Showing papers by "Banaras Hindu University published in 2021"

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

Abstract: In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

The journal coverage of Web of Science, Scopus and Dimensions: A comparative analysis

Abstract: Traditionally, Web of Science and Scopus have been the two most widely used databases for bibliometric analyses. However, during the last few years some new scholarly databases, such as Dimensions, have come up. Several previous studies have compared different databases, either through a direct comparison of article coverage or by comparing the citations across the databases. This article aims to present a comparative analysis of the journal coverage of the three databases (Web of Science, Scopus and Dimensions), with the objective to describe, understand and visualize the differences in them. The most recent master journal lists of the three databases is used for analysis. The results indicate that the databases have significantly different journal coverage, with the Web of Science being most selective and Dimensions being the most exhaustive. About 99.11% and 96.61% of the journals indexed in Web of Science are also indexed in Scopus and Dimensions, respectively. Scopus has 96.42% of its indexed journals also covered by Dimensions. Dimensions database has the most exhaustive journal coverage, with 82.22% more journals than Web of Science and 48.17% more journals than Scopus. This article also analysed the research outputs for 20 selected countries for the 2010–2018 period, as indexed in the three databases, and identified database-induced variations in research output volume, rank, global share and subject area composition for different countries. It is found that there are clearly visible variations in the research output from different countries in the three databases, along with differential coverage of different subject areas by the three databases. The analytical study provides an informative and practically useful picture of the journal coverage of Web of Science, Scopus and Dimensions databases.

Stigma and Discrimination During COVID-19 Pandemic.

Abstract: The COVID-19 pandemic has been instrumental in creating a dramatic shift from people's need to live in mutual association toward a desire to stigmatize distinctive others. Pandemic seems to be causing othering. Stated simply, stigmatization is a social process set to exclude those who are perceived to be a potential source of disease and may pose threat to the effective social living in the society. Based on the secondary evidence collected from news published online or in print, the present article delves into stigma associated with the COVID-19 pandemic among different social groups in the Indian society and the mounting cases of prejudice based on race, class, and religion. It also presents insights into the varied manifestations, and the deleterious consequences of COVID-19 inspired othering brought to its potential targets in India.

Cu(I)-Catalyzed Click Chemistry in Glycoscience and Their Diverse Applications.

Abstract: Copper(I)-catalyzed 1,3-dipolar cycloaddition between organic azides and terminal alkynes, commonly known as CuAAC or click chemistry, has been identified as one of the most successful, versatile, reliable, and modular strategies for the rapid and regioselective construction of 1,4-disubstituted 1,2,3-triazoles as diversely functionalized molecules. Carbohydrates, an integral part of living cells, have several fascinating features, including their structural diversity, biocompatibility, bioavailability, hydrophilicity, and superior ADME properties with minimal toxicity, which support increased demand to explore them as versatile scaffolds for easy access to diverse glycohybrids and well-defined glycoconjugates for complete chemical, biochemical, and pharmacological investigations. This review highlights the successful development of CuAAC or click chemistry in emerging areas of glycoscience, including the synthesis of triazole appended carbohydrate-containing molecular architectures (mainly glycohybrids, glycoconjugates, glycopolymers, glycopeptides, glycoproteins, glycolipids, glycoclusters, and glycodendrimers through regioselective triazole forming modular and bio-orthogonal coupling protocols). It discusses the widespread applications of these glycoproducts as enzyme inhibitors in drug discovery and development, sensing, gelation, chelation, glycosylation, and catalysis. This review also covers the impact of click chemistry and provides future perspectives on its role in various emerging disciplines of science and technology.

Evidence for the plant recruitment of beneficial microbes to suppress soil-borne pathogens.

Abstract: An emerging experimental framework suggests that plants under biotic stress may actively seek help from soil microbes, but empirical evidence underlying such a 'cry for help' strategy is limited. We used integrated microbial community profiling, pathogen and plant transcriptive gene quantification and culture-based methods to systematically investigate a three-way interaction between the wheat plant, wheat-associated microbiomes and Fusarium pseudograminearum (Fp). A clear enrichment of a dominant bacterium, Stenotrophomonas rhizophila (SR80), was observed in both the rhizosphere and root endosphere of Fp-infected wheat. SR80 reached 3.7 × 107 cells g-1 in the rhizosphere and accounted for up to 11.4% of the microbes in the root endosphere. Its abundance had a positive linear correlation with the pathogen load at base stems and expression of multiple defence genes in top leaves. Upon re-introduction in soils, SR80 enhanced plant growth, both the below-ground and above-ground, and induced strong disease resistance by boosting plant defence in the above-ground plant parts, but only when the pathogen was present. Together, the bacterium SR80 seems to have acted as an early warning system for plant defence. This work provides novel evidence for the potential protection of plants against pathogens by an enriched beneficial microbe via modulation of the plant immune system.

