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Authors = Vipul Kumar

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18 pages, 678 KiB  
Review
Predicting Outcome after Acute Severe Ulcerative Colitis: A Contemporary Review and Areas for Future Research
by Sudheer Kumar Vuyyuru, Olga Maria Nardone and Vipul Jairath
J. Clin. Med. 2024, 13(15), 4509; https://doi.org/10.3390/jcm13154509 - 1 Aug 2024
Cited by 4 | Viewed by 2921
Abstract
Acute Severe Ulcerative Colitis (ASUC) is a severe form of ulcerative colitis relapse which requires hospitalization and intensive medical intervention to avoid colectomy. The timely recognition of patients at risk of corticosteroid failure and the early initiation of medical rescue therapy are paramount [...] Read more.
Acute Severe Ulcerative Colitis (ASUC) is a severe form of ulcerative colitis relapse which requires hospitalization and intensive medical intervention to avoid colectomy. The timely recognition of patients at risk of corticosteroid failure and the early initiation of medical rescue therapy are paramount in the management of ASUC. The choice of medical rescue therapy is influenced by multiple factors, especially patient’s prior treatment history. This decision should involve the patient and ideally a multidisciplinary team of healthcare professionals, including gastroenterologists, radiologists, surgeons and enterostomal therapists. Although several predictive models have been developed to predict corticosteroid failure in ASUC, there is no single validated tool that is universally utilized. At present, infliximab and cyclosporine are the only agents systematically evaluated and recommended for medical rescue therapy, with recent reports of off-label utilization of tofacitinib and upadacitinib in small case series. The available evidence regarding the efficacy and safety of these oral small molecules for ASUC is insufficient to provide definitive recommendations. Early decision-making to assess the response to medical rescue therapy is essential, and the decision to pursue surgery in the case of treatment failure should not be delayed. Full article
(This article belongs to the Section Gastroenterology & Hepatopancreatobiliary Medicine)
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19 pages, 7318 KiB  
Article
Screening of the Biocontrol Efficacy of Potent Trichoderma Strains against Fusarium oxysporum f.sp. ciceri and Scelrotium rolfsii Causing Wilt and Collar Rot in Chickpea
by Ranjna Kumari, Vipul Kumar, Ananta Prasad Arukha, Muhammad Fazle Rabbee, Fuad Ameen and Bhupendra Koul
Microorganisms 2024, 12(7), 1280; https://doi.org/10.3390/microorganisms12071280 - 24 Jun 2024
Cited by 10 | Viewed by 2977
Abstract
Chickpeas contribute to half of the pulses produced in India and are an excellent source of protein, fibers, carbohydrates, minerals, and vitamins. However, the combination of the wilt and root rot diseases drastically lowers its yield. The use of antagonist microbes that restrict [...] Read more.
Chickpeas contribute to half of the pulses produced in India and are an excellent source of protein, fibers, carbohydrates, minerals, and vitamins. However, the combination of the wilt and root rot diseases drastically lowers its yield. The use of antagonist microbes that restrict the growth of other phytopathogens is an ecofriendly approach to combat the serious threats raised by the plant pathogens. Trichoderma spp. are well known as biocontrol agents, especially against soil- and seed-borne phytopathogens. In this study, 21 Trichoderma isolates that were collected from different rhizospheric soils were evaluated against two notorious soil-borne pathogens, such as Fusarium oxysproum f.sp. ciceri and Sclerotium rolfsii. The maximum percentage of inhibition against the tested pathogens was observed in Trichoderma isolate PBT13 (72.97%, 61.1%) followed by PBT3 (72.23%, 59.3%). The mycelial extension rate method, dual culture (antagonism), production of cell-wall degrading enzymes (CWDs), and antifungal metabolites (by GC-MS) were used as selection criteria for potent Trichoderma isolates. Among the 21 isolates, PBT3, PBT4, PBT9, and PBT13 exhibited high antagonistic activity, production of antifungal metabolites, and chitinase and β-1,3-glucanase activity. These four species were subjected