Search results for: potential spike

Authors: Der-Feng Guo

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Optoelectronic switches have attracted a considerable attention in the semiconductor research field due to their potential applications in optical computing systems and optoelectronic integrated circuits (OEICs). With high gains and high-speed operations, npn heterostructures can be used to produce promising optoelectronic switches. It is known that the bulk barrier and heterostructure-induced potential spike act important roles in the characteristics of the npn heterostructures. To investigate the effects of bulk barrier and potential spike heights on the optoelectronic switching of the npn heterostructures, GaAs/InGaP and AlGaAs/GaAs/InAlGaP npn heterostructural optoelectronic switches (HSOSs) have been fabricated in this work. It is seen that the illumination decreases the switching voltage Vs and increases the switching current Is, and thus the OFF state is under dark and ON state under illumination in the optical switching of the GaAs/InGaP HSOS characteristics. But in the AlGaAs/GaAs/InAlGaP HSOS characteristics, the Vs and Is present contrary trends, and the OFF state is under illumination and ON state under dark. The studied HSOSs show quite different switching variations with incident light, which are mainly attributed to the bulk barrier and potential spike heights affected by photogenerated carriers.

Keywords: bulk barrier, heterostructure, optoelectronic switch, potential spike

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Authors: Gyaltsen Dakpa, K. J. Senthil Kumar, Nai-Wen Tsao, Sheng-Yang Wang

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Context: Coronavirus disease 2019 (COVID-19) is a severe respiratory illness caused by the SARS-CoV-2 virus. One of the hallmarks of COVID-19 is a change in metabolism, which can lead to increased severity and mortality. The mechanism of SARS-CoV-2-mediated perturbations of metabolic pathways has yet to be fully understood. Research Aim: This study aimed to investigate the metabolic alteration caused by SARS-CoV-2 spike protein in Phorbol 12-myristate 13-acetate (PMA)-induced human monocytes (THP-1) and to examine the regulatory effect of natural compounds like Antcins A on SARS-CoV-2 spike protein-induced metabolic alteration. Methodology: The study used a combination of proton nuclear magnetic resonance (1H-NMR) and MetaboAnalyst 5.0 software. THP-1 cells were treated with SARS-CoV-2 spike protein or control, and the metabolomic profiles of the cells were compared. Antcin A was also added to the cells to assess its regulatory effect on SARS-CoV-2 spike protein-induced metabolic alteration. Findings: The study results showed that treatment with SARS-CoV-2 spike protein significantly altered the metabolomic profiles of THP-1 cells. Eight metabolites, including glycerol-phosphocholine, glycine, canadine, sarcosine, phosphoenolpyruvic acid, glutamine, glutamate, and N, N-dimethylglycine, were significantly different between control and spike-protein treatment groups. Antcin A significantly reversed the changes in these metabolites. In addition, treatment with antacid A significantly inhibited SARS-CoV-2 spike protein-mediated up-regulation of TLR-4 and ACE2 receptors. Theoretical Importance The findings of this study suggest that SARS-CoV-2 spike protein can cause significant metabolic alterations in THP-1 cells. Antcin A, a natural compound, has the potential to reverse these metabolic alterations and may be a potential candidate for developing preventive or therapeutic agents for COVID-19. Data Collection: The data for this study was collected from THP-1 cells that were treated with SARS-CoV-2 spike protein or a control. The metabolomic profiles of the cells were then compared using 1H-NMR and MetaboAnalyst 5.0 software. Analysis Procedures: The metabolomic profiles of the THP-1 cells were analyzed using 1H-NMR and MetaboAnalyst 5.0 software. The software was used to identify and quantify the cells' metabolites and compare the control and spike-protein treatment groups. Questions Addressed: The question addressed by this study was whether SARS-CoV-2 spike protein could cause metabolic alterations in THP-1 cells and whether Antcin A can reverse these alterations. Conclusion: The findings of this study suggest that SARS-CoV-2 spike protein can cause significant metabolic alterations in THP-1 cells. Antcin A, a natural compound, has the potential to reverse these metabolic alterations and may be a potential candidate for developing preventive or therapeutic agents for COVID-19.

Keywords: SARS-CoV-2-spike, ¹H-NMR, metabolomics, antcin-A, taiwanofungus camphoratus

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Authors: Shatha A. Yousif, Hatem Jasim, Ali R. Abas, Dheya P. Yousef

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To study the effect of the cross direction in bead wheat, three hybrid combinations (Babyle 113 , Iratome), (Sawa , Tamose2) and (Al Hashymya Al Iraq) were tested for plant height, number of tillers/m, number of grains per spike, weight of grains per spike, 1000-grain weight and grain yield. The results revealed that the direction of the cross had significant effect the number of grain/spike, tillers/m and grain yields. Grain yield was positively and significantly correlated with 1000-grain weight, number of grains per spike and tillers. Depend on the result of heritability and genetic advance it was suggested that 1000-grain weight number of grains per spike and tillers should be given emphasis for future wheat yield improvement programs.

Keywords: correlation, genetic advance, heritability, wheat, yield traits

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Authors: Aghasadeghi MR., Bahramali G., Sadat SM., Sadeghi SA., Yousefi M., Khodaei K., Ghorbani M., Sadat Larijani M.

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Background:The emerging COVID-19 pandemic is a serious concernfor the public health worldwide. Despite the many mutations in the virus genome, it is important to find an effective vaccine against viral mutations. Therefore, in current study, we aimed at immunoinformatic evaluation of the virus proteins immunogenicity to design a preventive vaccine candidate, which could elicit humoral and cellular immune responses as well. Methods:Three antigenic regions are included;Spike, Membrane, and Nucleocapsid amino acid sequences were obtained, and possible fusion proteins were assessed andcompared by immunogenicity, structural features, and population coverage. The best fusion protein was also evaluated for MHC-I and MHC-II T-cell epitopes and the linear and conformational B-cell epitopes. Results: Among the four predicted models, the truncated Spike protein in fusion with M and N proteins is composed of 24 highly immunogenic human MHC class I and 29 MHC class II, along with 14 B-cell linear and 61 discontinues epitopes. Also, the selected protein has high antigenicity and acceptable population coverage of 82.95% in Iran and 92.51% in Europe. Conclusion: The data indicate that the truncated Spike-M-N SARS-CoV-2form which could be potential targets of neutralizing antibodies. The protein also has the ability to stimulate humoral and cellular immunity. The in silico study provided the fusion protein as a potential preventive vaccine candidate for further in vivo evaluation.