Prospects for beyond the Standard Model physics searches at the Deep Underground Neutrino Experiment: DUNE Collaboration.

Abstract: The Deep Underground Neutrino Experiment (DUNE) will be a powerful tool for a variety of physics topics. The high-intensity proton beams provide a large neutrino flux, sampled by a near detector system consisting of a combination of capable precision detectors, and by the massive far detector system located deep underground. This configuration sets up DUNE as a machine for discovery, as it enables opportunities not only to perform precision neutrino measurements that may uncover deviations from the present three-flavor mixing paradigm, but also to discover new particles and unveil new interactions and symmetries beyond those predicted in the Standard Model (SM). Of the many potential beyond the Standard Model (BSM) topics DUNE will probe, this paper presents a selection of studies quantifying DUNE’s sensitivities to sterile neutrino mixing, heavy neutral leptons, non-standard interactions, CPT symmetry violation, Lorentz invariance violation, neutrino trident production, dark matter from both beam induced and cosmogenic sources, baryon number violation, and other new physics topics that complement those at high-energy colliders and significantly extend the present reach.

Coping with the Challenges of Abiotic Stress in Plants: New Dimensions in the Field Application of Nanoparticles.

Abstract: Abiotic stress in plants is a crucial issue worldwide, especially heavy-metal contaminants, salinity, and drought. These stresses may raise a lot of issues such as the generation of reactive oxygen species, membrane damage, loss of photosynthetic efficiency, etc. that could alter crop growth and developments by affecting biochemical, physiological, and molecular processes, causing a significant loss in productivity. To overcome the impact of these abiotic stressors, many strategies could be considered to support plant growth including the use of nanoparticles (NPs). However, the majority of studies have focused on understanding the toxicity of NPs on aquatic flora and fauna, and relatively less attention has been paid to the topic of the beneficial role of NPs in plants stress response, growth, and development. More scientific attention is required to understand the behavior of NPs on crops under these stress conditions. Therefore, the present work aims to comprehensively review the beneficial roles of NPs in plants under different abiotic stresses, especially heavy metals, salinity, and drought. This review provides deep insights about mechanisms of abiotic stress alleviation in plants under NP application.

Groundwater quality assessment using water quality index (WQI) under GIS framework

Abstract: Groundwater is an important source for drinking water supply in hard rock terrain of Bundelkhand massif particularly in District Mahoba, Uttar Pradesh, India. An attempt has been made in this work to understand the suitability of groundwater for human consumption. The parameters like pH, electrical conductivity, total dissolved solids, alkalinity, total hardness, calcium, magnesium, sodium, potassium, bicarbonate, sulfate, chloride, fluoride, nitrate, copper, manganese, silver, zinc, iron and nickel were analysed to estimate the groundwater quality. The water quality index (WQI) has been applied to categorize the water quality viz: excellent, good, poor, etc. which is quite useful to infer the quality of water to the people and policy makers in the concerned area. The WQI in the study area ranges from 4.75 to 115.93. The overall WQI in the study area indicates that the groundwater is safe and potable except few localized pockets in Charkhari and Jaitpur Blocks. The Hill-Piper Trilinear diagram reveals that the groundwater of the study area falls under Na+-Cl−, mixed Ca2+-Mg2+-Cl− and Ca2+- $${\text{HCO}}_{3}^{ - }$$ types. The granite-gneiss contains orthoclase feldspar and biotite minerals which after weathering yields bicarbonate and chloride rich groundwater. The correlation matrix has been created and analysed to observe their significant impetus on the assessment of groundwater quality. The current study suggests that the groundwater of the area under deteriorated water quality needs treatment before consumption and also to be protected from the perils of geogenic/anthropogenic contamination.