to molecular characterization using an internal transcribed spacer (ITS 1 and ITS4). The results of molecular characterization identified the four species as T. virnes, T. asperellum, T. lixii, and T. harzianum. Moreover, significant chitinase and β-1,3-glucanase activities of all Trichoderma isolates were recorded in the growth medium. Trichoderma harzianum (isolate PBT13) was found to exhibit the highest chitinase activity in terms of zone formation (4.40 ± 0.17 cm), whereas Trichoderma virens (isolate PBT3) exhibited the highest β-1,3-glucanase activity1.511 μmole/min. A GC-MS analysis of ethyl extracts from two isolates of Trichoderma (PBT9, PBT13) revealed the presence of 28 VOCs. Overall, this study suggests that these four Trichoderma strains are promising biological control agents (BCAs) and could be developed as bio-pesticides after stringent field trials for the management of soil-borne diseases of chickpeas. Full article
(This article belongs to the Special Issue Soil Fungi in Sustainable Agriculture, 2nd Edition)
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50 pages, 14108 KiB  
Review
Recent Progress and Prospect of Metal–Organic Framework-Based Nanozymes in Biomedical Application
by Anupriya Baranwal, Shakil Ahmed Polash, Vijay Kumar Aralappanavar, Bijay Kumar Behera, Vipul Bansal and Ravi Shukla
Nanomaterials 2024, 14(3), 244; https://doi.org/10.3390/nano14030244 - 23 Jan 2024
Cited by 20 | Viewed by 4925
Abstract
A nanozyme is a nanoscale material having enzyme-like properties. It exhibits several superior properties, including low preparation cost, robust catalytic activity, and long-term storage at ambient temperatures. Moreover, high stability enables repetitive use in multiple catalytic reactions. Hence, it is considered a potential [...] Read more.
A nanozyme is a nanoscale material having enzyme-like properties. It exhibits several superior properties, including low preparation cost, robust catalytic activity, and long-term storage at ambient temperatures. Moreover, high stability enables repetitive use in multiple catalytic reactions. Hence, it is considered a potential replacement for natural enzymes. Enormous research interest in nanozymes in the past two decades has made it imperative to look for better enzyme-mimicking materials for biomedical applications. Given this, research on metal–organic frameworks (MOFs) as a potential nanozyme material has gained momentum. MOFs are advanced hybrid materials made of inorganic metal ions and organic ligands. Their distinct composition, adaptable pore size, structural diversity, and ease in the tunability of physicochemical properties enable MOFs to mimic enzyme-like activities and act as promising nanozyme candidates. This review aims to discuss recent advances in the development of MOF-based nanozymes (MOF-NZs) and highlight their applications in the field of biomedicine. Firstly, different enzyme-mimetic activities exhibited by MOFs are discussed, and insights are given into various strategies to achieve them. Modification and functionalization strategies are deliberated to obtain MOF-NZs with enhanced catalytic activity. Subsequently, applications of MOF-NZs in the biosensing and therapeutics domain are discussed. Finally, the review is concluded by giving insights into the challenges encountered with MOF-NZs and possible directions to overcome them in the future. With this review, we aim to encourage consolidated efforts across enzyme engineering, nanotechnology, materials science, and biomedicine disciplines to inspire exciting innovations in this emerging yet promising field. Full article
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11 pages, 3620 KiB  
Article
Near Real-Time Detection and Moment Tensor Inversion of the 11 May 2022, Dharchula Earthquake
by Pankaj Kumar, Vipul Silwal, Rinku Mahanta, Vipin Kumar Maurya, Kamal, Mukat Lal Sharma and Ambikapathy Ammani
GeoHazards 2023, 4(4), 515-525; https://doi.org/10.3390/geohazards4040029 - 14 Dec 2023
Cited by 3 | Viewed by 2265
Abstract
On 11 May 2022, an earthquake of Mw 5.2 occurred in the Dharchula region of Uttarakhand Himalayas, India. The Uttarakhand State Earthquake Early Warning System (UEEWS) detected and transmitted the warning within 11.61 s from the origin time, taking only 4.26 s [...] Read more.