Keywords: SARS-CoV-2, immunoinformatic, protein, vaccine

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Authors: Giselle Tran, Ralitza Parina, Phuong T. Nguyen

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Background/Aims: Pancreatic cysts (PC) have recently become an increasingly common entity, often diagnosed as incidental findings on cross-sectional imaging. Clinically, management of the lesions is difficult because of uncertainties in their potential for malignant degeneration. Prior series have reported that carcinoembryonic antigen (CEA), a biomarker collected from cyst fluid aspiration, has a high diagnostic accuracy for discriminating between mucinous and non-mucinous lesions, at the patient’s initial presentation. To the author’s best knowledge, no prior studies have reported PC CEA levels obtained from endoscopic ultrasound fine-needle aspiration (EUS-FNA) over years of serial EUS surveillance imaging. Methods: We report a consecutive retrospective series of 624 patients who underwent EUS evaluation for a PC between 11/20/2009 and 11/13/2018. Of these patients, 401 patients had CEA values obtained at the point of entry. Of these, 157 patients had two or more CEA values obtained over the course of their EUS surveillance. Of the 157 patients (96 F, 61 M; mean age 68 [range, 62-76]), the mean interval of EUS follow-up was 29.7 months [3.5-128]. The mean number of EUS procedures was 3 [2-7]. To assess CEA value fluctuations, we defined an appreciable increase in CEA as "spikes" – two-times increase in CEA on a subsequent EUS-FNA of the same cyst, with the second CEA value being greater than 1000 ng/mL. Using this definition, cysts with a spike in CEA were compared to those without a spike in a bivariate analysis to determine if a CEA spike is associated with poorer outcomes and the presence of high-risk features. Results: Of the 157 patients analyzed, 29 had a spike in CEA. Of these 29 patients, 5 had a cyst with size increase >0.5cm (p=0.93); 2 had a large cyst, >3cm (p=0.77); 1 had a cyst that developed a new solid component (p=0.03); 7 had a cyst with a solid component at any time during surveillance (p=0.08); 21 had a complex cyst (p=0.34); 4 had a cyst categorized as "Statistically Higher Risk" based on molecular analysis (p=0.11); and 0 underwent surgical resection (p=0.28). Conclusion: With serial EUS imaging in the surveillance of PC, an increase in CEA level defined as a spike did not predict poorer outcomes. Most notably, a spike in CEA did not correlate with the number of patients sent to surgery or patients with an appreciable increase in cyst size. A spike in CEA did not correlate with the development of a solid nodule within the PC nor progression on molecular analysis. Future studies should focus on the selected use of CEA analysis when patients undergo EUS surveillance evaluation for PCs.

Keywords: carcinoembryonic antigen (CEA), endoscopic ultrasound (EUS), fine-needle aspiration (FNA), pancreatic cyst, spike

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Authors: Chen Chih-Cheng, Chen I-Cheng, Lee Yung-Tan, Kuo Yen-Whea, Yu Chin-Hung

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The purpose of this study is to construct a model for best spike player selection in a top volleyball tournament of the world. Data consisted of the records of 2013 World Grand Prix declared by International Volleyball Federation (FIVB). Simple Multiple-Attribute Rating Technique (SMART) was used for optimal decision-making model on the best spike player selection. The research results showed that the best spike player ranking by SMART is different than the ranking by FIVB. The results demonstrated the effectiveness and feasibility of the proposed model.

Keywords: simple multiple-attribute rating technique, World Grand Prix, best spike player, International Volleyball Federation

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Authors: Mohamad Ammar Ayass, Natalya Griko, Victor Pashkov, Wanying Cao, Kevin Zhu, Jin Zhang, Lina Abi Mosleh

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Respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for coronavirus disease 2019 (COVID-19). Early evidence pointed at the angiotensin-converting enzyme 2 (ACE-2) expressed on the epithelial cells of the lung as the main entry point of SARS-CoV-2 into the cells. The viral entry is mediated by the binding of the Receptor Binding Domain (RBD) of the spike protein that is expressed on the surface of the virus to the ACE-2 receptor. As the number of SARS-CoV-2 variants continues to increase, mutations arising in the RBD of SARS-CoV-2 may lead to the ineffectiveness of RBD targeted neutralizing antibodies. To address this limitation, the objective of this study is to develop a combination of aptamers that target different regions of the RBD, preventing the binding of the spike protein to ACE-2 receptor and subsequent viral entry and replication. A safe and innovative biomedical tool was developed to inhibit viral infection and reduce the harms of COVID-19. In the present study, DNA aptamers were developed against a recombinant trimer S protein using the Systematic Evolution of Ligands by Exponential enrichment (SELEX). Negative selection was introduced at round number 7 to select for aptamers that bind specifically to the RBD domain. A series of 9 aptamers (ADI2010, ADI2011, ADI201L, ADI203L, ADI205L, ADIR68, ADIR74, ADIR80, ADIR83) were selected and characterized with high binding affinity and specificity to the RBD of the spike protein. Aptamers (ADI25, ADI2009, ADI203L) were able to bind and pull down endogenous spike protein expressed on the surface of SARS-CoV-2 virus in COVID-19 positive patient samples and determined by liquid chromatography- tandem mass spectrometry analysis (LC-MS/MS). LC-MS/MS data confirmed that aptamers can bind to the RBD of the spike protein. Furthermore, results indicated that the combination of the 9 best aptamers inhibited the binding of the purified trimer spike protein to the ACE-2 receptor found on the surface of Vero E6 cells. In the same experiment, the combined aptamers displayed a better neutralizing effect than antibodies. The data suggests that the selected aptamers could be used in therapy to neutralize the effect of the SARS-CoV-2 virus by inhibiting the interaction between the RBD and ACE-2 receptor, preventing viral entry into target cells and therefore blocking viral replication.

