The spike protein of SARS-CoV-2 has been undergoing mutations and is highly glycosylated. It is critically important to investigate the biological significance of these mutations. Here, we ...investigated 80 variants and 26 glycosylation site modifications for the infectivity and reactivity to a panel of neutralizing antibodies and sera from convalescent patients. D614G, along with several variants containing both D614G and another amino acid change, were significantly more infectious. Most variants with amino acid change at receptor binding domain were less infectious, but variants including A475V, L452R, V483A, and F490L became resistant to some neutralizing antibodies. Moreover, the majority of glycosylation deletions were less infectious, whereas deletion of both N331 and N343 glycosylation drastically reduced infectivity, revealing the importance of glycosylation for viral infectivity. Interestingly, N234Q was markedly resistant to neutralizing antibodies, whereas N165Q became more sensitive. These findings could be of value in the development of vaccine and therapeutic antibodies.
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•Over 100 mutations were selected for analyses on their infectivity and antigenicity•The dominant D614G itself and combined with other mutations are more infectious•Ablation of both N331 and N343 glycosylation at RBD drastically reduced infectivity•Ten mutations such as N234Q, L452R, A475V, and V483A was markedly resistant to some mAbs
Eighty natural variants and 26 glycosylation spike mutants of SARS-CoV-2 were analyzed in terms of infectivity and antigenicity using high throughput pseudovirus assay in conjunction with neutralizing antibodies.
Abstract
An innovative nested array structure that can notably increase the DOF and the linear arrays’ direction of arrival (DOA) estimated performance is proposed. For the conventional nested array, ...we vectorize the ACM’s output of the whole array and then remove the repeated rows to get a virtual array’s output. In contrast with classical nested arrays, the superiority of the new nested array is that it utilizes the combination of reverse ordering and conjugation of the inner uniform linear array (ULA) for one of the two subarrays and the sparse outer ULA for another to increase the array aperture. This means the outer sparse ULA’s sensor spacing is approximately the length of the entire inner ULA in the classical nested array structure. Yet, it is about twice the length in the new nested array structure. We generate one lengthy consecutive virtual uniform array excluding any redundant virtual sensors by vectorizing the two subarrays’ cross-correlation matrix (CCM), which is mentioned above. With the export signal of the virtual array and its conjugate form of it, an equivalent covariance matrix of full rank is constructed, which is called the Toeplitz matrix, to compensate for the rank lack of the virtual array’s ACM. For the sake of obtaining the DOA of input signals, the conventional DOA estimation method will be implemented on the ACM. The increase in outer sparse ULA’s sensor spacing ensures an increase in virtual array aperture in principle, which means it is capable of increasing the number of DOA estimations, which is called DOF, and optimizing the DOA estimated performance in contrast with the ULA and classical nested arrays. Results from trials certify the preponderance of the proposed structure in the aspect of DOF and the accuracy of DOA estimation.
Pseudotyped viruses are useful virological tools because of their safety and versatility. On the basis of a vesicular stomatitis virus (VSV) pseudotyped virus production system, we developed a ...pseudotyped virus-based neutralization assay against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in biosafety level 2 facilities. Compared with the binding antibody test, the neutralization assay could discriminate the protective agents from the antibody family. This protocol includes production and titration of the SARS-CoV-2 S pseudotyped virus and the neutralization assay based on it. Various types of samples targeting virus attachment and entry could be evaluated for their potency, including serum samples derived from animals and humans, monoclonal antibodies and fusion inhibitors (peptides or small molecules). If the pseudotyped virus stock has been prepared in advance, it will take 2 days to get the potency data for the candidate samples. Experience in handling cells is needed before implementing this protocol.
Aims
The involvement of pyroptosis in ischemic stroke remains to be established. Therefore, we used the specific pyroptosis inhibitor Vx765 as an experimental intervention target in a murine model of ...stroke.
Methods
A total of 564 C57BL/6 mice were subjected to photothrombotic procedures and treated via gavage with Vx765 at 1‐hour post‐ischemia. We subsequently assessed the expression of Gasdermin D (GSDMD), inflammasomes, caspase‐1, and interleukin‐1β (IL‐1β) using immunofluorescence (IF) and Western blot (WB) analyses. We also examined ultrastructural changes of cortical neurons with transmission electron microscopy (TEM) and measured infarct volumes dynamically by magnetic resonance imaging (MRI). Moreover, we evaluated the neurologic deficits by modified neurological severity scores, the rotarod test, and Treadscan.
