nCoVDock2: a docking server to predict the binding modes between COVID-19 targets and its potential ligands.

The rapid emergence of SARS-CoV-2 variants with multi-sites mutations is considered as a major obstacle for the development of drugs and vaccines. Although most of the functional proteins essential for SARS-CoV-2 have been determined, the understanding of the COVID-19 target-ligand interactions remains a key challenge. The old version of this COVID-19 docking server was built in 2020, and free and open to all users. Here, we present nCoVDock2, a new docking server to predict the binding modes for targets from SARS-CoV-2. First, the new server supports more targets. We replaced the modeled structures with newly resolved structures and added more potential targets of COVID-19, especially for the variants. Second, for small molecule docking, Autodock Vina was upgraded to the latest version 1.2.0, and a new scoring function was added for peptide or antibody docking. Third, the input interface and molecular visualization were updated for a better user experience. The web server, together with an extensive help and tutorial, are freely available at: https://ncovdock2.schanglab.org.cn.

Prediction of atmospheric pollutants in urban environment based on coupled deep learning model and sensitivity analysis.

Accurate and efficient predictions of pollutants in the atmosphere provide a reliable basis for the scientific management of atmospheric pollution. This study develops a model that combines an attention mechanism, convolutional neural network (CNN), and long short-term memory (LSTM) unit to predict the O3 and PM2.5 levels in the atmosphere, as well as an air quality index (AQI). The prediction results given by the proposed model are compared with those from CNN-LSTM and LSTM models as well as random forest and support vector regression models. The proposed model achieves a correlation coefficient between the predicted and observed values of more than 0.90, outperforming the other four models. The model errors are also consistently lower when using the proposed approach. Sobol-based sensitivity analysis is applied to identify the variables that make the greatest contribution to the model prediction results. Taking the COVID-19 outbreak as the time boundary, we find some homology in the interactions among the pollutants and meteorological factors in the atmosphere during different periods. Solar irradiance is the most important factor for O3, CO is the most important factor for PM2.5, and particulate matter has the most significant effect on AQI. The key influencing factors are the same over the whole phase and before the COVID-19 outbreak, indicating that the impact of COVID-19 restrictions on AQI gradually stabilized. Removing variables that contribute the least to the prediction results without affecting the model prediction performance improves the modeling efficiency and reduces the computational costs.

The Spatial-Temporal Evolution and Influencing Factors of Public Attention to 5G: Empirical Analysis Based on Baidu Index from 2011 to 2021

The development of 5G (fifth-generation wireless systems) determines the future direction of technology and economy and has received extensive public attention. Studying the changing rules of public attention to 5G can provide an important guiding significance for the sustainable development of 5G. This paper takes Baidu Index as the measurement index of 5G public attention and analyzes the spatial and temporal evolution characteristics and influencing factors of public attention to 5G from 2011 to 2021 by using the elasticity coefficient, Gini coefficient, geographical concentration index, and panel data model. The results of the study show the following. (1) The public concern to 5G is generally on the rise, but the heat has declined in the past two years. (2) The public's 5G attention shows a seasonal effect, with the highest attention in March and June. (3) The spatial difference of 5G public attention is obvious. The eastern region has a high degree of attention, the internal differences between the eastern and western regions are obvious, and the central region is relatively balanced. (4) The factors such as local economic level, education level, Internet development, and media attention have significantly affected the public focus on 5G. Also, some suggestions are made for the sustainable development of 5G and the planning of 6G (sixth-generation wireless systems).

Viral inactivation by irradiation rays.

Viral infection can lead to serious illness and death around the world, as exemplified by the spread of COVID-19. Using irradiation rays can inactive virions through ionizing and non-ionizing effect. The application of light in viral inactivation and the underlying mechanisms are reviewed by the research group of Dayong Jin from University of Technology Sydney.

The top 100 most cited papers in insomnia: A bibliometric analysis.