Keywords: aptamer, ACE-2 receptor, binding inhibitor, COVID-19, spike protein, SARS-CoV-2, treatment

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Authors: Mohammad Hossein Modarressi, Mozhgan Mondeali, Khabat Barkhordari, Ali Etemadi

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The COVID-19 pandemic, caused by SARS-CoV-2, has led to significant concerns worldwide due to its catastrophic effects on public health. The SARS-CoV-2 infection is initiated with the binding of the receptor-binding domain (RBD) in its spike protein to the ACE2 receptor in the host cell membrane. Due to the error-prone entity of the viral RNA-dependent polymerase complex, the virus genome, including the coding region for the RBD, acquires new mutations, leading to the appearance of multiple variants. These variants can potentially impact transmission, virulence, antigenicity and evasive immune properties. S477N mutation located in the RBD has been observed in the SARS-CoV-2 omicron (B.1.1. 529) variant. In this study, we investigated the consequences of S477N mutation at the molecular level using computational approaches such as molecular dynamics simulation, protein-protein interaction analysis, immunoinformatics and free energy computation. We showed that displacement of Ser with Asn increases the stability of the spike protein and its affinity to ACE2 and thus increases the transmission potential of the virus. This mutation changes the folding and secondary structure of the spike protein. Also, it reduces antibody neutralization, raising concern about re-infection, vaccine breakthrough and therapeutic values.

Keywords: S477N, COVID-19, molecular dynamic, SARS-COV2 mutations

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Authors: Seyong Oh, Jin-Hong Park

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Recently, neuromorphic computing based on brain-inspired artificial neural networks (ANNs) has attracted huge amount of research interests due to the technological abilities to facilitate massively parallel, low-energy consuming, and event-driven computing. In particular, research on artificial synapse that imitate biological synapses responsible for human information processing and memory is in the spotlight. Here, we demonstrate a photosynaptic device, wherein a synaptic weight is governed by a mixed spike consisting of voltage and light spikes. Compared to the device operated only by the voltage spike, ∆G in the proposed photosynaptic device significantly increased from -2.32nS to 5.95nS with no degradation of nonlinearity (NL) (potentiation/depression values were changed from 4.24/8 to 5/8). Furthermore, the Modified National Institute of Standards and Technology (MNIST) digit pattern recognition rates improved from 36% and 49% to 50% and 62% in ANNs consisting of the synaptic devices with 20 and 100 weight states, respectively. We expect that the photosynaptic device technology processed by optoelectronic spike will play an important role in implementing the neuromorphic computing systems in the future.

Keywords: optoelectronic synapse, IGZO (Indium-Gallium-Zinc Oxide) photosynaptic device, optoelectronic spiking process, neuromorphic computing

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Authors: Abdullah Özköse, Ahmet Tamkoç

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This study aimed to determine some plant characteristics of perennial ryegrass (Lolium perenne L.) genotypes collected from the natural flora of Ankara and correlations between these characteristics. In order to evaluate for breeding purposes according to Turkey's environmental conditions, perennial ryegrass plants collected from natural pasture of Ankara at 2004 were utilized. The collected seeds of plants were sown in pots and seedlings were prepared in greenhouse. Seedlings were transplanted to the experimental field at 50x50 cm intervals in Randomized Complete Blocks Design in 2005. Data were obtained from the observations and measurements of 568 perennial ryegrasses in 2007 and 2008. Perennial ryegrass plants’ in the spring re-growth time, color, density, growth habit, tendency to inflorescences, time of inflorescence, plant height, length of upper internode, spike length, leaf length, leaf width, leaf area, leaf shape, number of spikelets per spike, seed yield per spike, and 1000 grain weight were investigated and correlation analyses were made on the data. Correlation coefficients were estimated between all paired combinations of the traits. The yield components exhibited varying trends of association among themselves. Seed yield per spike showed significant and positive association with number of spikelets per spike, 1000 grain weight, plant height, length of upper internode, spike length, leaf length, leaf width, leaf area and color, but significant and negative association with growth habit and in the spring re-growth time spring.

Keywords: correlation, morphological traits, Lolium perenne

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Authors: Javad Sarvestan, Zdenek Svoboda

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Force-time (F-T) curvature characteristics are globally referenced as the main indicators of athletic jump performance. Nevertheless, to the best of authors’ knowledge, no investigation tried to deeply study the relationship between F-T curve variables and real-game jump performance among elite volleyball players. To this end, this study was designated to investigate the association between F-T curve variables, including movement timings, force, velocity, power, rate of force development (RFD), modified reactive strength index (RSImod), and net impulse with spike jump height during real-game circumstances. Twelve young elite volleyball players performed 3 countermovement jump (CMJ) and 3 spike jump in real-game circumstances with 1-minute rest intervals to prevent fatigue. Shapiro-Wilk statistical test illustrated the normality of data distribution, and Pearson’s product correlation test portrayed a significant correlation between CMJ height and peak RFD (0.85), average RFD (r=0.81), RSImod (r=0.88) and concentric net impulse (r=0.98), and also significant correlation between spike jump height and peak RFD (0.73), average RFD (r=0.80), RSImod (r=0.62) and concentric net impulse (r=0.71). Multiple regression analysis also reported that these factors have a strong contribution in predicting of CMJ (98%) and spike jump (77%) heights. Outcomes of this study confirm that the RFD, concentric net impulse, and RSImod values could precisely monitor and track the volleyball attackers’ explosive strength, muscular stretch-shortening cycle function efficiency, and ultimate spike jump height. To this effect, volleyball coaches and trainers are advised to have an in-depth focus on their athletes’ progression or the impacts of strength trainings by observing and chasing the F-T curve variables such as RFD, net impulse, and RSImod.

