Browsing by Author "Rahul Kumar Mishra"

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Bayes analysis of abridged age specific fertility pattern using parametric models
(Taylor and Francis Ltd., 2022) Rahul Kumar Mishra; Satyanshu K. Upadhyay
The paper provides a Bayesian alternative to transform the abridged age-specific fertility data into an unabridged one. A model suitable for a binary type of fertility data is considered for the study. The success probabilities of the considered model are assumed to vary in accordance with some established parametric age-specific fertility models. Bayes analysis is done using uniform priors for the unknown parameters of the considered models. Since the posterior analysis involves analytically intractable form of integrals, the paper employs the Gibbs sampler algorithm with intermediate Metropolis-Hastings steps to draw the corresponding posterior samples. Numerical illustration is provided using grouped age-specific fertility rate data. Finally, a few standard Bayesian model comparison tools are used in order to recommend an appropriate model for the data in hand, keeping in view the intended objectives. © 2020 Taylor & Francis Group, LLC.
Bayes and classical prediction of total fertility rate of India using autoregressive integrated moving average model
(Natural Sciences Publishing, 2018) Praveen Kumar Tripathi; Rahul Kumar Mishra; S.K. Upadhyay
The paper illustrates a simple methodology to predict total fertility rate of India through an approximate Bayes analysis using a particular case of general autoregressive integrated moving average model. The corresponding results based on classical paradigm are also obtained especially using maximum likelihood estimators. The study first examines the data for its stationarity and the same is achieved by differencing the data twice. Once the stationarity is achieved, some specific cases of general autoregressive integrated moving average model are examined for the given time series data to find the most appropriate candidate. This is being done using Akaike's information criterion and Bayes information criterion. The selected specific case of the model is analyzed both in Bayesian and classical frameworks, the former using vague prior for the parameters. The posterior computation in Bayesian paradigm is done using Markov chain Monte Carlo simulation. The two paradigms ultimately focus on drawing relevant inferences including the short term predictions, both retrospectively and prospectively. The results are, in general, found to be satisfactory. © 2018 NSP.
Correction to: Novel genetic association of the Furin gene polymorphism rs1981458 with COVID-19 severity among Indian populations (Scientific Reports, (2024), 14, 1, (7822), 10.1038/s41598-024-54607-7)
(Nature Research, 2024) Rudra Kumar Pandey; Anshika Srivastava; Rahul Kumar Mishra; Prajjval Pratap Singh; Gyaneshwer Chaubey
Correction to: Scientific Reportshttps://doi.org/10.1038/s41598-024-54607-7, published online 03 April 2024 The original version of this Article contained errors in the Material and Methods section and in the legend of Figure 3 (A, B, C). In the Material and Methods section, under the subheading ‘Insilco analysis’, “To analyse the TMPRSS2 expression in various human tissues, the GTEx portal database (http://www.gtexportal.org/home/) was used.” now reads: “To analyse the FURIN expression in various human tissues, the GTEx portal database (http://www.gtexportal.org/home/) was used.” In the legend of Figure 3, “(A) and (B) display the allele frequency distribution of rs2070788 across Indian populations in a frequency map and the corresponding COVID-19 Case Fatality Rate (CFR) as of August 30th, 2021.” now reads: “(A) and (B) display the allele frequency distribution of rs1981458 across Indian populations in a frequency map and the corresponding COVID-19 Case Fatality Rate (CFR) as of August 30th, 2021.” “The linear regression graph depicts the association between the rs1981458 allele frequency of the TMPRSS2 gene with COVID-19 CFR.” now reads: “The linear regression graph depicts the association between the rs1981458 allele frequency of the FURIN gene with COVID-19 CFR.” The original Article has been corrected. © The Author(s) 2024.