On 11 May 2022, an earthquake of Mw 5.2 occurred in the Dharchula region of Uttarakhand Himalayas, India. The Uttarakhand State Earthquake Early Warning System (UEEWS) detected and transmitted the warning within 11.61 s from the origin time, taking only 4.26 s for processing, location, and magnitude estimation and warning dissemination. The complete analysis was performed using three seconds of waveforms. Using the initial earthquake parameters provided by the UEEWS, moment tensor inversion was performed using the broadband seismometers network installed in northern India. The moment tensor (MT) inversion was performed for the event using both the body waves and the surface waves. The first motion polarity was used along with waveform data to enhance the solution’s stability. This paper discusses the importance of real-time event detection and efforts towards real-time MT source inversion of earthquakes in the Uttarakhand Himalayas. Relocation of two past earthquakes near Dharchula is also undertaken in this study. The outcome of this study provides insights into mitigating seismic hazards, understanding earthquake source mechanisms, and enhancing knowledge of local fault structures. Full article
(This article belongs to the Special Issue Active Faulting and Seismicity)
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37 pages, 10689 KiB  
Review
Journey of Trichoderma from Pilot Scale to Mass Production: A Review
by Vipul Kumar, Bhupendra Koul, Pooja Taak, Dhananjay Yadav and Minseok Song
Agriculture 2023, 13(10), 2022; https://doi.org/10.3390/agriculture13102022 - 18 Oct 2023
Cited by 20 | Viewed by 17500
Abstract
Trichoderma spp. has the ability to inhibit fungal plant pathogens through several mechanisms like the production of hydrolytic enzymes, mycoparasitism, coiling, and antibiosis and is therefore recommended as a potential and native biocontrol agent for effective control of soil-transmitted diseases. Various species of [...] Read more.
Trichoderma spp. has the ability to inhibit fungal plant pathogens through several mechanisms like the production of hydrolytic enzymes, mycoparasitism, coiling, and antibiosis and is therefore recommended as a potential and native biocontrol agent for effective control of soil-transmitted diseases. Various species of Trichoderma, like T. virens, T. asperellum, T. harzianum, etc., have been explored for their biocontrol activity against phytopathogens. There are different Trichoderma species and strains with respect to plant pathogens. Efforts have been made to develop effective and efficient methods, such as microencapsulation use of different polymers, adjuvants, or carriers, to increase the shelf-life and efficacy of Trichoderma formulations. The crucial aspects for the success of a biocontrol agent include developing and validating formulations, improvement in shelf-life, cost-effectiveness, easy accessibility, improved delivery systems, broad spectrum in action, robust performance (biocontrol), and integrative strategies for sustainable disease management. This review focuses on recent developments in the isolation, identification, preservation, substrates, consortium, quality control, mass production, delivery methods, field performance, registration, and commercialization of Trichoderma formulations for strategic development of next-generation multifunctional biological control formulations. Full article
(This article belongs to the Section Crop Protection, Diseases, Pests and Weeds)
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21 pages, 14620 KiB  
Article
Fractals as Julia and Mandelbrot Sets of Complex Cosine Functions via Fixed Point Iterations
by Anita Tomar, Vipul Kumar, Udhamvir Singh Rana and Mohammad Sajid
Symmetry 2023, 15(2), 478; https://doi.org/10.3390/sym15020478 - 10 Feb 2023
Cited by 14 | Viewed by 3488
Abstract
In this manuscript, we explore stunning fractals as Julia and Mandelbrot sets of complexvalued cosine functions by establishing the escape radii via a four-step iteration scheme extended with s-convexity. We furnish some illustrations to determine the alteration in generated graphical images and study [...] Read more.