Keywords: net impulse, reactive strength index, rate of force development, stretch-shortening cycle

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Authors: Hassane Ben Slimane, Dennai Benmoussa, Abderrachid Helmaoui

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We have theoretically calculated the photovoltaic conversion efficiency of a graded interface CdS/CIGS solar cell, which can be experimentally fabricated. Because the conduction band discontinuity or spike in an abrupt heterojunction CdS/CIGS solar cell can hinder the separation of hole-electron by electric field, a graded interface layer is uses to eliminate the spike and reduces recombination in space charge region. This paper describes the role of the graded band gap interface layer in decreasing the performance of the heterojunction cell. By optimizing the thickness of the graded region, an improvement of conversion efficiency has been observed in comparison to the conventional CIGS system.

Keywords: heterojunction, solar cell, graded interface, CIGS

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Authors: Omvati Verma, Shyamashrre Roy

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A field experiment was conducted with three basal nitrogen levels (90, 120 and 150 kg N/ha) and five foliar application of urea (absolute control, water spray, 3% urea spray at anthesis, 7 and 14 days after anthesis) at G.B. Pant University of Agriculture & Technology, Pantnagar, U.S. Nagar (Uttarakhand) during rabi season in a factorial randomized block design with three replications. Results revealed that nitrogen application of 150 kg/ha produced the highest seed yield, straw and biological yield and it was significantly superior to 90 kg N/ha and was at par with 120 kg N/ha. The number of tillers increased significantly with increase in nitrogen doses up to 150 kg N/ha. Spike length, number of grains per spike, grain weight per spike and thousand seed weight showed significantly higher values with 120 kg N/ha than 90 kg N/ha and were at par with that of 150 kg N/ha. Also, plant height showed similar trend. Leaf area index and chlorophyll content showed significant increase with an increase in nitrogen levels at different stages. In the case of foliar spray treatments, urea spray at anthesis showed highest value for yield and yield attributes. In case of spike length and thousand seed weight, it was similar with the urea spray at 7 and 14 days after anthesis, but for rest of the yield attributes, it was significantly higher than rest of the treatments. Among seed quality parameters protein and sedimentation value showed significant increase due to increase in nitrogen rates whereas, starch and hectolitre weight had a decreasing trend. Wet gluten content was not influenced by nitrogen levels. Foliar urea spray at anthesis resulted in highest value of protein and hectolitre weight whereas, urea spray at 7 days after anthesis showed highest value of sedimentation value and wet gluten content.

Keywords: foliar application, nitrogenous fertilizer, seed quality, yield

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Authors: A. Bruce Janati, Muhammad Umair Khan, Naif Alghassab, Ibrahim Alzeir, Assem Mahmoud, M. Sammour

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Rationale: Lennox-Gastaut syndrome(LGS) is an electro-clinical syndrome composed of the triad of mental retardation, multiple seizure types, and the characteristic generalized slow spike-wave complexes in the EEG. In this article, we report on two patients with LGS whose brain MRI showed dysgenesis of corpus callosum(CC). We review the literature and stress the role of CC in the genesis of secondary bilateral synchrony(SBS). Method: This was a clinical study conducted at King Khalid Hospital. Results: The EEG was consistent with LGS in patient 1 and unilateral slow spike-wave complexes in patient 2. The MRI showed hypoplasia of the splenium of CC in patient 1, and global hypoplasia of CC combined with Joubert syndrome in patient 2. Conclusion: Based on the data, we proffer the following hypotheses: 1-Hypoplasia of CC interferes with functional integrity of this structure. 2-The genu of CC plays a pivotal role in the genesis of secondary bilateral synchrony. 3-Electrodecremental seizures in LGS emanate from pacemakers generated in the brain stem, in particular the mesencephalon projecting abnormal signals to the cortex via thalamic nuclei. 4-Unilateral slow spike-wave complexes in the context of mental retardation and multiple seizure types may represent a variant of LGS, justifying neuroimaging studies.

Keywords: EEG, Lennox-Gastaut syndrome, corpus callosum , MRI

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Authors: Mostafa Mohammadpour, Christoph Kapeller, Christy Li, Josef Scharinger, Christoph Guger

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Interictal spikes provide valuable information on electrocorticography (ECoG), which aids in surgical planning for patients who suffer from refractory epilepsy. However, the shape and temporal dynamics of these spikes remain unclear. The purpose of this work was to analyze the shape of interictal spikes and measure their distance to the seizure onset zone (SOZ) to use in epilepsy surgery. Thirteen patients' data from the iEEG portal were retrospectively studied. For analysis, half an hour of ECoG data was used from each patient, with the data being truncated before the onset of a seizure. Spikes were first detected and grouped in a sequence, then clustered into interictal epileptiform discharges (IEDs) and non-IED groups using two-step clustering. The distance of the spikes from IED and non-IED groups to SOZ was quantified and compared using the Wilcoxon rank-sum test. Spikes in the IED group tended to be in SOZ or close to it, while spikes in the non-IED group were in distance of SOZ or non-SOZ area. At the group level, the distribution for sharp wave, positive baseline shift, slow wave, and slow wave to sharp wave ratio was significantly different for IED and non-IED groups. The distance of the IED cluster was 10.00mm and significantly closer to the SOZ than the 17.65mm for non-IEDs. These findings provide insights into the shape and spatiotemporal dynamics of spikes that could influence the network mechanisms underlying refractory epilepsy.

Keywords: spike propagation, spike pattern, clustering, SOZ

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Authors: Helan Satish, M. Ramasubba Reddy

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The simulation of an endocardial cell for gene mutation in the cardiac sodium ion channel NaV1.5, encoded by SCN5A gene, is discussed. The characterization of Brugada Syndrome by loss of function effect on SCN5A mutation due to L812Q mutant present in the DII-S4 transmembrane region of the NaV1.5 channel protein and its effect in an endocardial cell is studied. Ten Tusscher model of human ventricular action potential is modified to incorporate the changes contributed by L812Q mutant in the endocardial cells. Results show that BrS-associated SCN5A mutation causes reduction in the inward sodium current by modifications in the channel gating dynamics such as delayed activation, enhanced inactivation, and slowed recovery from inactivation in the endocardial cell. A decrease in the inward sodium current was also observed, which affects depolarization phase (Phase 0) that leads to reduction in the spike amplitude of the cardiac action potential.

