Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel evolutionary divergent RNA virus, is responsible for the present devastating COVID-19 pandemic. To explore the genomic ...signatures, we comprehensively analyzed 2,492 complete and/or near-complete genome sequences of SARS-CoV-2 strains reported from across the globe to the GISAID database up to 30 March 2020. Genome-wide annotations revealed 1,516 nucleotide-level variations at different positions throughout the entire genome of SARS-CoV-2. Moreover, nucleotide (nt) deletion analysis found twelve deletion sites throughout the genome other than previously reported deletions at coding sequence of the ORF8 (open reading frame), spike, and ORF7a proteins, specifically in polyprotein ORF1ab (n = 9), ORF10 (n = 1), and 3´-UTR (n = 2). Evidence from the systematic gene-level mutational and protein profile analyses revealed a large number of amino acid (aa) substitutions (n = 744), demonstrating the viral proteins heterogeneous. Notably, residues of receptor-binding domain (RBD) showing crucial interactions with angiotensin-converting enzyme 2 (ACE2) and cross-reacting neutralizing antibody were found to be conserved among the analyzed virus strains, except for replacement of lysine with arginine at 378th position of the cryptic epitope of a Shanghai isolate, hCoV-19/Shanghai/SH0007/2020 (EPI_ISL_416320). Furthermore, our results of the preliminary epidemiological data on SARS-CoV-2 infections revealed that frequency of aa mutations were relatively higher in the SARS-CoV-2 genome sequences of Europe (43.07%) followed by Asia (38.09%), and North America (29.64%) while case fatality rates remained higher in the European temperate countries, such as Italy, Spain, Netherlands, France, England and Belgium. Thus, the present method of genome annotation employed at this early pandemic stage could be a promising tool for monitoring and tracking the continuously evolving pandemic situation, the associated genetic variants, and their implications for the development of effective control and prophylaxis strategies.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
The emerged novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has created a global health crisis that warrants an accurate and detailed characterization of the rapidly ...evolving viral genome for understanding its epidemiology, pathogenesis, and containment. Here, we explored 61,485 sequences of the nucleocapsid (N) protein, a potent diagnostic and prophylactic target, for identifying the mutations to review their roles in real‐time polymerase chain reaction based diagnosis and observe consequent impacts. Compared to the Wuhan reference strain, a total of 1034 unique nucleotide mutations were identified in the mutant strains (49.15%, n = 30,221) globally. Of these mutations, 367 occupy primer binding sites including the 3′‐end mismatch to the primer‐pair of 11 well‐characterized primer sets. Noteworthily, CDC (USA) recommended the N2 primer set contained a lower mismatch than the other primer sets. Moreover, 684 amino acid (aa) substitutions were located across 317 (75.66% of total aa) unique positions including 82, 21, and 83 of those in the RNA binding N‐terminal domain (NTD), SR‐rich region, and C‐terminal dimerization domain, respectively. Moreover, 11 in‐frame deletions, mostly (n = 10) within the highly flexible linker region, were revealed, and the rest was within the NTD region. Furthermore, we predicted the possible consequence of high‐frequency mutations (≥20) and deletions on the tertiary structure of the N protein. Remarkably, we observed that a high frequency (67.94% of mutated sequences) co‐occuring mutations (R203K and G204R) destabilized and decreased overall structural flexibility. The N protein of SARS‐CoV‐2 comprises an average of 1.2 mutations per strain compared to 4.4 and 0.4 in Middle East respiratory syndrome‐related coronavirus and SARS‐CoV, respectively. Despite being proposed as the alternative target to spike protein for vaccine and therapeutics, the ongoing evolution of the N protein may challenge these endeavors, thus needing further immunoinformatics analyses. Therefore, continuous monitoring is required for tracing the ongoing evolution of the SARS‐CoV‐2 N protein in prophylactic and diagnostic interventions.
Highlights
Analyzing 61,485 sequences of the nucleocapsid (N) protein, 1034 unique nucleotide mutations were identified in the mutant strains (49.15%, n=30,221) globally.
Of these mutations, 367 occupy primer binding sites including the 3'‐end mismatch to the primer‐pair of 11 well‐characterized primer sets.
In total, 684 amino acid (aa) substitutions in 317 unique positions including 82, 21, and 83 in RNA binding N‐terminal domain (NTD), SR‐rich region, and C‐terminal dimerization domain (CTD), respectively were detected.
Eleven in‐frame deletions found, mostly (n = 10) within the highly flexible linker region of the SARS‐CoV‐2 N protein.
