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The SARS-CoV-2 Omicron variant containing 15 mutations, including the unique Q493R, in the spike protein receptor binding domain (S1-RBD) is highly infectious. While comparison with previously reported mutations provide some insights, the mechanism underlying the increased infections and the impact of the reversal of the unique Q493R mutation seen in BA.4, BA.5, BA.2.75, BQ.1 and XBB lineages is not yet completely understood. Here, using structural modelling and molecular dynamics (MD) simulations, we show that the Omicron mutations increases the affinity of S1-RBD for ACE2, and a reversal of the unique Q493R mutation further increases the ACE2-S1-RBD affinity. Specifically, we performed all atom, explicit solvent MD simulations using a modelled structure of the Omicron S1-RBD-ACE2 and compared the trajectories with the WT complex revealing a substantial reduction in the Cα-atom fluctuation in the Omicron S1-RBD and increased hydrogen bond and other interactions. Residue level analysis revealed an alteration in the interaction between several residues including a switch in the interaction of ACE2 D38 from S1-RBD Y449 in the WT complex to the mutated R residue (Q493R) in Omicron complex. Importantly, simulations with Revertant (Omicron without the Q493R mutation) complex revealed further enhancement of the interaction between S1-RBD and ACE2. Thus, results presented here not only provide insights into the increased infectious potential of the Omicron variant but also a mechanistic basis for the reversal of the Q493R mutation seen in some Omicron lineages and will aid in understanding the impact of mutations in SARS-CoV-2 evolution.

Background: SARS-CoV-2 variants continue to spread throughout the world and cause waves of COVID-19 infections. It is important to find effective antiviral drugs to combat SARS-CoV-2 and its variants. The main protease (Mpro) of SARS-CoV-2 is a promising therapeutic target due to its crucial role in viral replication and its conservation in all the variants. Therefore, the aim of this work was to identify an effective inhibitor of Mpro. Methods: We studied around 200 antimicrobial peptides using in silico methods including molecular docking and allergenicity and toxicity prediction. One selected antiviral peptide was studied experimentally using a Bioluminescence Resonance Energy Transfer (BRET)-based Mpro biosensor, which reports Mpro activity through a decrease in energy transfer. Results: Molecular docking identified one natural antimicrobial peptide, Protegrin-2, with high binding affinity and stable interactions with Mpro allosteric residues. Furthermore, free energy calculations and molecular dynamics simulation illustrated a high affinity interaction between the two. We also determined the impact of the binding of Protegrin-2 to Mpro using a BRET-based assay, showing that it inhibits the proteolytic cleavage activity of Mpro. Conclusions: Our in silico and experimental studies identified Protegrin-2 as a potent inhibitor of Mpro that could be pursued further towards drug development against COVID-19 infection.

The study aimed to estimate the dietary intake of vitamin A and its major food sources among rural pregnant women from the southwest region of Bangladesh. A multi-stage random cluster sampling method was used to select the respondents (N = 1012). A semi-structured questionnaire was used to collect the data, and statistical analysis was conducted using IBM SPSS 20.0. The mean age of the respondents was 23.27 ± 5.23 years, and the majority were in their second (48%) and third trimester (49%). The mean dietary intake of vitamin A was 392 ± 566 μg Retinol Activity Equivalent (RAE)/day (51% of Recommended Dietary Allowance). The contribution of β-carotene (plant source) and retinol (animal source) in vitamin A intake was about 60% and 40%, respectively. The major β-carotene contributing food groups were vegetables (dark and light) and tubers, and food items were colocasia, potato, beans, brinjal, and ripe tomatoes. On the other hand, the major retinol-contributing food groups were fish, eggs, and milk, and food items were small fish, Rui (carp) fish, and cow’s milk. It was also observed that the consumption of food items from β-carotene and retinol-contributing food groups did not differ significantly among the three groups of respondents, but the variations in the amount of the different food items consumed were significant. Dietary vitamin A intake is low among pregnant women in the South-West region of Bangladesh. Hence, they are at a greater risk of adverse materno-fetal health outcomes associated with vitamin A deficiency.