Results
Elevated expression of GSDMD and GSDMD p30, the pore‐forming subunit, was evident in the peri‐ischemic region on days one and three post‐ischemia. The neuronal plasma, nuclear, and mitochondrial membranes showed ultrastructural damage at day three post‐stroke. Elevated expression of inflammasomes, caspase‐1, and IL‐1β was also present on days one and three post‐injury. There were significant differences between Vx765‐treated and vehicle groups in mean infarct volumes (14.36 vs 21.52 mm3; 12.34 vs 18.56 mm3; 4.13 vs 10.06 mm3; P < .05 at day one, three, and seven post‐surgery, respectively). Mice treated with Vx765 showed better motor recovery as assessed by serial behavior tests and had better neuronal survival, which was attributable to pyroptosis inhibition, as illustrated by downregulated expression of the effector protein GSDMD, inflammasomes, caspase‐1, and IL‐1β. Besides, treatment with Vx765 preserved neuronal membrane structures after the ischemic injury.
Conclusions
Pyroptosis emerges as an important pathway for neuronal death in an acute ischemic stroke. Vx765, a low molecular weight drug that has proven safe in clinical epilepsy trials, has potential therapeutic value for cerebral ischemia by targeting the canonical inflammasome pathway of pyroptosis.
Emitter localization is an active research topic in electronic reconnaissance. Recently, passive synthetic aperture (PSA) has been used to determine the azimuth and range distance of the emitter. ...However, the existing methods approximate the distance equation of the spaceborne model through the airborne model, resulting in a large positioning error. In this article, an emitter localization algorithm based on PSA in the spaceborne model is proposed. First, the phase of the received signal is accumulated by using the symmetry of the Doppler history of the received signal in long synthetic aperture time, improving the azimuth positioning accuracy. The effective velocity is then used to establish the nonlinear equations of range distance. A modulus function is used to solve the equations, correcting the range positioning error in the spaceborne model. Finally, the influence of noise, satellite position error, and satellite speed error on the positioning results is analyzed. The error matrix of the proposed method in wide swath is obtained. Simulation results show that the positioning accuracy of this method is one order of magnitude higher than that of traditional single-satellite positioning methods. The effectiveness of the proposed method is verified through actual satellite experiments.
Passive synthetic aperture (PSA) is recently used in passive localization, due to its high precision and high resolution. However, the unknown parameters of the radiation sources will cause the ...Doppler signal to distort, which will affect the localization accuracy. To solve the problem, this article proposes a passive localization algorithm based on range migration difference (RMD) and nonuniform fast Fourier transform (NUFFT) for pulse repetition interval (PRI)-staggered radar signal. The main idea is to use the RMD to compensate for the PRI estimation errors, and then the azimuth distance can be derived by conducting quadratic polynomial fitting on the trajectory of range migration. Moreover, nonuniform sampling of the Doppler signal caused by staggered PRI is corrected by achieving NUFFT via the convolution function. Therefore, the Doppler rate and zero-Doppler time can be estimated by designing different matched filters in the frequency domain, and the carrier frequency estimation error is eliminated by searching the output peak value of the matched filters under different residential frequency offsets (RFOs). The simulation results show that the proposed RMD-NUFFT method can not only eliminate the impact of radar parameter estimation error on localization accuracy but also achieve accurate parameter estimation for nonuniformly sampled signals, improving the positioning accuracy of the target. Furthermore, compared with the traditional direction of arrival (DOA), frequency of arrival (FOA), and time difference of arrival (TDOA), the localization accuracy of the proposed algorithm has a significant improvement. The estimation error of source position does not exceed 800 m with SNR not less than −5 dB, which proves the effectiveness of the proposed method.
Pseudoviruses are useful virological tools because of their safety and versatility, especially for emerging and re-emerging viruses. Due to its high pathogenicity and infectivity and the lack of ...effective vaccines and therapeutics, live SARS-CoV-2 has to be handled under biosafety level 3 conditions, which has hindered the development of vaccines and therapeutics. Based on a VSV pseudovirus production system, a pseudovirus-based neutralization assay has been developed for evaluating neutralizing antibodies against SARS-CoV-2 in biosafety level 2 facilities. The key parameters for this assay were optimized, including cell types, cell numbers, virus inoculum. When tested against the SARS-CoV-2 pseudovirus, SARS-CoV-2 convalescent patient sera showed high neutralizing potency, which underscore its potential as therapeutics. The limit of detection for this assay was determined as 22.1 and 43.2 for human and mouse serum samples respectively using a panel of 120 negative samples. The cutoff values were set as 30 and 50 for human and mouse serum samples, respectively. This assay showed relatively low coefficient of variations with 15.9% and 16.2% for the intra- and inter-assay analyses respectively. Taken together, we established a robust pseudovirus-based neutralization assay for SARS-CoV-2 and are glad to share pseudoviruses and related protocols with the developers of vaccines or therapeutics to fight against this lethal virus.