Effect of sowing dates and harvesting on fruit setting, fruit traits, seed yield and profitability of cucumber
(EM International, 2016) Ramashanker Singh; Aniruddh Pratap Singh; Rahul Kumar Mishra; Deepak Kumar Jaiswal; S.N. Singh
An experiment was conducted in completely randomized block design with three replications to determine the optimum date of sowing and best harvesting stage for getting the good seed yield of cucumber during winter season of 2007 and 2008. Sowing date of 1st March produced highest percentage of fruit set (46.05), fruits/plant (3.15), fruit length (20.35 cm), fruit diameter (7.17 cm) and fruit weight (398.45 g). Minimum percentage of fruit set and fruit weight was recorded with sowing on 30th April. However, fruits/plant, fruit length and fruit diameter was registered minimum under sowing on 15th January. Harvesting stage did not bring the significant influence on vine length, branches/vine, fruit set and fruit length of cucumber. However, fruit diameter and fruit weight was recorded maximum at harvesting stage 7 (40 DAA). The minimum fruit diameter and fruit weight was recorded with harvesting stage 1 (28 DAA). The seed yield and seed germination was also registered higher value with sowing date of 1st March. The sowing date of 30th April recorded minimum seed yield and seed germination. Harvesting stage 7 (40 DAA) recorded seed yield and seed germination. The minimum value of seed yield and seed germination was recorded with harvesting stage 1 (28 DAA). Economic analysis of data indicated that maximum net return of Rs 17059 and B:C ratio of 2.44 was recorded with sowing date 4 (1st March). However, minimum net return and B:C ratio with sowing date 1 (15th January). Harvesting stage of 7 (40 DAA) registered highest net return and B:C ratio.
Genetic Diversity and Spatiotemporal Distribution of SARS-CoV-2 Alpha Variant in India
(Multidisciplinary Digital Publishing Institute (MDPI), 2023) Jahnavi Parasar; Rudra Kumar Pandey; Yashvant Patel; Prajjval Pratap Singh; Anshika Srivastava; Rahul Kumar Mishra; Bhupendra Kumar; Niraj Rai; Vijaya Nath Mishra; Pankaj Shrivastava; P. B. Kavi Kishor; Prashanth Suravajhala; Rakesh Tamang; Ajai Kumar Pathak; Gyaneshwer Chaubey
After the spill to humans, in the evolutionary timeline of SARS-CoV-2, several positively selected variants have emerged. A phylogeographic study on these variants can reveal their spatial and temporal distribution. In December 2020, the alpha variant of the severe acute respiratory syndrome coronavirus (SARS-CoV-2), which has been designated as a variant of concern (VOC) by the WHO, was discovered in the south-eastern United Kingdom (UK). Slowly, it expanded across India, with a considerable number of cases, particularly in North India. This study focuses on determining the prevalence and expansion of the Alpha variants in various parts of India mainly by using phylospatial analysis. The genetic diversity estimation has helped us to understand various evolutionary forces that have shaped the spatial distribution of this variant during its peak. Overall, our study paves the way to understanding the evolution and expansion of a virus variant, which may help to mitigate in the case of any future wave. © 2023 by the authors.
Multiple Domestication Centers of the Indian Pig Population
(Oxford University Press, 2025) Shailesh Desai; Prajjval Pratap Singh; Rudra Kumar Pandey; Rahul Kumar Mishra; Akhilesh Kumar Chaubey; Ajit Kumar; Sachin Kumar Tiwary; Sandeep Kumar Gupta; A. Achilli; Nicola Rambaldi Migliore; G. Chaubey
The domestication of animals is a major milestone in human history and has been studied in various fields. Pig domestication, in particular, has been widely studied, and it is believed that India is one of at least six domestication centers. However, there is a lack of systematic studies using high-resolution genetic markers, including complete mitogenomes, to investigate the domestication and genetic roots of pigs in India. In the present study, we investigated the origin and evolution of Indian pigs using mitochondrial genetic data to complement archaeological data sets. The phylogenetic status of Indian pig breeds was determined by analyzing all available mitochondrial data, incorporating a global data set of 239 mitogenomes. The Bayesian and maximum likelihood tree analyses unveiled at least eight haplogroups diverging from three main branches, two of which are geographically restricted to India. We propose that the North Indian domestic haplogroup might represent an independent in situ domestication event in North India, probably dating before ∼5,000 YBP. An additional North East Indian domestic haplogroup is nested within a widespread Asian clade that also includes Indian mitogenomes from the Andaman and Nicobar Islands that diverged more recently from distinct East and Southeast Asian roots. In conclusion, we propose that North Indian farmers could have been responsible for the independent domestication of local wild boars giving rise to the current domestic lineage identified in North India. At least one additional domestic lineage arrived in India more recently and remained mainly localized in the northeast. Domestic mitogenomes from the Indian islands show a notable connection with pig populations from Vietnam, and their arrival might be related to Austroasiatic-speaking human populations. Overall, this study provides valuable insights into the complex dynamics of pig domestication in India. © The Author(s) 2025. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.