Keywords: SCN5A gene mutation, sodium channel, Brugada syndrome, cardiac arrhythmia, action potential

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Authors: Dileep Kumar, Janhavi Ramchandra Rao Kumar, Rao

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COVID-19 has ravaged the globe, and it is spreading its Spectre day by day. In the absence of established drugs, this disease has created havoc. Some of the infected persons are symptomatic or asymptomatic. The respiratory system, cardiac system, digestive system, etc. in human beings are affected by this virus. In our present investigation, we have undertaken a study of the Indian Ayurvedic herb, Ocimum sanctum against SARS-CoV-2 using molecular docking and dynamics studies. The docking analysis was performed on the Glide module of Schrödinger suite on two different proteins from SARS-CoV-2 viz. NSP15 Endoribonuclease and spike receptor-binding domain. MM-GBSA based binding free energy calculations also suggest the most favorable binding affinities of carvacrol, β elemene, and β caryophyllene with binding energies of −61.61, 58.23, and −54.19 Kcal/mol respectively with spike receptor-binding domain and NSP15 Endoribonuclease. It rekindles our hope for the design and development of new drug candidates for the treatment of COVID19.

Keywords: molecular docking, COVID-19, ocimum sanctum, binding energy

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Authors: Alireza Jalalvand, Maryam Saleh, Somayeh Behjat Khatouni, Zahra Bahri Najafi, Foroozan Fatahinia, Narges Ismailzadeh, Behrokh Farahmand

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Object: In the last two decades, the recent outbreak of Coronavirus (SARS-CoV-2) imposed a global pandemic in the world. Despite the increasing prevalence of the disease, there are no effective drugs to treat it. A suitable and rapid way to afford an effective drug and treat the global pandemic is a computational drug study. This study used molecular docking methods to examine the potential inhibition of over 50 antiviral drugs against three fundamental proteins of SARS-CoV-2. METHODS: Through a literature review, three important proteins (a key protease, RNA-dependent RNA polymerase (RdRp), and spike) were selected as drug targets. Three-dimensional (3D) structures of protease, spike, and RdRP proteins were obtained from the Protein Data Bank. Protein had minimal energy. Over 50 antiviral drugs were considered candidates for protein inhibition and their 3D structures were obtained from drug banks. The Autodock 4.2 software was used to define the molecular docking settings and run the algorithm. RESULTS: Five drugs, including indinavir, lopinavir, saquinavir, nelfinavir, and remdesivir, exhibited the highest inhibitory potency against all three proteins based on the binding energies and drug binding positions deduced from docking and hydrogen-bonding analysis. Conclusions: According to the results, among the drugs mentioned, saquinavir and lopinavir showed the highest inhibitory potency against all three proteins compared to other drugs. It may enter laboratory phase studies as a dual-drug treatment to inhibit SARS-CoV-2.

Keywords: covid-19, drug repositioning, molecular docking, lopinavir, saquinavir

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Authors: Ratul Das

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The present experimental study insights the decontamination of instantaneous velocity fluctuations captured by Acoustic Doppler Velocimeter (ADV) in gravel-bed streams to ascertain near-bed turbulence for low Reynolds number. The interference between incidental and reflected pulses produce spikes in the ADV data especially in the near-bed flow zone and therefore filtering the data are very essential. Nortek’s Vectrino four-receiver ADV probe was used to capture the instantaneous three-dimensional velocity fluctuations over a non-cohesive bed. A spike removal algorithm based on the acceleration threshold method was applied to note the bed roughness and its influence on velocity fluctuations and velocity power spectra in the carrier fluid. The velocity power spectra of despiked signals with a best combination of velocity threshold (VT) and acceleration threshold (AT) are proposed which ascertained velocity power spectra a satisfactory fit with the Kolmogorov “–5/3 scaling-law” in the inertial sub-range. Also, velocity distributions below the roughness crest level fairly follows a third-degree polynomial series.

Keywords: acoustic doppler velocimeter, gravel-bed, spike removal, reynolds shear stress, near-bed turbulence, velocity power spectra

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Authors: D. S. Gurjar, R. Kaur, K. P. Singh, R. Singh

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A greater volume of wastewater generate from urban areas in India. Due to the adequate availability, less energy requirement and nutrient richness, farmers of urban and peri-urban areas are deliberately using wastewater to grow high value vegetable crops. Wastewater contains pathogens and toxic pollutants, which can enter in the food chain system while using wastewater for irrigating vegetable crops. Hence, wastewater can use for growing commercial flower crops that may avoid food chain contamination. Tuberose (Polianthes tuberosa L.) is one of the most important commercially grown, cultivated over 30, 000 ha area, flower crop in India. Its popularity is mainly due to the sweet fragrance as well as the long keeping quality of the flower spikes. The flower spikes of tuberose has high market price and usually blooms during summer and rainy seasons when there is meager supply of other flowers in the market. It has high irrigation water requirement and fresh water supply is inadequate in tuberose growing areas of India. Therefore, wastewater may fulfill the water and nutrients requirements and may enhance the productivity of tuberose. Keeping in view, the present study was carried out at WTC farm of ICAR-Indian Agricultural Research Institute, New Delhi in 2014-15. Prajwal was the variety of test crop. The seven treatments were taken as T-1. Wastewater irrigation at 0.6 ID/CPE, T-2: Wastewater irrigation at 0.8 ID/CPE, T-3: Wastewater irrigation at 1.0 ID/CPE, T-4: Wastewater irrigation at 1.2 ID/CPE, T-5: Wastewater irrigation at 1.4 ID/CPE, T-6: Conjunctive use of Groundwater and Wastewater irrigation at 1.0 ID/CPE in cyclic mode, T-7: Control (Groundwater irrigation at 1.0 ID/CPE) in randomized block design with three replication. Wastewater and groundwater samples were collected on monthly basis (April 2014 to March 2015) and analyzed for different parameters of irrigation quality (pH, EC, SAR, RSC), pollution hazard (BOD, toxic heavy metals and Faecal coliforms) and nutrients potential (N, P, K, Cu, Fe, Mn, Zn) as per standard methods. After harvest of tuberose crop, soil samples were also collected and analyzed for different parameters of soil quality as per standard methods. The vegetative growth and flower parameters were recorded at flowering stage of tuberose plants. Results indicated that wastewater samples had higher nutrient potential, pollution hazard as compared to groundwater used in experimental crop. Soil quality parameters such as pH EC, available phosphorous & potassium and heavy metals (Cu, Fe, Mn, Zn, Cd. Pb, Ni, Cr, Co, As) were not significantly changed whereas organic carbon and available nitrogen were significant higher in the treatments where wastewater irrigations were given at 1.2 and 1.4 ID/CPE as compared to groundwater irrigations. Significantly higher plant height (68.47 cm), leaves per plant (78.35), spike length (99.93 cm), rachis length (37.40 cm), numbers of florets per spike (56.53), cut spike yield (0.93 lakh/ha) and loose flower yield (8.5 t/ha) were observed in the treatment of Wastewater irrigation at 1.2 ID/CPE. Study concluded that given quality of wastewater improves the productivity of tuberose without an adverse impact on soil quality/health. However, its long term impacts need to be further evaluated.