Corneal injuries play a significant role in global visual impairment, underscoring the demand for innovative biomaterials with specific attributes such as adhesion, cohesion, and regenerative potential. In this study, we have developed a biocompatible bioadhesive for corneal reconstruction. Derived from Collagen type I, naturally present in human corneal stromal tissue, the bioadhesive was cross-linked with modified polyethylene glycol diacrylate (PEGDA-DOPA), rendering it curable through visible light exposure and exhibiting superior adhesion to biological tissues even in wet conditions. The physicochemical characteristics of the proposed bioadhesive were customized by manipulating the concentration of its precursor polymers and adjusting the duration of photocrosslinking. To identify the optimal sample with maximum adhesion, mechanical strength, and biocompatibility, characterization tests were conducted. The optimal specimen, consisting of 30 % (w/v) PEGDA-DOPA and cured with visible light for 5 min, exhibited commendable adhesive strength of 783.6 kPa and shear strength of 53.7 kPa, surpassing that of commercialized eye adhesives.Additionally, biocompatibility test results indicated a notably high survival rate (>100 %) of keratocytes seeded on the hydrogel adhesive after 7 days of incubation. Consequently, this designed bioadhesive, characterized by high adhesion strength, robust mechanical strength, and excellent biocompatibility, is anticipated to enhance the spontaneous repair process of damaged corneal stromal tissue., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Published by Elsevier B.V.)

NanoLuc (NLuc) luciferase has found extensive application in designing a range of biological assays, including gene expression analysis, protein-protein interaction, and protein conformational changes due to its enhanced brightness and small size. However, questions related to its mechanism of interaction with the substrate, furimazine, as well as bioluminescence activity remain elusive. Here, we combined molecular dynamics (MD) simulation and mutational analysis to show that the R162A mutation results in a decreased but stable bioluminescence activity of NLuc in living cells and in vitro. Specifically, we performed multiple, all-atom, explicit solvent MD simulations of the apo and furimazine-docked (holo) NLuc structures revealing differential dynamics of the protein in the absence and presence of the ligand. Further, analysis of trajectories for hydrogen bonds (H-bonds) formed between NLuc and furimazine revealed substantial H-bond interaction between R162 and Q32 residues. Mutation of the two residues in NLuc revealed a decreased but stable activity of the R162A, but not Q32A, mutant NLuc in live cell and in vitro assays performed using lysates prepared from cells expressing the proteins and with the furimazine substrate. In addition to highlighting the role of the R162 residue in NLuc activity, we believe that the mutant NLuc will find wide application in designing in vitro assays requiring extended monitoring of NLuc bioluminescence activity. SIGNIFICANCE: Bioluminescence has been extensively utilized in developing a variety of biological and biomedical assays. In this regard, engineering of brighter bioluminescent proteins, i.e. luciferases, has played a significant role. This is acutely exemplified by the engineering of the NLuc luciferase, which is small in size and displays much enhanced bioluminescence and thermal stability compared to previously available luciferases. While enhanced bioluminescent activity is desirable in a multitude of biological and biomedical assays, it would also be useful to develop variants of the protein that display a prolonged bioluminescence activity. This is specifically relevant in designing assays that require bioluminescence for extended periods, such as in the case of biosensors designed for monitoring slow enzymatic or cellular signaling reactions, without necessitating multiple rounds of luciferase substrate addition or any specialized reagents that result in increased assay costs. In the current manuscript, we report a mutant NLuc that possesses a stable and prolonged bioluminescence activity, albeit lower than the wild-type NLuc, and envisage a wider application of the mutant NLuc in designing biosensors for monitoring slower biological and biomedical events., Competing Interests: Declaration of competing interest The authors have declared no conflict of interest., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Zinc (Zn)-based alloys and composites are gaining increasing interest as promising biodegradable implant materials due to their appropriate biodegradation rates and biological functionalities. However, the inadequate mechanical strength and ductility of pure Zn have restricted its application. In this study, Zn matrix composites (ZMCs) reinforced with 0.1-0.4 wt.