Novel genetic association of the Furin gene polymorphism rs1981458 with COVID-19 severity among Indian populations
(Nature Research, 2024) Rudra Kumar Pandey; Anshika Srivastava; Rahul Kumar Mishra; Prajjval Pratap Singh; Gyaneshwer Chaubey
SARS CoV-2, the causative agent for the ongoing COVID-19 pandemic, it enters the host cell by activating the ACE2 receptor with the help of two proteasesi.e., Furin and TMPRSS2. Therefore, variations in these genes may account for differential susceptibility and severity between populations. Previous studies have shown that the role of ACE2 and TMPRSS2 gene variants in understanding COVID-19 susceptibility among Indian populations. Nevertheless, a knowledge gap exists concerning the COVID-19 susceptibility of Furin gene variants among diverse South Asian ethnic groups. Investigating the role of Furin gene variants and their global phylogeographic structure is essential to comprehensively understanding COVID-19 susceptibility in these populations. We have used 450 samples from diverse Indian states and performed linear regression to analyse the Furin gene variant's with COVID-19 Case Fatality Rate (CFR) that could be epidemiologically associated with disease severity outcomes. Associated genetic variants were further evaluated for their expression and regulatory potential through various Insilco analyses. Additionally, we examined the Furin gene using next-generation sequencing (NGS) data from 393 diverse global samples, with a particular emphasis on South Asia, to investigate its Phylogeographic structure among diverse world populations. We found a significant positive association for the SNP rs1981458 with COVID-19 CFR (p < 0.05) among diverse Indian populations at different timelines of the first and second waves. Further, QTL and other regulatory analyses showed various significant associations for positive regulatory roles of rs1981458 and Furin gene, mainly in Immune cells and virus infection process, highlighting their role in host immunity and viral assembly and processing. The Furin protein–protein interaction suggested that COVID-19 may contribute to Pulmonary arterial hypertension via a typical inflammation mechanism. The phylogeographic architecture of the Furin gene demonstrated a closer genetic affinity of South Asia with West Eurasian populations. Therefore, it is worth proposing that for the Furin gene, the COVID-19 susceptibility of South Asians will be more similar to the West Eurasian population. Our previous studies on the ACE2 and TMPRSS2 genes showed genetic affinity of South Asian with East Eurasians and West Eurasians, respectively. Therefore, with the collective information from these three important genes (ACE2, TMPRSS2 and Furin) we modelled COVID-19 susceptibilityof South Asia in between these two major ancestries with an inclination towards West Eurasia. In conclusion, this study, for the first time, concluded the role of rs1981458 in COVID-19 severity among the Indian population and outlined its regulatory potential.This study also highlights that the genetic structure for COVID-19 susceptibilityof South Asia is distinct, however, inclined to the West Eurasian population. We believe this insight may be utilised as a genetic biomarker to identify vulnerable populations, which might be directly relevant for developing policies and allocating resources more effectively during an epidemic. © The Author(s) 2024.