In this manuscript, we explore stunning fractals as Julia and Mandelbrot sets of complexvalued cosine functions by establishing the escape radii via a four-step iteration scheme extended with s-convexity. We furnish some illustrations to determine the alteration in generated graphical images and study the consequences of underlying parameters on the variation of dynamics, colour, time of generation, and shape of generated fractals. The black points in the obtained fractals are the “non-chaotic” points and the dynamical behaviour in the black area is easily predictable. The coloured points are the points that “escape”, that is, they tend to infinity under one of iterative methods based on a four-step fixed-point iteration scheme extended with s-convexity. The different colours tell us how quickly a point escapes. The order of escaping of coloured points is red, orange, yellow, green, blue, and violet, that is, the red point is the fastest to escape while the violet point is the slowest to escape. Mostly, these generated fractals have symmetry. The Julia set, where we find all of the chaotic behaviour for the dynamical system, marks the boundary between these two categories of behaviour points. The Mandelbrot set, which was originally observed in 1980 by Benoit Mandelbrot and is particularly important in dynamics, is the collection of all feasible Julia sets. It perfectly sums up the Julia sets. Full article
(This article belongs to the Section Mathematics)
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21 pages, 4195 KiB  
Article
A Low-Loss Impedance Transformer-Less Fish-Tail-Shaped MS-to-WG Transition for K-/Ka-/Q-/U-Band Applications
by Atul Varshney, Vipul Sharma, Chittaranjan Nayak, Amit Kumar Goyal and Yehia Massoud
Electronics 2023, 12(3), 670; https://doi.org/10.3390/electronics12030670 - 29 Jan 2023
Cited by 22 | Viewed by 2228
Abstract
This paper presents a low-loss, high-transmission, broadside-coupled, transverse, reciprocal, two-port, and nature-inspired Ka-band transition design to move the electromagnetic energy of a rectangular waveguide (RWG) to the microstrip (MS) line. The proposed transition is simple in structure, with an excellent insertion loss, S [...] Read more.
This paper presents a low-loss, high-transmission, broadside-coupled, transverse, reciprocal, two-port, and nature-inspired Ka-band transition design to move the electromagnetic energy of a rectangular waveguide (RWG) to the microstrip (MS) line. The proposed transition is simple in structure, with an excellent insertion loss, S12/S21, (IL) near −0.40 dB and return loss, S11/S22, of <−21 dB, while the VSWR value is very close to one. Thus, this transition is an outstanding candidate for MIC/MMIC-based millimeter wave, military, and RADAR applications, as well as in wireless and satellite communications as a compatible connector. This transition also provides a bandwidth of 21.50 GHz (23.52–45.0 GHz) for the abovementioned microwave applications, at a <−10 dB return loss (RL). The proposed transition model also exhibits a −15 dB absolute bandwidth of 27.06–23.44 GHz, with an insertion loss < −0.60 dB. Due to a return loss of <−15 dB over an ultra-wide bandwidth, the proposed transition is not only a good candidate for full Ka-band (26–40 GHz) applications but also covers applications for K-band from 23.74 GHz to 26.0 GHz, Q-band applications from 33.0 to 45.0 GHz, and U-band applications from 40.0 GHz to 45 GHz, with approximately 97% power transmission between the transmission lines and only 3% power reflections. The impedance matching at the designed frequency between the RWG and MS line is achieved by flaring one end of the MS line inside the RWG in a fishtail shape, without the need for a quarter-wave/tapered/exponential/Binomial, or multi-section Chebyshev transformer. The main goal of this research was to design a multi-section impedance-transformer-free, simple, and easy-to-fabricate MS line, to share electromagnetic (EM) energy between an MS line and RWG in 30 GHz satellite applications and 30 GHz high-frequency applications, for interconnects screen printed on an organic substrate for flexible, wearable, textile conformal antennas. This work also presents an exact RLC electrical equivalence model of the MS line (fishtail) to RWG transition at 30 GHz. The novelty of this work is that the proposed transition can be used for four microwave bands of electromagnetic energy transmission, with extremely low reflection, and with a compact, simple-design MS line, and simple RWG. Full article
(This article belongs to the Section Microwave and Wireless Communications)
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14 pages, 3523 KiB  
Article
Physicochemical, Morphological, and Functional Characterization of Edible Anthocyanin-Enriched Aloevera Coatings on Fresh Figs (Ficus carica L.)
by Sawsan Ali Al-Hilifi, Rawdah Mahmood Al-Ali, Orass T. Al-Ibresam, Nishant Kumar, Saeed Paidari, Anka Trajkovska Petkoska and Vipul Agarwal
Gels 2022, 8(10), 645; https://doi.org/10.3390/gels8100645 - 11 Oct 2022
Cited by 25 | Viewed by 3802
Abstract
In the present investigation, Aloe vera gel (AVG)-based edible coatings enriched with anthocyanin were prepared. We investigated the effect of different formulations of aloe-vera-based edible coatings, such as neat AVG (T1), AVG with glycerol (T2), Aloe vera with 0.2% anthocyanin + glycerol (T3), [...] Read more.