Essential Oils and Their Application in Food Safety

Abstract: Food industries are facing ry faces a great challenge due to contamination of food products with different microbes such as bacteria, fungi, viruses, parasites etc. These microbes deteriorate food items both by producing different toxins during pre and post-harvest processing. They not only deteriorate food but also contaminate them with different toxins. Mycotoxins are one of theamong most potent and well-studied toxic food contaminant of fungal origin causing severe health hazard to human health hazard. UseApplication of synthetic chemicals as food preservatives in food system pose a real scourge in the present scenario is being discouraged due to their bio-incompatibility, and non-biodegradability and environmental non-sustainability. Therefore, plant based antimicrobials including essential oils have developed cumulative interest come up as potential replacement alternative of these popular synthetic preservatives because of their ecofriendly nature and generally recognized as safe (GRAS) status. However, the practical Worldwide utilization of essential oils as plant based and efficient antimicrobial in the food industry is challenging due to their volatile nature, less solubility and high instability. The recent application of different delivery strategies viz. nanoencapsulation, active packaging and polymer based coating are effectively addressed these challenges and improve the bioefficacy as well as controlled release of essential oils. This challenge can be overcome by nanoencapsulation. Nanoencapsulation is an interesting and emerging technique that raises the physico-chemical properties, as well as slow release of essential oils for improving food safety. This article provides an detailed overview on essential oils for preservation of stored foods against bacteria, fungi and mycotoxins of antimicrobial plant based food preservatives, their along with specialized mechanismmode of action and technological advancement by using different delivery systems for their effective application in food and agricultural industries smart green preservative.in their application for food preservation.

Beneficial microbiomes for bioremediation of diverse contaminated environments for environmental sustainability: present status and future challenges

Abstract: Over the past few decades, the rapid development of agriculture and industries has resulted in contamination of the environment by diverse pollutants, including heavy metals, polychlorinated biphenyls, plastics, and various agrochemicals. Their presence in the environment is of great concern due to their toxicity and non-biodegradable nature. Their interaction with each other and coexistence in the environment greatly influence and threaten the ecological environment and human health. Furthermore, the presence of these pollutants affects the soil quality and fertility. Physicochemical techniques are used to remediate such environments, but they are less effective and demand high costs of operation. Bioremediation is an efficient, widespread, cost-effective, and eco-friendly cleanup tool. The use of microorganisms has received significant attention as an efficient biotechnological strategy to decontaminate the environment. Bioremediation through microorganisms appears to be an economically viable and efficient approach because it poses the lowest risk to the environment. This technique utilizes the metabolic potential of microorganisms to clean up contaminated environments. Many microbial genera have been known to be involved in bioremediation, including Alcaligenes, Arthrobacter, Aspergillus, Bacillus, Burkholderia, Mucor, Penicillium, Pseudomonas, Stenotrophomonas, Talaromyces, and Trichoderma. Archaea, including Natrialba and Haloferax, from extreme environments have also been reported as potent bioresources for biological remediation. Thus, utilizing microbes for managing environmental pollution is promising technology, and, in fact, the microbes provide a useful podium that can be used for an enhanced bioremediation model of diverse environmental pollutants.

The role of disinfectants and sanitizers during COVID-19 pandemic: advantages and deleterious effects on humans and the environment.

Abstract: Disinfectants and sanitizers are essential preventive agents against the coronavirus disease 2019 (COVID-19) pandemic; however, the pandemic crisis was marred by undue hype, which led to the indiscriminate use of disinfectants and sanitizers. Despite demonstrating a beneficial role in the control and prevention of COVID-19, there are crucial concerns regarding the large-scale use of disinfectants and sanitizers, including the side effects on human and animal health along with harmful impacts exerted on the environment and ecological balance. This article discusses the roles of disinfectants and sanitizers in the control and prevention of the current pandemic and highlights updated disinfection techniques against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This article provides evidence of the deleterious effects of disinfectants and sanitizers exerted on humans, animals, and the environment as well as suggests mitigation strategies to reduce these effects. Additionally, potential technologies and approaches for the reduction of these effects and the development of safe, affordable, and effective disinfectants are discussed, particularly, eco-friendly technologies using nanotechnology and nanomedicine.