% graphene nanoplatelets (GNP) fabricated via powder metallurgy were investigated as potential biodegradable implant materials. The microstructures, mechanical properties, and corrosion behaviors of the GNP-reinforced ZMCs were characterized using optical microscopy, scanning electron microscopy combined with energy-dispersive X-ray spectroscopy, Raman spectroscopy, compression testing, and electrochemical and immersion testing in Hanks' balanced salt solution (HBSS). The microstructural study revealed that the GNP was uniformly dispersed in the ZMCs after ball milling and sintering at 420°C for 6 h. The microhardness, compressive yield strength, ultimate compressive strength, and compressive strain of the ZMC-0.2GNP were 69 HV, 123 MPa, 247 MPa, and 23 %, respectively, improvements of ∼ 18 %, 50%, ∼ 28%, and ∼ 15% compared to pure Zn. The corrosion rate of the ZMCs were lower than that of the pure Zn in HBSS, and the ZMC-0.2GNP composite exhibited the lowest corrosion rate of 0.09 mm/y as measured by electrochemical testing. Biocompatibility assessment indicated that the diluted extracts of pure Zn and GNP-reinforced ZMCs with concentrations of 12.5% and 6.25% exhibited no cytotoxicity after cell culturing for up to 5 days, and the diluted extracts of ZMC-0.2 GNP composite revealed more than 90% cell viability after cell culturing of 3 days, showing the satisfying cytocompatibility. STATEMENT OF SIGNIFICANCE: Biodegradable Zn is a promising candidate material for orthopedic implant applications. Nonetheless, the inadequate mechanical strength and ductility of pure Zn limited its clinical application. In this study, Zn matrix composites (ZMCs) reinforced with 0.1-0.4 wt.% graphene nanoplatelets (GNP) were developed via powder metallurgy, and the reinforcing efficacy of GNP on their mechanical properties was investigated. The addition of GNP significantly improved the compressive properties of ZMCs, with the Zn-0.2GNP composite exhibiting the best compressive properties, including 123 MPa compressive yield strength, 247 MPa ultimate compressive strength, and 22.9% compressive strain. Further, the 12.5% concentration extract of the ZMCs exhibited no cytotoxicity after cell culturing for 5 d toward SaOS2 cells., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022. Published by Elsevier Ltd.)

The user does not have any idea about the credibility of outcomes from deep neural networks (DNN) when uncertainty quantification (UQ) is not employed. However, current Deep UQ classification models capture mostly epistemic uncertainty. Therefore, this paper aims to propose an aleatory-aware Deep UQ method for classification problems. First, we train DNNs through transfer learning and collect numeric output posteriors for all training samples instead of logical outputs. Then we determine the probability of happening a certain class from K-nearest output posteriors of the same DNN in training samples. We name this probability as opacity score, as the paper focuses on the detection of opacity on X-ray images. This score reflects the level of aleatory on the sample. When the NN is certain on the classification of the sample, the probability of happening a class becomes much higher than the probabilities of others. Probabilities for different classes become close to each other for a highly uncertain classification outcome. To capture the epistemic uncertainty, we train multiple DNNs with different random initializations, model selection, and augmentations to observe the effect of these training parameters on prediction and uncertainty. To reduce execution time, we first obtain features from the pre-trained NN. Then we apply features to the ensemble of fully connected layers to get