the peptide-binding and dimerization sites of neurophysin.(ABSTRACT TRUNCATED AT 250 WORDS)
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Sardana V, Breslow E. Proton magnetic resonance and binding studies of proteolytically modified neurophysins. J Biol Chem 1984; 259:3669-79. [PMID: 6706974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The proton NMR spectra and role in peptide binding of carboxyl-terminal and NH2-terminal neurophysin residues were studied by preparation of bovine neurophysin-I derivatives from which residues 90-92 had been cleaved by carboxypeptidase or residues 1-8 excised by trypsin. The carboxypeptidase-treated protein showed normal peptide-binding behavior. NMR comparisons of this derivative and the native protein allowed identification of proton resonances associated with residues 89-92, confirmed a lack of functional role for this region of the protein, and permitted new observations on the behavior of neurophysin's aromatic residues. The trypsin-treated protein bound peptide with an affinity only 1/50 that of the native protein at pH 6 but evinced the same binding specificity and pH dependence of binding as the native protein. These results argued against direct interaction of residues in the 1-8 sequence with bound peptide and for a role for these residues, particularly Arg-8, in conformational stabilization of the active site; this role is held to be additional to the reported influence of 1-8 on dimerization. NMR comparisons of the trypsin product and native protein allowed preliminary assignment of a set of alkyl proton resonances to residues within the 1-8 sequence and were compatible with a restricted environment for Arg-8. Conformational differences between native and trypsin-treated proteins were manifest particularly by differences in the NMR spectra of Phe and Tyr-49 ring protons. The behavior of Phe ring protons was consistent with the reported decreased dimerization constant of the trypsin product and suggested participation of Phe-22 or -35 in dimerization. The behavior of Tyr-49 provided the first direct evidence of a change in secondary or tertiary structure associated with excision of residues 1-8. Suggested mechanisms by which this conformational change reduces binding include a direct effect on Tyr-49 and/or a conformational rearrangement of active site residues near Tyr-49.
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