Potentialities of bioinspired metal and metal oxide nanoparticles in biomedical sciences

Abstract: To date, various reports have shown that metallic gold bhasma at the nanoscale form was used as medicine as early as 2500 B.C. in India, China, and Egypt. Owing to their unique physicochemical, biological, and electronic properties, they have broad utilities in energy, environment, agriculture and more recently, the biomedical field. The biomedical domain has been used in drug delivery, imaging, diagnostics, therapeutics, and biosensing applications. In this review, we will discuss and highlight the increasing control over metal and metal oxide nanoparticle structures as smart nanomaterials utilized in the biomedical domain to advance the role of biosynthesized nanoparticles for improving human health through wide applications in the targeted drug delivery, controlled release drug delivery, wound dressing, tissue scaffolding, and medical implants. In addition, we have discussed concerns related to the role of these types of nanoparticles as an anti-viral agent by majorly highlighting the ways to combat the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic, along with their prospects.

Microstructure, pathophysiology, and potential therapeutics of COVID-19: A comprehensive review.

Abstract: There have been over seven million cases and almost 413 372 deaths globally due to the novel coronavirus (2019-nCoV) associated disease COVID-19, as of 11 June 2020. Phylogenetic analysis suggests that there is a common source for these infections. The overall sequence similarities between the spike protein of 2019-nCoV and that of SARS-CoV are known to be around 76% to 78% and 73% to 76% for the whole protein and receptor-binding domain (RBD), respectively. Thus, they have the potential to serve as the drug and/or vaccine candidate. However, the individual response against 2019-nCoV differs due to genetic variations in the human population. Understanding the variations in angiotensin-converting enzyme 2 (ACE2) and human leukocyte antigen (HLA) that may affect the severity of 2019-nCoV infection could help in identifying individuals at a higher risk from the COVID-19. A number of potential drugs/vaccines as well as antibody/cytokine-based therapeutics are in various developmental stages of preclinical/clinical trials against SARS-CoV, MERS-CoV, and 2019-nCoV with substantial cross-reactivity, and may be used against COVID-19. For diagnosis, the reverse-transcription polymerase chain reaction is the gold standard test for initial diagnosis of COVID-19. A kit based on serological tests are also recommended for investigating the spread of COVID-19 but this is challenging due to the antibodies cross-reactivity. This review comprehensively summarizes the recent reports available regarding the host-pathogen interaction, morphological and genomic structure of the virus, and the diagnostic techniques as well as the available potential therapeutics against COVID-19.

The state of the art of deep learning models in medical science and their challenges

Abstract: With time, AI technologies have matured well and resonated in various domains of applied sciences and engineering. The sub-domains of AI, machine learning (ML), deep learning (DL), and associated statistical tools are getting more attention. Therefore, various machine learning models are being created to take advantage of the data available and accomplish tasks, such as automatic prediction, classification, clustering, segmentation and anomaly detection, etc. Tasks like classification need labeled data used to train the models to achieve a reliable accuracy. This study shows the systematic review of promising research areas and applications of DL models in medical diagnosis and medical healthcare systems. The prevalent DL models, their architectures, and related pros, cons are discussed to clarify their prospects. Many deep learning networks have been useful in the field of medical image processing for prognosis and diagnosis of life-threatening ailments (e.g., breast cancer, lung cancer, and brain tumor, etc.), which stand as an error-prone and tedious task for doctors and specialists when performed manually. Medical images are processed using these DL methods to solve various tasks like prediction, segmentation, and classification with accuracy bypassing human abilities. However, the current DL models have some limitations that encourage the researchers to seek further improvement.

Impact of social media advertisements on the transmission dynamics of COVID-19 pandemic in India.

Abstract: In this paper, we propose a mathematical model to assess the impact of social media advertisements in combating the coronavirus pandemic in India. We assume that dissemination of awareness among susceptible individuals modifies public attitudes and behaviours towards this contagious disease which results in reducing the chance of contact with the coronavirus and hence decreasing the disease transmission. Moreover, the individual's behavioral response in the presence of global information campaigns accelerate the rate of hospitalization of symptomatic individuals and also encourage the asymptomatic individuals for conducting health protocols, such as self-isolation, social distancing, etc. We calibrate the proposed model with the cumulative confirmed COVID-19 cases for the Republic of India. We estimate eight epidemiologically important parameters, and also the size of basic reproduction number for India. We find that the basic reproduction number for India is greater than unity, which represents the substantial outbreak of COVID-19 in the country. Sophisticated techniques of sensitivity analysis are employed to determine the impacts of model parameters on basic reproduction number and symptomatic infected population. Our results reveal that to reduce disease burden in India, non-pharmaceutical interventions strategies should be implemented effectively to decrease basic reproduction number below unity. Continuous propagation of awareness through the internet and social media platforms should be regularly circulated by the health authorities/government officials for hospitalization of symptomatic individuals and quarantine of asymptomatic individuals to control the prevalence of disease in India.