The N protein of SARS‐CoV‐2 comprises an average of 1.2 mutations per strain compared to 4.4 and 0.4 in MERS‐CoV and SARS‐CoV, respectively.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Extrusion of foods is an emerging technology for the food industries to process and market a large number of products of varying size, shape, texture, and taste. Extrusion cooking technology has led ...to production of wide variety of products like pasta, breakfast cereals, bread crumbs, biscuits, crackers, croutons, baby foods, snack foods, confectionery items, chewing gum, texturized vegetable protein (TVP), modified starch, pet foods, dried soups, dry beverage mixes etc. The functional properties of extruded foods plays an important role for their acceptability which include water absorption, water solubility, oil absorption indexes, expansion index, bulk density and viscosity of the dough. The aim of this review is to give the detailed outlines about the potential of extrusion technology in development of different types of products and the role of extrusion-operating conditions and their effect on product development resulting in quality changes i.e physical, chemical, and nutritional, experienced during the extrusion process.
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BFBNIB, GIS, IJS, KISLJ, NUK, PNG, UL, UM, UPUK
A focused library of novel bis-heterocycles encompassing 2-mercapto benzothiazole and 1,2,3-triazoles were synthesized using click chemistry approach. The synthesized compounds have been tested for ...their anti-inflammatory activity by using biochemical cyclooxygenase (COX) activity assays and carrageenan-induced hind paw edema. Among the tested compounds, compound 4d demonstrated a potent selective COX-2 inhibition with COX-2/COX-1 ratio of 0.44. Results from carrageenan-induced hind paw edema showed that compounds 4a, 4d, 4e and 4f posses significant anti-inflammatory activity as compared to the standard drug Ibuprofen. The compounds showing significant activity were further subjected to anti-nociceptive activity by writhing test. These four compounds have shown comparable activity with the standard Ibuprofen. Further ulcerogenic studies shows that none of these compounds causing gastric ulceration.
Novel bis-heterocycles encompassing 2-mercapto benzothiazole and 1,2,3-triazoles demonstrated a potent selective COX-2 inhibition and significant anti-inflammatory activity as compared to the standard drug Ibuprofen without causing any ulceration. Display omitted
► New bis-heterocycles bearing 2-mercapto benzothiazole and triazoles were synthesized. ► Some of the compounds demonstrated a potent selective COX-2 inhibition. ► Molecular docking study also confirms strong binding potential towards COX-2. ► Significant anti-inflammatory activity in vivo was observed as compared to Ibuprofen. ► Compounds 4d and 4e are showing better analgesic activity compared to Ibuprofen.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
In this paper, a method using higher order statistical moments of EEG signals calculated in the empirical mode decomposition (EMD) domain is proposed for detecting seizure and epilepsy. The ...appropriateness of these moments in distinguishing the EEG signals is investigated through an extensive analysis in the EMD domain. An artificial neural network is employed as the classifier of the EEG signals wherein these moments are used as features. The performance of the proposed method is studied using a publicly available benchmark database for various classification cases that include healthy, interictal (seizure-free interval) and ictal (seizure), healthy and seizure, nonseizure and seizure, and interictal and ictal, and compared with that of several recent methods based on time-frequency analysis and statistical moments. It is shown that the proposed method can provide, in almost all the cases, 100% accuracy, sensitivity, and specificity, especially in the case of discriminating seizure activities from the nonseizure ones for patients with epilepsy while being much faster as compared to the time-frequency analysis-based techniques.