Keywords: conjunctive use, irrigation, tuberose, wastewater

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Authors: Azizurahman Sakhizadah, Tsugiyuki Masunaga

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The use of sulfur fertilizer by Afghanistan farmers for wheat production has never been practiced, although sulfur deficiency has been expected for wheat production. A field experiment was conducted at Poza e Ishan Research Station Farm, Baghlan province, Afghanistan to examine the effect of sulfur fertilizer on growth and yield components of wheat. The experiment was laid out in randomize complete block design (RCBD), having three replications and eight treatments. The initial soil of experiment was alkaline (pH8.4), with textural class of sandy clay loam, available sulfur (40.8) mg kg-1, and Olsen-P (28.8) mg kg-1. Wheat variety, Kabul 013 was cultivated from November 2015 to June 2016. The recommended doses of nitrogen and Phosphors (Urea and DAP at 250 and 125 kg ha-1) were applied by broadcasting except control plot. Sulfur was applied by foliar spray (K2 SO4) at the rate of 10, 20, and 30 kg ha-1, split at tillering and flowering stages. The results demonstrated that sulfur application positively influenced on growth and yield of wheat crop with combination of nitrogen. Plant did not respond to sole sulfur application. Plant height, spike length, spikelet's number spike-1, were increased and yield g m-2 was also increased by 1.2, 19.1 and 25.1 % for 10, 20 and 30 kg sulfur ha-1 application.

Keywords: sulfur, nitrogen, wheat, foliar

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Authors: Sun Zhe, Ruggero Micheletto

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The research of neural network is very important for the development of advanced next generation intelligent devices and the medical treatment. The most important part of the neural network research is the learning. The process of learning in our brain is essentially several adjustment processes of connection strength between neurons. It is very difficult to figure out how this mechanism works in the complex network and how the connection strength influences brain functions. For this reason, we made a model with only two coupled neurons and studied the influence of connection strength between them. To emulate the neuronal activity of realistic neurons, we prefer to use the Izhikevich neuron model. This model can simulate the neuron variables accurately and it’s simplicity is very suitable to implement on computers. In this research, the parameter ρ is used to estimate the correlation coefficient between spike train of two coupling neurons.We think the results is very important for figuring out the mechanism between synchronization of coupling neurons and synaptic plasticity. The result also presented the importance of the spike frequency adaptation in complex systems.

Keywords: neural networks, noise, stochastic processes, coupled neurons, correlation coefficient, synchronization, pacemaker, synaptic plasticity

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Authors: Michael Fundator

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Groundbreaking application of biomathematical and biochemical research in neural networks processes to formation of non-canonical bases, islands, and analog bases in DNA and mRNA at or near the transcription that contradicts the long anticipated statistical assumptions for the distribution of bases and analog bases compounds is implemented through statistical and stochastic methods apparatus with addition of quantum principles, where the usual transience of Poisson spike train becomes very instrumental tool for finding even almost periodical type of solutions to Fokker-Plank stochastic differential equation. Present article develops new multidimensional methods of finding solutions to stochastic differential equations based on more rigorous approach to mathematical apparatus through Kolmogorov-Chentsov continuity theorem that allows the stochastic processes with jumps under certain conditions to have γ-Holder continuous modification that is used as basis for finding analogous parallels in dynamics of neutral networks and formation of analog bases and transcription in DNA.

Keywords: Fokker-Plank stochastic differential equation, Kolmogorov-Chentsov continuity theorem, neural networks, translation and transcription

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Authors: Omar Ibrahim, Aly A. Gaafar, K. A. Ratib

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Two field experiments in micro plots were carried out during the winter seasons of 2012/2013 and 2013/2014, Soil Salinity Laboratory, Alexandria, Egypt, to study the effect of three levels of salicylic acid (SA) as a growth regulator (0, 50, 100 ppm) and three rates of nitrogen fertilizer (75, 100, 125 kg N/feddan) on growth and yield of a spring wheat (Giza 168). The experimental design was a split plot with the main plots in randomized complete block design (RCBD) and four replicates. The results indicated that increasing nitrogen fertilizer rates resulted in insignificant effect on both plant height (cm) and grain weight/spike only. However, a significant effect was observed in all the other studied characters due to the increase in nitrogen fertilizer. On the other hand, increasing salicylic acid rates resulted in insignificant effect in all the studied characters except for chlorophyll a, chlorophyll b, number of grain/spike, and grain yield (gm/ plot). The highest effects on grain yield in wheat were obtained by the rate of 125 kg/feddan of nitrogen fertilizer and 100 ppm of salicylic acid. In conclusion, the data indicated that a high grain yield could be obtained by adding 100 kg/feddan of nitrogen fertilizer and spraying of 50 ppm of salicylic acid with no significant difference with the highest rates. Finally, the interaction had no significant effect on all the studied characters.