Mapping subnational HIV mortality in six Latin American countries with incomplete vital registration systems

Abstract: Background Human immunodeficiency virus (HIV) remains a public health priority in Latin America. While the burden of HIV is historically concentrated in urban areas and high-risk groups, subnational estimates that cover multiple countries and years are missing. This paucity is partially due to incomplete vital registration (VR) systems and statistical challenges related to estimating mortality rates in areas with low numbers of HIV deaths. In this analysis, we address this gap and provide novel estimates of the HIV mortality rate and the number of HIV deaths by age group, sex, and municipality in Brazil, Colombia, Costa Rica, Ecuador, Guatemala, and Mexico. Methods We performed an ecological study using VR data ranging from 2000 to 2017, dependent on individual country data availability. We modeled HIV mortality using a Bayesian spatially explicit mixed-effects regression model that incorporates prior information on VR completeness. We calibrated our results to the Global Burden of Disease Study 2017. Results All countries displayed over a 40-fold difference in HIV mortality between municipalities with the highest and lowest age-standardized HIV mortality rate in the last year of study for men, and over a 20-fold difference for women. Despite decreases in national HIV mortality in all countries—apart from Ecuador—across the period of study, we found broad variation in relative changes in HIV mortality at the municipality level and increasing relative inequality over time in all countries. In all six countries included in this analysis, 50% or more HIV deaths were concentrated in fewer than 10% of municipalities in the latest year of study. In addition, national age patterns reflected shifts in mortality to older age groups—the median age group among decedents ranged from 30 to 45 years of age at the municipality level in Brazil, Colombia, and Mexico in 2017. Conclusions Our subnational estimates of HIV mortality revealed significant spatial variation and diverging local trends in HIV mortality over time and by age. This analysis provides a framework for incorporating data and uncertainty from incomplete VR systems and can help guide more geographically precise public health intervention to support HIV-related care and reduce HIV-related deaths.

Supernova neutrino burst detection with the Deep Underground Neutrino Experiment

Abstract: The Deep Underground Neutrino Experiment (DUNE), a 40-kton underground liquid argon time projection chamber experiment, will be sensitive to the electron-neutrino flavor component of the burst of neutrinos expected from the next Galactic core-collapse supernova. Such an observation will bring unique insight into the astrophysics of core collapse as well as into the properties of neutrinos. The general capabilities of DUNE for neutrino detection in the relevant few- to few-tens-of-MeV neutrino energy range will be described. As an example, DUNE's ability to constrain the $ u_e$ spectral parameters of the neutrino burst will be considered.

Silver Nanoparticles Synthesized Using Carica papaya Leaf Extract (AgNPs-PLE) Causes Cell Cycle Arrest and Apoptosis in Human Prostate (DU145) Cancer Cells

Abstract: Treatment of cancer has been limited by the poor efficacy and toxicity profiles of available drugs There is a growing demand to develop alternative approaches to combat cancer such as use of nano-formulation-based drugs Here, we report biosynthesis and characterization of silver nanoparticles (AgNPs) with papaya leaf extract (PLE) and its anti-cancer properties against different human cancer cells Purified nanoparticles were characterized by standard techniques, such as TEM, STM, SEM, EDS, XRD, and FTIR Furthermore, cytotoxic activity of AgNPs-PLE was carried out against different human cancer cells and non-tumorigenic human keratinocytes cells AgNPs-PLE when compared with AgNPs-citric acid or PLE showed better efficacy against cancer cells and was also relatively less toxic to normal cells Treatment of DU145 cells with AgNPs-PLE (05–50 μg/ml) for 24–48 h lowered total cell number by 24–36% (P < 005) Inhibition of cell growth was linked with arrest of cell cycle at G2/M phase at 24 h, while G1 and G2/M phase arrests at 48 h ROS production was observed at earlier time points in presence of AgNPs-PLE, suggesting its role behind apoptosis in DU145 cells Induction of apoptosis (57%) was revealed by AO/EB staining in DU145 cells along with induction of Bax, cleaved caspase-3, and cleaved PARP proteins G1-S phase cell cycle check point marker, cyclin D1 was down-regulated along with an increase in cip1/p21 and kip1/p27 tumor suppressor proteins by AgNPs-PLE These findings suggest the anti-cancer properties of AgNPs-PLE