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Antimicrobial and scar preventive wound dressings were developed by coating a blend of chitosan (CS), polyethylene glycol (PEG) and polyvinyl pyrolidone (PVP) on the cotton fabric and ...subsequent freeze drying. The miscibility of blend systems and functional group interaction were investigated by attenuated total reflectance-infra red spectroscopy. The scanning electron microscopy of the coated fabric revealed porous structure. The porosity of the material was 54–70% and the pore size was in the range of 75-120μm depending on the blend composition. The air permeability diminished as the PVP content increased. The water vapour transmission rate was in the range of 2000–3500g/m2day which may offer to be proper material for the wound dressing with moderate exudate absorption. Tetracycline hydrochloride was used as model drug within the hydrogel matrix. The cumulative release of drug was found to be ∼80% of the total loading after ∼48h. The drug loaded dressings showed good antimicrobial nature against both gram positive and gram negative bacteria. In vivo wound healing and tissue compatibility studies were carried out over a period of 21 days on full-thickness skin wounds created on male Wistar rats. Fast healing was observed in drug loaded dressing treated wounds with minimum scarring, as compared to the other groups. These results suggest that drug loaded dressing could provide scar preventive wound healing.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Eggplant or brinjal (Solanum melongena) is a popular vegetable grown throughout Asia where it is attacked by brinjal fruit and shoot borer (BFSB) (Leucinodes orbonalis). Yield losses in Bangladesh ...have been reported up to 86% and farmers rely primarily on frequent insecticide applications to reduce injury. Bangladesh has developed and released four brinjal varieties producing Cry1Ac (Bt brinjal) and is the first country to do so. We report on the first replicated field trials comparing four Bt brinjal varieties to their non-Bt isolines, with and without standard insecticide spray regimes. Results of the two-year study (2016-17) indicated Bt varieties had increased fruit production and minimal BFSB fruit infestation compared with their respective non-Bt isolines. Fruit infestation for Bt varieties varied from 0-2.27% in 2016, 0% in 2017, and was not significantly affected by the spray regime in either year. In contrast, fruit infestation in non-Bt lines reached 36.70% in 2016 and 45.51% in 2017, even with weekly spraying. An economic analysis revealed that all Bt lines had higher gross returns than their non-Bt isolines. The non-sprayed non-Bt isolines resulted in negative returns in most cases. Maximum fruit yield was obtained from sprayed plots compared to non-sprayed plots, indicating that other insects such as whiteflies, thrips and mites can reduce plant vigor and subsequent fruit weight. Statistically similar densities of non-target arthropods, including beneficial arthropods, were generally observed in both Bt and non-Bt varieties. An additional trial that focused on a single Bt variety and its isoline provided similar results on infestation levels, with and without sprays, and similarly demonstrated higher gross returns and no significant effects on non-target arthropods. Together, these studies indicate that the four Bt brinjal lines are extremely effective at controlling BFSB in Bangladesh without affecting other arthropods, and provide greater economic returns than their non-Bt isolines.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Staphylococcus aureus is responsible for large numbers of hospital-related and community-acquired infections. In this study, we investigated the presence of S. aureus and methicillin-resistant S. ...aureus (MRSA) in 100 samples from animals (55 cattle, 36 dogs, and 9 cats) and 150 samples from hospitalized human patients. The samples were collected from healthy and diseased animals and from diseased humans and included milk, wound swab, pus, exudates, nasal swab and diabetic ulcer. Initially, S. aureus was isolated and identified by colony morphology, Gram staining, and biochemical tests (catalase and coagulase tests). The S. aureus-positive samples were examined by polymerase chain reaction (PCR) to determine their MRSA status.
Of the 100 animal samples, 29 were positive for S. aureus. Four samples (13.8%) from dogs were MRSA-positive, but samples from cattle and cats were MRSA-negative. Of the 150 human samples we collected, 64 were S. aureus-positive and, of these, 34 (53.1%) were MRSA-positive. Most (28%) of the MRSA samples were isolated from surgical wound swabs, followed by the pus from skin infections (11%), exudates from diabetic ulcers (6%), exudates from burns (4%), and aural swabs (3%). By contrast, a low MRSA detection rate (n = 4) was seen in the non-human isolates, where all MRSA bacteria were isolated from nasal swabs from dogs. The antimicrobials susceptibility testing results showed that S. aureus isolates with mecA genes showed resistance to penicillin (100%), oxacillin (100%), erythromycin (73.5%), ciprofloxacin (70.6%), and gentamicin (67.7%). The lowest resistance was found against ceftazidime, and no vancomycin-resistant isolates were obtained.
We detected S. aureus and MRSA in both human and canine specimens. Isolates were found to be resistant to some of the antimicrobials available locally. MRSA carriage in humans and animals appears to be a great threat to effective antimicrobials treatment. The prudent use of antimicrobials will reduce the antimicrobial resistance. Our findings will help to find the most appropriate treatment and to reduce antimicrobial resistance in the future by implementing prudent use of antimicrobials. Further studies are required to better understand the epidemiology of MRSA human-animal inter-species transmission in Bangladesh.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Different energy sources and converters need to be integrated to meet sustained load demands while accommodating various natural conditions. This paper focuses on the integration of photovoltaic ...(PV), fuel cell (FC) and ultra-capacitor (UC) systems for sustained power generation. In the proposed system, during adequate insolation, the PV system feeds the electrolyzer to produce hydrogen for future use and transfers energy to the load side if possible. Whenever the PV system cannot completely meet load demands, the FC system provides power to meet the remaining load. If the rate of load demand increases the outside limits of FC capability, the UC bank meets the load demand above that which is provided by PV and FC systems. The main contribution of this work is the hybridization of alternate energy sources with FC systems using long and short-term storage strategies with appropriate power controllers and control strategies to build an autonomous system, with a pragmatic design and dynamic model proposed for a PV/FC/UC hybrid power generation system. The model is developed and applied in the MATLAB
®, Simulink
® and SimPowerSystems
® environment, based on the mathematical and electrical models developed for the proposed system.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
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