Outlier maternal haplogroups N5 and X2 and their potential role in elevated tuberculosis prevalence among the Sahariya tribe
(Elsevier B.V., 2025) Debashruti Das; Prajjval Pratap Singh; Shailesh Desai; Rahul Kumar Mishra; Pankaj Shrivastava; Prashanth N. Suravajhala; Rakesh Tamang; G. Chaubey
India bears the largest burden of tuberculosis (TB) cases in the world. Prior studies have highlighted significantly higher pulmonary TB among the Sahariya tribal population in Central India. The disease susceptibility of a population to disease may be influenced by genetic ancestry. In this context, we investigated the maternal genetic ancestry of the Sahariya in relation to their neighbouring tribal populations. For this study, we used the largest available dataset (n = 729), comprising 140 Sahariya individuals and 589 individuals from adjacent caste and tribal groups (including 50 newly sequenced samples). Our detailed mtDNA analysis revealed the exclusive presence of two rare haplogroups N5 and X2 which are completely absent in neighbouring tribal and caste populations. Further examination of the phylogeographic origins of the branches of haplogroups N5 and X2 suggests that these unique founder haplogroup branches (N5a and X2a) were likely introduced into the Sahariya from the western regions of the Indian subcontinent. The temporal expansion of these haplogroups indicates a gene flow from the western area to the Sahariya population during the early Iron Age. In addition to that, we have also analysed 33 SNPs for six TB-associated genes. We observed a single SNP (rs4958847-IRGM1) where the minor allele frequency was significantly different in Sahariya with their neighbouring populations. Consequently, our analysis of maternal genetic ancestry and known associated autosomal genes provides insights that may help explain the higher prevalence of TB among the Sahariya compared to their neighbouring populations. © 2025 Elsevier B.V. and Mitochondria Research Society
Parametric Bayes Analyses to Study the Age-Specific Fertility Patterns
(Taylor and Francis Ltd., 2019) Rahul Kumar Mishra; Satyanshu K. Upadhyay
Synoptic Abstract: The article considers various parametric models proposed for studying age-specific fertility patterns and develops a Bayesian alternative for their analyses. The analysis is done using weak proper priors for the parameters. Since the posterior analysis involves analytically intractable integrals, the article uses Metropolis algorithm to draw the corresponding posterior samples and hence obtains the sample based inferences. The maximum likelihood estimates of parameters are also obtained by non-linear optimization technique. Such estimates are used as an aid to our Bayesian computation. The considered models are finally compared using different Bayesian model selection tools to recommend an appropriate model for the situation under consideration. Finally, numerical illustration is provided for two different datasets in order to check the feasibility of the models with changing fertility patterns over time. © 2018, © 2018 Taylor & Francis Group, LLC.
Reconstructing the population history of the Nicobarese
(Springer Nature, 2024) Rahul Kumar Mishra; Prajjval Pratap Singh; Niraj Rai; Shailesh Desai; Pratik Pandey; Sachin Kr. Tiwary; Rakesh Tamang; Prashanth Suravajhala; Pankaj Shrivastava; Kumarasamy Thangaraj; George van Driem; Gyaneshwer Chaubey
The Nicobarese are the major tribal groups in the Nicobar district, situated south of the Andaman group of Islands. Linguistic phylogeny suggests that the linguistic ancestors of the Nicobarese settled the Nicobar archipelago in the early Holocene. So far, genetic research on them is low-resolution and restricted to the haploid DNA markers. Therefore, in the present analysis, we have used the high-resolution biparental (1554 published and 5 newly genotyped Nicobarese individuals) and uniparental genetic markers and looked at the genetic association of Nicobarese with the South and Southeast Asian populations. We report a common ancestral component shared among the Austroasiatic of South and Southeast Asia. Our analyses have suggested that the Nicobarese peoples retain this ancestral Austroasiatic predominant component in their genomes in the highest proportion. On the Southeast Asian mainland, the Htin Mal, who speak an Austroasiatic language of the Khmuic branch, represent a population that has preserved their ethnic distinctness from other groups over time and consequently shown the highest drift with the Nicobarese. The analysis based on haplotypes indicated a significant level of genomic segment sharing across linguistic groups, indicating an ancient broader distribution of Austroasiatic populations in Southeast Asia. Based on the temporal analyses of haploid DNA, it is suggested that the forebears of the Nicobarese people may have arrived on the Nicobar Islands in the last 5000 YBP. Therefore, among the modern populations, the Nicobarese peoples and the Htin Mal language community represent good genetic proxies for ancient Austroasiatics. © The Author(s), under exclusive licence to European Society of Human Genetics 2024.