In the present investigation, Aloe vera gel (AVG)-based edible coatings enriched with anthocyanin were prepared. We investigated the effect of different formulations of aloe-vera-based edible coatings, such as neat AVG (T1), AVG with glycerol (T2), Aloe vera with 0.2% anthocyanin + glycerol (T3), and AVG with 0.5% anthocyanin + glycerol (T4), on the postharvest quality of fig (Ficus carica L.) fruits under refrigerated conditions (4 °C) for up to 12 days of storage with 2-day examination intervals. The results of the present study revealed that the T4 treatment was the most effective for reducing the weight loss in fig fruits throughout the storage period (~4%), followed by T3, T2, and T1. The minimum weight loss after 12 days of storage (3.76%) was recorded for the T4 treatment, followed by T3 (4.34%), which was significantly higher than that of uncoated fruit (~11%). The best quality attributes, such as the total soluble solids (TSS), titratable acidity (TA), and pH, were also demonstrated by the T3 and T4 treatments. The T4 coating caused a marginal change of 0.16 in the fruit titratable acidity, compared to the change of 0.33 in the untreated fruit control after 12 days of storage at 4 °C. Similarly, the total soluble solids in the T4-coated fruits increased marginally (0.43 °Brix) compared to the uncoated control fruits (>2 °Brix) after 12 days of storage at 4 °C. The results revealed that the incorporation of anthocyanin content into AVG is a promising technology for the development of active edible coatings to extend the shelf life of fig fruits. Full article
(This article belongs to the Special Issue Bioactive Gel Films and Coatings Applied in Active Food Packaging)
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23 pages, 4205 KiB  
Article
A Low Dose Combination of Withaferin A and Caffeic Acid Phenethyl Ester Possesses Anti-Metastatic Potential In Vitro: Molecular Targets and Mechanisms
by Anissa Nofita Sari, Jaspreet Kaur Dhanjal, Ahmed Elwakeel, Vipul Kumar, Hazna Noor Meidinna, Huayue Zhang, Yoshiyuki Ishida, Keiji Terao, Durai Sundar, Sunil C. Kaul and Renu Wadhwa
Cancers 2022, 14(3), 787; https://doi.org/10.3390/cancers14030787 - 3 Feb 2022
Cited by 21 | Viewed by 5328
Abstract
Withaferin A (Wi-A) and Caffeic Acid Phenethyl Ester (CAPE) are the bioactive ingredients of Ashwagandha (Withania somnifera) and propolis, respectively. Both of these natural compounds have been shown to possess anticancer activity. In the present study, we recruited a low dose [...] Read more.
Withaferin A (Wi-A) and Caffeic Acid Phenethyl Ester (CAPE) are the bioactive ingredients of Ashwagandha (Withania somnifera) and propolis, respectively. Both of these natural compounds have been shown to possess anticancer activity. In the present study, we recruited a low dose of each of these compounds and developed a combination that exhibited remarkably potent anti-migratory and anti-angiogenic activities. Extensive molecular analyses including a cDNA array and expression analyses of the specific gene targets demonstrated that such activities are mediated through their effect on cell adhesion/tight junction proteins (Claudins, E-cadherin), inhibition of canonical Wnt/β-catenin signaling pathways and the consequent downregulation of EMT-signaling proteins (Vimentin, MMPs, VEGF and VEGFR) that play a critical role in cancer metastasis. The data supported that this novel combination of Wi-A and CAPE (Wi-ACAPE, containing 0.5 µM of Wi-A and 10 µM of CAPE) may be recruited for the treatment of metastatic and aggressive cancers and, hence, warrant further evaluation by recruiting a variety of experimental and clinical metastatic models. Full article
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15 pages, 4278 KiB  
Article
6+: A Novel Approach for Building Extraction from a Medium Resolution Multi-Spectral Satellite
by Mayank Dixit, Kuldeep Chaurasia, Vipul Kumar Mishra, Dilbag Singh and Heung-No Lee
Sustainability 2022, 14(3), 1615; https://doi.org/10.3390/su14031615 - 29 Jan 2022
Cited by 7 | Viewed by 3282
Abstract
For smart, sustainable cities and urban planning, building extraction through satellite images becomes a crucial activity. It is challenging in the medium spatial resolution. This work proposes a novel methodology named ‘6+’ for improving building extraction in 10 m medium spatial resolution multispectral [...] Read more.