Keywords: growth regulator, nitrogen fertilizer, spring wheat, salicylic acid

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Authors: Atlal El-Assaad

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Viruses change with time through mutations and result in new variants that may persist or disappear. A Mutation refers to an actual change in the virus genetic sequence, and a variant is a viral genome that may contain one or more mutations. Critical mutations may cause the virus to be more transmissible, with high disease severity, and more vulnerable to diagnostics, therapeutics, and vaccines. Thus, variants carrying such mutations may increase the risk to human health and are considered variants of concern (VOC). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) - the contagious in humans, positive-sense single-stranded RNA virus that caused coronavirus disease 2019 (COVID-19) - has been studied thoroughly, and several variants were revealed across the world with their corresponding mutations. SARS-CoV-2 has four structural proteins, known as the S (spike), E (envelope), M (membrane), and N (nucleocapsid) proteins, but prior study and vaccines development focused on genetic mutations in the S protein due to its vital role in allowing the virus to attach and fuse with the membrane of a host cell. Specifically, subunit S1 catalyzes attachment, whereas subunit S2 mediates fusion. In this perspective, we studied all charged amino acid mutations of the SARS-CoV-2 viral spike protein S1 when bound to Antibody CC12.1 in a crystal structure and assessed the effect of different mutations. We generated all missense mutants of SARS-CoV-2 protein amino acids (AAs) within the SARS-CoV-2:CC12.1 complex model. To generate the family of mutants in each complex, we mutated every charged amino acid with all other charged amino acids (Lysine (K), Arginine (R), Glutamic Acid (E), and Aspartic Acid (D)) and studied the new binding of the complex after each mutation. We applied Poisson-Boltzmann electrostatic calculations feeding into free energy calculations to determine the effect of each mutation on binding. After analyzing our data, we identified charged amino acids keys for binding. Furthermore, we validated those findings against published experimental genetic data. Our results are the first to propose in silico potential life-threatening mutations of SARS-CoV-2 beyond the present mutations found in the five common variants found worldwide.

Keywords: SARS-CoV-2, variant, ionic amino acid, protein-protein interactions, missense mutation, AESOP

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Authors: Gordana Branković, Dejan Dodig, Vesna Pajić, Vesna Kandić, Desimir Knežević, Nenad Đurić

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The wheat grain quality properties are influenced by genotype, environmental conditions and genotype × environment interaction (GEI). The increasing request of more nutritious wheat products will direct future breeding programmes. Therefore, the aim of investigation was to determine: i) variability of the protein content (PC), wet gluten content (WG) and Zeleny sedimentation volume (ZS); ii) components of variance, heritability in a broad sense (hb2), and expected genetic advance as percent of mean (GAM) for PC, WG, and ZS; iii) correlations between PC, WG, ZS, and most important agronomic traits; in order to assess expected breeding success versus environmental impact for these quality traits. The plant material consisted of 30 genotypes of bread wheat (Triticum aestivum L. ssp. aestivum) and durum wheat (Triticum durum Desf.). The trials were sown at the three test locations in Serbia: Rimski Šančevi, Zemun Polje and Padinska Skela during 2010-2011 and 2011-2012. The experiments were set as randomized complete block design with four replications. The plot consisted of five rows of 1 m2 (5 × 0.2 m × 1 m). PC, WG and ZS were determined by the use of Near infrared spectrometry (NIRS) with the Infraneo analyser (Chopin Technologies, France). PC, WG and ZS, in bread wheat, were in the range 13.4-16.4%, 22.8-30.3%, and 39.4-67.1 mL, respectively, and in durum wheat, in the range 15.3-18.1%, 28.9-36.3%, 37.4-48.3 mL, respectively. The dominant component of variance for PC, WG, and ZS, in bread wheat, was genotype with the genetic variance/GEI variance (VG/VG × E) relation of 3.2, 2.9 and 1.0, respectively, and in durum wheat was GEI with the VG/VG × E relation of 0.70, 0.69 and 0.49, respectively. hb2 and GAM values for PC, WG and ZS, in bread wheat, were 94.9% and 12.6%, 93.7% and 18.4%, and 86.2% and 28.1%, respectively, and in durum wheat, 80.7% and 7.6%, 79.7% and 10.2%, and 74% and 11.2%, respectively. The most consistent through six environments, statistically significant correlations, for bread wheat, were between PC and spike length (-0.312 to -0.637); PC, WG, ZS and grain number per spike (-0.320 to -0.620; -0.369 to -0.567; -0.301 to -0.378, respectively); PC and grain thickness (0.338 to 0.566), and for durum wheat, were between PC, WG, ZS and yield (-0.290 to -0.690; -0.433 to -0.753; -0.297 to -0.660, respectively); PC and plant height (-0.314 to -0.521); PC, WG and spike length (-0.298 to -0.597; -0.293 to -0.627, respectively); PC, WG and grain thickness (0.260 to 0.575; 0.269 to 0.498, respectively); PC, WG and grain vitreousness (0.278 to 0.665; 0.357 to 0.690, respectively). Breeding success can be anticipated for ZS in bread wheat due to coupled high values for hb2 and GAM, suggesting existence of additive genetic effects, and also for WG in bread wheat, due to very high hb2 and medium high GAM. The small, and medium, negative correlations between PC, WG, ZS, and yield or yield components, indicate difficulties to select simultaneously for high quality and yield, depending on linkage for particular genetic arrangements to be broken by recombination.