the distribution of opacity score during the test. We also train several ResNet and DenseNet DNNs to observe the effect of model selection on prediction and uncertainty. The paper also demonstrates a patient referral framework based on the proposed uncertainty quantification. The scripts of the proposed method are available at the following link: https://github.com/dipuk0506/Aleatory-aware-UQ., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Source-separating sanitation systems offer the possibility of recycling nutrients present in wastewater as crop fertilisers. Thereby, they can reduce agriculture's impacts on global sources, sinks, and cycles for nitrogen and phosphorous, as well as their associated environmental costs. However, it has been broadly assumed that people would be reluctant to perform the new sanitation behaviours that are necessary for implementing such systems in practice. Yet, few studies have tried to systematically gather evidence in support of this assumption. To address this gap, we surveyed 3763 people at 20 universities in 16 countries using a standardised questionnaire. We identified and systematically assessed cross-cultural and country-level explanatory factors that were strongly associated with people's willingness to consume food grown using human urine as fertiliser. Overall, 68% of the respondents favoured recycling human urine, 59% stated a willingness to eat urine-fertilised food, and only 11% believed that urine posed health risks that could not be mitigated by treatment. Most people did not expect to pay less for urine-fertilised food, but only 15% were willing to pay a price premium. Consumer perceptions were found to differ greatly by country and the strongest predictive factors for acceptance overall were cognitive factors (perceptions of risks and benefits) and social norms. Increasing awareness and building trust among consumers about the effectiveness of new sanitation systems via cognitive and normative messaging can help increase acceptance. Based on our findings, we believe that in many countries, acceptance by food consumers will not be the major social barrier to closing the loop on human urine. That a potential market exists for urine-fertilised food, however, needs to be communicated to other stakeholders in the sanitation service chain., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 The Author(s). Published by Elsevier B.V. All rights reserved.)

Pseudo-graphite from the University of Idaho Thermolyzed Asphalt Reaction also known as GUITAR is a new form of carbon. It shares morphological features with graphites, including basal and edge planes. Unlike graphites and other sp 2 -hybridized carbons, GUITAR has fast heterogeneous electron transfer across its basal planes and resistance to corrosion similar to boron-doped diamond electrodes. In this contribution GUITAR electrodes were examined as sensors for aqueous free chlorine (HOCl and OCl - ) at pH 7.0 with cyclic voltammetric (CV) and chronoamperometric (CA) methods. Using CV at 50 mV s -1 GUITAR has a limit of detection of 1.0 μmol L -1 , linear range of 0-5,000 μmol L -1 , sensitivity of 215.8 μA L mmol -1 cm -2 and a signal stability of 4 days in constant exposure to 1 mmol L -1 free chlorine in pH 7.0, 0.1 mol L -1 phosphate buffer system. After 7 days of exposure GUITAR electrodes lost 37% of the former sensitivity, which was recovered by an in-situ regeneration procedure. The common aqueous ions, Ca 2+ , Na + , NO 3 - , SO 4 2- , Cl - , CO 3 2- and dissolved oxygen did not affect the response of the GUITAR-based sensor. The combination of limit of detection, linear range, sensitivity, sensor lifetime and its relative lack of interferences indicate that GUITAR is one of the best performers in free chlorine sensors., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Herein we have developed an optimized analytical method for the simultaneous quantification of a fungicide, thiophanate-methyl, and its metabolite, carbendazim, in pear cultivated under open-field conditions using liquid chromatography-triple quadrupole mass spectrometry (LC-MS/MS). Due to the problem of partitioning associated with using acetonitrile and salts, methanol was used for sample extraction; the extract was then filtered using a vacuum filter, and cleaned-up