For smart, sustainable cities and urban planning, building extraction through satellite images becomes a crucial activity. It is challenging in the medium spatial resolution. This work proposes a novel methodology named ‘6+’ for improving building extraction in 10 m medium spatial resolution multispectral satellite images. Data resources used are Sentinel-2A satellite images and OpenStreetMap (OSM). The proposed methodology merges the available high-resolution bands, super-resolved Short-Wave InfraRed (SWIR) bands, and an Enhanced Normalized Difference Impervious Surface Index (ENDISI) built-up index-based image to produce enhanced multispectral satellite images that contain additional information on impervious surfaces for improving building extraction results. The proposed methodology produces a novel building extraction dataset named ‘6+’. Another dataset named ‘6 band’ is also prepared for comparison by merging super-resolved bands 11 and 12 along with all the highest spatial resolution bands. The building ground truths are prepared using OSM shapefiles. The models specific for extracting buildings, i.e., BRRNet, JointNet, SegUnet, Dilated-ResUnet, and other Unet based encoder-decoder models with a backbone of various state-of-art image segmentation algorithms, are applied on both datasets. The comparative analyses of all models applied to the ‘6+’ dataset achieve a better performance in terms of F1-Score and Intersection over Union (IoU) than the ‘6 band’ dataset. Full article
(This article belongs to the Special Issue Sustainable Smart Cities and Societies Using Emerging Technologies)
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15 pages, 16345 KiB  
Article
Enhanced Network Intrusion Detection System
by Ketan Kotecha, Raghav Verma, Prahalad V. Rao, Priyanshu Prasad, Vipul Kumar Mishra, Tapas Badal, Divyansh Jain, Deepak Garg and Shakti Sharma
Sensors 2021, 21(23), 7835; https://doi.org/10.3390/s21237835 - 25 Nov 2021
Cited by 19 | Viewed by 4190
Abstract
A reasonably good network intrusion detection system generally requires a high detection rate and a low false alarm rate in order to predict anomalies more accurately. Older datasets cannot capture the schema of a set of modern attacks; therefore, modelling based on these [...] Read more.
A reasonably good network intrusion detection system generally requires a high detection rate and a low false alarm rate in order to predict anomalies more accurately. Older datasets cannot capture the schema of a set of modern attacks; therefore, modelling based on these datasets lacked sufficient generalizability. This paper operates on the UNSW-NB15 Dataset, which is currently one of the best representatives of modern attacks and suggests various models. We discuss various models and conclude our discussion with the model that performs the best using various kinds of evaluation metrics. Alongside modelling, a comprehensive data analysis on the features of the dataset itself using our understanding of correlation, variance, and similar factors for a wider picture is done for better modelling. Furthermore, hypothetical ponderings are discussed for potential network intrusion detection systems, including suggestions on prospective modelling and dataset generation as well. Full article
(This article belongs to the Special Issue Smart Mobile-Internet of Things (M-IoT))
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16 pages, 1730 KiB  
Article
Background Invariant Faster Motion Modeling for Drone Action Recognition
by Ketan Kotecha, Deepak Garg, Balmukund Mishra, Pratik Narang and Vipul Kumar Mishra
Drones 2021, 5(3), 87; https://doi.org/10.3390/drones5030087 - 31 Aug 2021
Cited by 14 | Viewed by 4113
Abstract
Visual data collected from drones has opened a new direction for surveillance applications and has recently attracted considerable attention among computer vision researchers. Due to the availability and increasing use of the drone for both public and private sectors, it is a critical [...] Read more.