Respiration rate is an essential indicator of vital signs, which can demonstrate the physiological condition of the human body and provide clues to some diseases. Commercial Wi-Fi devices can provide ...a non-invasive, cost-effective and long-term respiration rate-monitoring scheme for home scenarios. However, previous studies show that the breathing depth and location may affect the detectability of respiratory signals. In this study, we leverage the variation of the Doppler spectral energy extracted from the channel state information (CSI) collected by Wi-Fi devices to track the chest displacement induced by respiration. First, the random phase is eliminated by phase-fitting method to obtain the complex CSI containing the Doppler shift. Then, the multipath decomposition of CSI is carried out to obtain the channel impulse response, which eliminates the interference phase of the time delay and retains the Doppler shift. The dynamic path units are also separate from the multipath, which overcomes the indoor multipath effect. Finally, we conduct a time-frequency analysis to dynamic units to accumulate Doppler spectral energy. Based on these ideas, we design a complete respiration rate-monitoring system to obtain the respiration rate by using the consistency between the Doppler energy change period and the respiratory cycle. We evaluate our system through extensive experiments in several typical home environments filled with multipath. Experimental results show that the errors of the three scenarios are approximate, the maximum error is less than 0.7 bpm, and the average errors are approximately 0.15 bpm. This result indicates that our scheme can achieve high precision respiration monitoring and has good anti-multipath ability compared with existing methods.
A heterogeneous sensing multiunmanned aerial vehicle (UAV) system is developed to track a moving target undergoing unknown motion. Using heterogeneous sensors for tracking can increase robustness and ...reduce costs. However, the formation configuration of the multi-UAV system needs to be designed to ensure the best estimation performance. A metric based on the Fisher information matrix is used to determine the best formation configuration since the state covariance matrix was proven to be lower bounded by the Cramer-Rao lower bound. In other words, the determinant value of the Fisher information matrix is designed to be the cost function, and limitation of the field of view (FOV), limitation of the tracking distance, and avoiding inter-UAV collisions are considered as constraints. Finally, the generated optimal formation configuration is converted to the relative position for the distributed controller of the UAVs to achieve tracking. Controllers for UAVs are designed to ensure that tracking of the target is achieved in the optimal configuration with the constraints satisfied. In addition to performing the theoretical analysis, experiments and simulations were conducted to verify the efficacy of the developed heterogeneous sensing system.
Radio frequency fingerprint identification (RFFI) is a physical layer security methodology to recognize individual devices by leveraging hardware imperfections inevitably induced in the manufacturing ...process. However, the performance degradation caused by the time-varying channel impacts and interferences has severely restricted the development of RFFI. To this end, we present a channel-agnostic RFFI system, which consists of three modules, i.e., signal preprocessing module, feature extraction module, and classification module. In the signal preprocessing module, we first propose a novel approach, referred to as limiter-based spectral circular shift bidirectional division (LB-SCSBD), to generate two parallel spectral quotient (SQ) sequences. Then, we define the spectral quotient constellation (SQC) symbols according to different modulation formats, and thereby transform the SQ sequences into four magnitude-based sequences in terms of two channel-robust signal representations, i.e., the SQ magnitude (SQM) and SQC error vector magnitude (SQC-EVM). In the feature extraction module, we present a moment-based statistical feature extractor (MB-SFE) to extract the device-specific information from the above four sequences. In the classification module, the extracted statistics are fed into the multi-class support vector machine (SVM) for training and testing. We take WiFi as a case study and evaluate the performance of the proposed RFFI system by classifying eight simulated device models and six universal software radio peripheral (USRP) transmitter radios. Experimental results show that (i) the proposed method achieves the accuracies of 99.84% and 98.26% with eight devices in QPSK and 16QAM cases, as well as the accuracy of 92.42% with six USRP devices (ii) the proposed method exhibits superior classification performance in comparison to some existing RFFI methods, leading to a significant accuracy improvement of at least 38.33%.
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