Studying C-reactive protein and D-dimer levels in blood may prevent severe complications: A study in Bangladeshi COVID-19 patients
(Frontiers Media S.A., 2022) Gazi Nurun Nahar Sultana; Anshika Srivastava; Khalida Akhtaar; Prajjval Pratap Singh; Md. Anarul Islam; Rahul Kumar Mishra; Gyaneshwer Chaubey
The ongoing COVID-19 pandemic has been a scientific, medical and social challenge. Since clinical course of this disease is largely unpredictable and can develop rapidly causing severe complications, it is important to identify laboratory biomarkers, which may help to classify patient’s severity during initial stage. Previous studies have suggested C—reactive protein (inflammatory) and D-dimer (biochemical) as an effective biomarker. The differential severity in patients across the world and our limited understanding in the progression of the disease calls for a multi-country analysis for biomarkers. Therefore, we have analyzed these biomarkers among 228 Bangladeshi COVID-19 patients. We observed significant association of COVID-19 severity with these two biomarkers. Thus, we suggest to use these biomarkers for Bangladeshi COVID-19 patients for better disease monitoring. Such validated preventive measures may decrease the case fatality ratio substantially. Copyright © 2022 Sultana, Srivastava, Akhtaar, Singh, Islam, Mishra and Chaubey.
Vaccine hesitancy for coronavirus SARS-CoV-2 in Varanasi India
(Frontiers Media S.A., 2022) Utkarsh Srivastava; Avanish Kumar Tripathi; Jagjeet Kaur; Sabita Devi; Shipra Verma; Vanya Singh; Debashruti Das; Prajjval Pratap Singh; Rahul Kumar Mishra; Nikhil A. Kumar; Vijaya Nath Mishra; Pradeep Kumar; Vandana Rai; Rakesh Tamang; Prashanth Suravajhala; Rakesh Pandey; Gyaneshwer Chaubey
With the rollout of the world's largest vaccine drive for SARS-CoV-2 by the Government of India on January 16 2021, India had targeted to vaccinate its entire population by the end of 2021. Struggling with vaccine procurement and production earlier, India overcome these hurdles, but the Indian population still did not seem to be mobilizing swiftly toward vaccination centers. The severe second wave has slowed the vaccination pace and was also one of the major contributing factors to vaccine hesitancy. To understand the nature of vaccine hesitancy and its underlying factors, we conducted extensive online and offline surveys in Varanasi and adjoining regions using structured questions. Most respondents were students (0.633). However, respondents from other occupations, such as government officials (0.10), have also participated in the study. Interestingly, most people (0.75) relied on fake news and did not take COVID-19 seriously. Most importantly, we noticed that a substantial proportion of respondents (relative frequency 0.151; mean age 24.8 years) reported that they were still not interested in vaccination. We observed a significant association between vaccine hesitancy and socioeconomic status (χ2 = 307.6, p < 0.001). However, we failed to detect any association between vaccine hesitancy and gender (χ2 = 0.007, p > 0.5). People who have neither been vaccinated nor have ever been infected may become the medium for spreading the virus and creating new variants, which may lead to the vaccine-resistant variant. We expect this extensive survey to help the Government upgrade their vaccination policies for COVID-19 in North India. Copyright © 2022 Srivastava, Tripathi, Kaur, Devi, Verma, Singh, Das, Singh, Mishra, Kumar, Mishra, Kumar, Rai, Tamang, Suravajhala, Pandey and Chaubey.