Visual data collected from drones has opened a new direction for surveillance applications and has recently attracted considerable attention among computer vision researchers. Due to the availability and increasing use of the drone for both public and private sectors, it is a critical futuristic technology to solve multiple surveillance problems in remote areas. One of the fundamental challenges in recognizing crowd monitoring videos’ human action is the precise modeling of an individual’s motion feature. Most state-of-the-art methods heavily rely on optical flow for motion modeling and representation, and motion modeling through optical flow is a time-consuming process. This article underlines this issue and provides a novel architecture that eliminates the dependency on optical flow. The proposed architecture uses two sub-modules, FMFM (faster motion feature modeling) and AAR (accurate action recognition), to accurately classify the aerial surveillance action. Another critical issue in aerial surveillance is a deficiency of the dataset. Out of few datasets proposed recently, most of them have multiple humans performing different actions in the same scene, such as a crowd monitoring video, and hence not suitable for directly applying to the training of action recognition models. Given this, we have proposed a novel dataset captured from top view aerial surveillance that has a good variety in terms of actors, daytime, and environment. The proposed architecture has shown the capability to be applied in different terrain as it removes the background before using the action recognition model. The proposed architecture is validated through the experiment with varying investigation levels and achieves a remarkable performance of 0.90 validation accuracy in aerial action recognition. Full article
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12 pages, 3616 KiB  
Article
Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity
by Vipul Kumar, Jasdeep Singh, Seyed E. Hasnain and Durai Sundar
Int. J. Mol. Sci. 2021, 22(17), 9131; https://doi.org/10.3390/ijms22179131 - 24 Aug 2021
Cited by 64 | Viewed by 6414
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) outbreak in December 2019 has caused a global pandemic. The rapid mutation rate in the virus has created alarming situations worldwide and is being attributed to the false negativity in RT-PCR tests. It has also [...] Read more.
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) outbreak in December 2019 has caused a global pandemic. The rapid mutation rate in the virus has created alarming situations worldwide and is being attributed to the false negativity in RT-PCR tests. It has also increased the chances of reinfection and immune escape. Recently various lineages namely, B.1.1.7 (Alpha), B.1.617.1 (Kappa), B.1.617.2 (Delta) and B.1.617.3 have caused rapid infection around the globe. To understand the biophysical perspective, we have performed molecular dynamic simulations of four different spikes (receptor binding domain)-hACE2 complexes, namely wildtype (WT), Alpha variant (N501Y spike mutant), Kappa (L452R, E484Q) and Delta (L452R, T478K), and compared their dynamics, binding energy and molecular interactions. Our results show that mutation has caused significant increase in the binding energy between the spike and hACE2 in Alpha and Kappa variants. In the case of Kappa and Delta variants, the mutations at L452R, T478K and E484Q increased the stability and intra-chain interactions in the spike protein, which may change the interaction ability of neutralizing antibodies to these spike variants. Further, we found that the Alpha variant had increased hydrogen interaction with Lys353 of hACE2 and more binding affinity in comparison to WT. The current study provides the biophysical basis for understanding the molecular mechanism and rationale behind the increase in the transmissivity and infectivity of the mutants compared to wild-type SARS-CoV-2. Full article
(This article belongs to the Special Issue Frontiers in Protein Structure Research)
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16 pages, 2597 KiB  
Article
Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications
by Jasdeep Singh, Jasmine Samal, Vipul Kumar, Jyoti Sharma, Usha Agrawal, Nasreen Z. Ehtesham, Durai Sundar, Syed Asad Rahman, Subhash Hira and Seyed E. Hasnain
Viruses 2021, 13(3), 439; https://doi.org/10.3390/v13030439 - 9 Mar 2021
Cited by 98 | Viewed by 11186
Abstract
SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus 2) has accumulated multiple mutations during its global circulation. Recently, three SARS-CoV-2 lineages, B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1), have emerged in the United Kingdom, South Africa and Brazil, respectively. Here, we have presented global viewpoint on [...] Read more.
SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus 2) has accumulated multiple mutations during its global circulation. Recently, three SARS-CoV-2 lineages, B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1), have emerged in the United Kingdom, South Africa and Brazil, respectively. Here, we have presented global viewpoint on implications of emerging SARS-CoV-2 variants based on structural–function impact of crucial mutations occurring in its spike (S), ORF8 and nucleocapsid (N) proteins. While the N501Y mutation was observed in all three lineages, the 501Y.V1 and P.1 accumulated a different set of mutations in the S protein. The missense mutational effects were predicted through a COVID-19 dedicated resource followed by atomistic molecular dynamics simulations. Current findings indicate that some mutations in the S protein might lead to higher affinity with host receptors and resistance against antibodies, but not all are due to different antibody binding (epitope) regions. Mutations may, however, result in diagnostic tests failures and possible interference with binding of newly identified anti-viral candidates against SARS-CoV-2, likely necessitating roll out of recurring “flu-like shots” annually for tackling COVID-19. The functional relevance of these mutations has been described in terms of modulation of host tropism, antibody resistance, diagnostic sensitivity and therapeutic candidates. Besides global economic losses, post-vaccine reinfections with emerging variants can have significant clinical, therapeutic and public health impacts. Full article
(This article belongs to the Special Issue Viral Genetic Diversity)
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25 pages, 4769 KiB  
Article
Identification and Characterization of MortaparibPlus—A Novel Triazole Derivative That Targets Mortalin-p53 Interaction and Inhibits Cancer-Cell Proliferation by Wild-Type p53-Dependent and -Independent Mechanisms
by Anissa Nofita Sari, Ahmed Elwakeel, Jaspreet Kaur Dhanjal, Vipul Kumar, Durai Sundar, Sunil C. Kaul and Renu Wadhwa
Cancers 2021, 13(4), 835; https://doi.org/10.3390/cancers13040835 - 17 Feb 2021
Cited by 19 | Viewed by 5357
Abstract
p53 has an essential role in suppressing the carcinogenesis process by inducing cell cycle arrest/apoptosis/senescence. Mortalin/GRP75 is a member of the Hsp70 protein family that binds to p53 causing its sequestration in the cell cytoplasm. Hence, p53 cannot translocate to the nucleus to [...] Read more.
p53 has an essential role in suppressing the carcinogenesis process by inducing cell cycle arrest/apoptosis/senescence. Mortalin/GRP75 is a member of the Hsp70 protein family that binds to p53 causing its sequestration in the cell cytoplasm. Hence, p53 cannot translocate to the nucleus to execute its canonical tumour suppression function as a transcription factor. Abrogation of mortalin-p53 interaction and subsequent reactivation of p53’s tumour suppression function has been anticipated as a possible approach in developing a novel cancer therapeutic drug candidate. A chemical library was screened in a high-content screening system to identify potential mortalin-p53 interaction disruptors. By four rounds of visual assays for mortalin and p53, we identified a novel synthetic small-molecule triazole derivative (4-[(1E)-2-(2-phenylindol-3-yl)-1-azavinyl]-1,2,4-triazole, henceforth named MortaparibPlus). Its activities were validated using multiple bioinformatics and experimental approaches in colorectal cancer cells possessing either wild-type (HCT116) or mutant (DLD-1) p53. Bioinformatics and computational analyses predicted the ability of MortaparibPlus to competitively prevent the interaction of mortalin with p53 as it interacted with the p53 binding site of mortalin. Immunoprecipitation analyses demonstrated the abrogation of mortalin-p53 complex formation in MortaparibPlus-treated cells that showed growth arrest and apoptosis mediated by activation of p21WAF1, or BAX and PUMA signalling, respectively. Furthermore, we demonstrate that MortaparibPlus-induced cytotoxicity to cancer cells is mediated by multiple mechanisms that included the inhibition of PARP1, up-regulation of p73, and also the down-regulation of mortalin and CARF proteins that play critical roles in carcinogenesis. MortaparibPlus is a novel multimodal candidate anticancer drug that warrants further experimental and clinical attention. Full article
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