Keywords: bread and durum wheat, genetic advance, protein and wet gluten content, Zeleny sedimentation volume

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Authors: Syed Muhammad Awais Tahir, Syed Hossein Raza Hamdani

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In the last two years, there has been a substantial increase in the rate of satellite launches. To keep up with the technology, it is imperative that the launch cost must be made affordable, especially in developing and underdeveloped countries. Launch cost is directly affected by the launch vehicle’s aerodynamic performance. Pegasus-XL SLV (Satellite Launch Vehicle) has been serving as a commercial SLV for the last 26 years, commencing its commercial flight operation from the six operational sites all around the US and Europe, and the Marshal Islands. Aerodynamic heating and drag contribute largely to Pegasus’s flight performance. The objective of this study is to reduce the aerodynamic heating and drag on Pegasus’s body significantly for supersonic and hypersonic flight regimes. Aerodynamic data for Pegasus’s first flight has been validated through CFD (Computational Fluid Dynamics), and then drag and aerodynamic heating is reduced by using a combination of a forward-facing cylindrical spike and a conical aero-disk at the actual operational flight conditions. CFD analysis using ANSYS fluent will be carried out for Mach no. ranges from 0.83 to 7.8, and AoA (Angle of Attack) ranges from -4 to +24 degrees for both simple and spiked-configuration, and then the comparison will be drawn using a variety of graphs and contours. Expected drag reduction for supersonic flight is to be around 15% to 25%, and for hypersonic flight is to be around 30% to 50%, especially for AoA < 15⁰. A 5% to 10% reduction in aerodynamic heating is expected to be achieved for hypersonic regions. In conclusion, the aerodynamic performance of air-launched Pegasus-XL SLV can be further enhanced, leading to its optimal fuel usage to achieve a more economical orbital flight.

Keywords: aerodynamics, pegasus-XL, drag reduction, aerodynamic heating, satellite launch vehicle, SLV, spike, aero-disk

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Authors: Zelalem Bitew, Adane Kassa, Beyene Misgan

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In this study, a sensitive and selective voltammetric method based on poly(diphenylamine-4-sulfonic acid) modified glassy carbon electrode (poly(DPASA)/GCE) was developed for determination of gallic acid. Appearance of an irreversible oxidative peak at both bare GCE and poly(DPASA)/GCE for gallic acid with about three folds current enhancement and much reduced potential at poly(DPASA)/GCE showed catalytic property of the modifier towards oxidation of gallic acid. Under optimized conditions, Adsorptive stripping square wave voltammetric peak current response of the poly(DPASA)/GCE showed linear dependence with gallic acid concentration in the range 5.00 × 10-7 − 3.00 × 10-4 mol L-1 with limit of detection of 4.35 × 10-9. Spike recovery results between 94.62-99.63, 95.00-99.80 and 97.25-103.20% of gallic acid in honey, raw peanut, and commercial peanut butter samples respectively, interference recovery results with less than 4.11% error in the presence of uric acid and ascorbic acid, lower LOD and relatively wider dynamic range than most of the previously reported methods validated the potential applicability of the method based on poly(DPASA)/GCE for determination of gallic acid real samples including in honey and peanut samples.

Keywords: gallic acid, diphenyl amine sulfonic acid, adsorptive anodic striping square wave voltammetry, honey, peanut

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Authors: Manal Kamel, Sara Maher, Hanan El Baz, Faten Salah, Omar Sayyouh, Zeinab Demerdash

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In the recent COVID 19 pandemic, experts of public health have emphasized testing, tracking infected people, and tracing their contacts as an effective strategy to reduce the spread of the virus. Development of rapid and sensitive diagnostic assays to replace reverse transcription polymerase chain reaction (RT-PCR) is mandatory..Our innovative test strip relying on the application of nanoparticles conjugated to recombinant nanobodies for SARS-COV-2 spike protein (S1) & angiotensin-converting enzyme 2 (that is responsible for the virus entry into host cells) for rapid detection of SARS-COV-2 spike protein (S1) in saliva or sputum specimens. Comparative tests with RT-PCR will be held to estimate the significant effect of using COVID 19 nanobodies for the first time in the development of lateral flow test strip. The SARS-CoV-2 S1 (3 ng of recombinant proteins) was detected by our developed LFIA in saliva specimen of COVID-19 Patients No cross-reaction was detected with Middle East respiratory syndrome coronavirus (MERS-CoV) or SARS- CoV antigens..Our developed system revealed 96 % sensitivity and 100% specificity for saliva samples compared to 89 % and 100% sensitivity and specificity for nasopharyngeal swabs. providing a reliable alternative for the painful and uncomfortable nasopharyngeal swab process and the complexes, time consuming PCR test. An increase in testing compliances to be expected.

Keywords: COVID 19, diagnosis, LFIA, nanobodies, ACE2

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Authors: Shenghong Huang, Weirong Wang, Xisheng Luo, Xinzhu Li, Xinwen Zhao

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Understanding of material mixing induced by Richtmyer-Meshkov instability (RMI) at extreme shock compressing conditions (high energy density environment: P >> 100GPa, T >> 10000k) is of great significance in engineering and science, such as inertial confinement fusion(ICF), supersonic combustion, etc. Turbulent mixing induced by RMI is a kind of complex fluid dynamics, which is closely related with hydrodynamic conditions, thermodynamic states, material physical properties such as compressibility, strength, surface tension and viscosity, etc. as well as initial perturbation on interface. For phenomena in ordinary thermodynamic conditions (low energy density environment), many investigations have been conducted and many progresses have been reported, while for mixing in extreme thermodynamic conditions, the evolution may be very different due to ionization as well as large difference of material physical properties, which is full of scientific problems and academic interests. In this investigation, the first principle based molecular dynamic method is applied to study metal Lithium and gas Hydrogen (Li-H2) interface mixing in micro/meso scale regime at different shock compressing loading speed ranging from 3 km/s to 30 km/s. It's found that, 1) Different from low-speed shock compressing cases, in high-speed shock compresing (>9km/s) cases, a strong acceleration of metal/gas interface after strong shock compression is observed numerically, leading to a strong phase inverse and spike growing with a relative larger linear rate. And more specially, the spike growing rate is observed to be increased with shock loading speed, presenting large discrepancy with available empirical RMI models; 2) Ionization is happened in shock font zone at high-speed loading cases(>9km/s). An additional local electric field induced by the inhomogeneous diffusion of electrons and nuclei after shock font is observed to occur near the metal/gas interface, leading to a large acceleration of nuclei in this zone; 3) In conclusion, the work of additional electric field contributes to a mechanism of RMI in micro/meso scale regime at extreme shock compressing conditions, i.e., a Rayleigh-Taylor instability(RTI) is induced by additional electric field during RMI mixing process and thus a larger linear growing rate of interface spike.

Keywords: ionization, micro/meso scale, material mixing, shock

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