using C 18 QuEChERS bulk sorbent following dispersive solid-phase extraction (d-SPE) procedure. Since a common problem, "matrix effect", associated with the matrix was observed in LC-MS/MS, calibration curves for both thiophanate-methyl and carbendazim were constructed in the matrix using seven different concentration levels. Excellent linearity was observed, with determinant coefficient (R 2 ) ≥ 0.9990. The limits of quantification (LOQs) were ≤0.02 mg/kg, satisfactory in terms of the maximum residue limits. Methods were validated at two fortification concentrations (10 × LOQ and 50 × LOQ); the experiments were repeated three times for each level and the average recoveries were 75.00-84.92%, with the coefficient of variation (CV) being ≤5.78%. The developed analytical method was applied to pear samples previously sprayed with commercial thiophanate-methyl formulation four times on different days during pre-harvest treatment. The parent compound was converted to its metabolites and the total residues degraded continuously until harvest. The data obtained in this study could help set safety guidelines for thiophanate-methyl in pear., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Objectives: Physical inactivity is an established risk factor for non-communicable diseases (NCD) and identified as the major public health concern worldwide. However, nationally representative and internationally comparable data on physical activity (PA) are lacking in Bangladesh. The objective of this paper was to determine nationally representative prevalence of PA levels among Bangladeshi adults., Study Design: Cross-sectional survey., Methods: Data, on PA for this paper, were analysed from the NCD risk factors survey 2010 in Bangladesh. A standardized approach known as STEPS (STEPSwise approach to Surveillance for NCD risk factors) was followed for this survey. A total of 9275 adults (aged ≥ 25 years) were interviewed. Data on PA were processed and analysed according to Global Physical Activity Questionnaire (GPAQ) version 2 analysis framework., Results: Of total 9275 respondents 4312 were men and 4963 women with a mean age of 42.4 (±13.5) years. Median MET-minutes of total PA in a typical week was double in rural areas (3360) than urban (1680) areas. The overall country wide prevalence of low PA was 34.5% (95% confidence interval, 33.5-35.5), urban 37.7% (36.3-39.1) and rural 31.6% (30.3-32.9). Women in general were more inactive (women, 53.6% [52.2-55.0], men 15.4% [14.9-17.1]). The main contributions to total PA were from work (urban 47.0%, rural 61.0%), and active commuting (38.0%, 30.0%) domains. Leisure-time PA represented only a small proportion (15.0%, 9.0%)., Conclusions: Insufficient physical activity is highly prevalent among the Bangladeshi adult population. Promoting overall PA at leisure-time and commuting considering country context can be feasible options with special attention to the women., (Copyright © 2016 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.)

Relative bioavailability of vitamin B-6 from tuna, whole wheat bread and peanut butter was investigated in eight men. The study was divided into a 10-day adjustment and three, 14-day experimental periods in a 3 X 3 Latin square design. Vitamin B-6 intake was set at 1.6 mg/day, with 50% of the intake coming from one of the three experimental foods and 50% from a basal diet. Daily complete urine and fecal collections were made. Urine was analyzed for 4-pyridoxic acid (4PA) and vitamin B-6, fecal samples for vitamin B-6 and plasma (sampled every 5 days) for pyridoxal 5'-phosphate (PLP). Mean values +/- SD for the adjustment, tuna, whole wheat bread and peanut butter periods were: 5.65 +/- 1.76, 4.89 +/- 1.10, 3.62 +/- 0.66 and 2.80 +/- 0.50 mumol/day for 4-pyridoxic acid; 0.98 +/- 0.34, 1.05 +/- 0.20, 0.76 +/- 0.09 and 0.68 +/- 0.19 mumol/day for urinary vitamin B-6; 2.72 +/- 0.94, 3.08 +/- 0.73, 3.80 +/- 0.78 and 4.42 +/- 1.03 mumol/day for fecal vitamin B-6 and 65.0 +/- 23.30, 64.8 +/- 29.80, 49.3 +/- 14.40 and 48.4 +/- 20.20 nM for plasma pyridoxal 5'-phosphate, respectively. 4PA and urinary vitamin B-6 excretion were significantly (P less than or equal to 0.01) higher in the tuna period than in either the whole wheat bread or peanut butter periods.(ABSTRACT TRUNCATED AT 250 WORDS)