Objective: The number of citations to a paper represents the weight of that work in a particular area of interest. Several highly cited papers are listed in the bibliometric analysis. This study aimed to identify and analyze the 100 most cited papers in insomnia research that might appeal to researchers and clinicians. Methods: We reviewed the Web of Science (WOS) Core Collection database to identify articles from 1985 to 24 March 2022. The R bibliometric package was used to further analyze citation counts, authors, year of publication, source journal, geographical origin, subject, article type, and level of evidence. Word co-occurrence in 100 articles was visualized using VOS viewer software. Results: A total of 44,654 manuscripts were searched on the Web of Science. Between 2001 and 2021, the top 100 influential manuscripts were published, with a total citation frequency of 38,463. The top countries and institutions contributing to the field were the U.S. and Duke University. Morin C.M. was the most productive author, ranking first in citations. Sleep had the highest number of manuscripts published in the top 100 (n = 31), followed by Sleep Medicine Reviews (n = 9). The most cited manuscript (Bastien et al., Sleep Medicine, 2001; 3,384 citations) reported clinical validation of the Insomnia Severity Index (ISI) as a brief screening indicator for insomnia and as an outcome indicator for treatment studies. Co-occurrence analyses suggest that psychiatric disorders combined with insomnia and cognitive behavioral therapy remain future research trends. Conclusion: This study provides a detailed list of the most cited articles on insomnia. The analysis provides researchers and clinicians with a detailed overview of the most cited papers on insomnia over the past two decades. Notably, COVID-19, anxiety, depression, CBT, and sleep microstructure are potential areas of focus for future research.

A national risk analysis model (NRAM) for the assessment of COVID-19 epidemic.

COVID-19 has caused a critical health concern and severe economic crisis worldwide. With multiple variants, the epidemic has triggered waves of mass transmission for nearly 3 years. In order to coordinate epidemic control and economic development, it is important to support decision-making on precautions or prevention measures based on the risk analysis for different countries. This study proposes a national risk analysis model (NRAM) combining Bayesian network (BN) with other methods. The model is built and applied through three steps. (1) The key factors affecting the epidemic spreading are identified to form the nodes of BN. Then, each node can be assigned state values after data collection and analysis. (2) The model (NRAM) will be built through the determination of the structure and parameters of the network based on some integrated methods. (3) The model will be applied to scenario deduction and sensitivity analysis to support decision-making in the context of COVID-19. Through the comparison with other models, NRAM shows better performance in the assessment of spreading risk at different countries. Moreover, the model reveals that the higher education level and stricter government measures can achieve better epidemic prevention and control effects. This study provides a new insight into the prevention and control of COVID-19 at the national level.

The application of network agenda setting model during the COVID-19 pandemic based on latent dirichlet allocation topic modeling

Based on Network Agenda Setting Model, this study collected 42,516 media reports from Party Media, commercial media, and We Media of China during the COVID-19 pandemic. We trained LDA models for topic clustering through unsupervised machine learning. Questionnaires (N = 470) and social network analysis methods were then applied to examine the correlation between media network agendas and public network agendas in terms of explicit and implicit topics. The study found that the media reports could be classified into 14 topics by the LDA topic modeling, and the three types of media presented homogeneity in the topics of their reports, yet had their own characteristics;there was a significant correlation between the media network agenda and the public network agenda, and the We Media reports had the most prominent effect on the public network agenda;the correlation between the media agenda and the implicit public agenda was higher than that of the explicit public agenda. Overall, findings showed a significant correlation between network agendas among different media.

Frailty is an independent determinant of COVID-19 vaccine hesitancy in the elderly: a cross-sectional study.

COVID-19 vaccines have become an important hope for slowing down or stopping the pandemic. As the population ages, older adults will comprise a greater proportion of the vaccinated population. We aimed to assess influencing factors of COVID-19 vaccine hesitancy in older adults. For this aim, We conducted a cross-sectional study on a questionnaire survey of the elderly over 65 years living in the community of Haikou City from August 1st to September 30th, 2021. Univariate and multivariate Logistic regression analyses were performed to identify factors related to vaccine hesitancy. We analyzed completed questionnaires from 225 respondents (42.2% women, mean age 73.4±6.2 years). There were 99 people in the vaccine hesitation group and 126 people in the vaccine acceptance group, the incidence of vaccine hesitation in the elderly population is about44%（99/225）. The incidence of frailty in the vaccine hesitation group was much higher than that in the vaccine trust group (62.63 vs. 30.95%, P＜0.001). The risk factors of vaccine hesitancy in the elderly aged 70-75years and over 75 years were 2.987 times and 3.587 times higher than that in the population aged 65-70 years (OR=2.987,95%CI: 1.424-6.265, P＜0.001; OR=3.587,95% CI:1.804-7.131, P＜0.001). Frailty is also an independent risk factor of vaccine hesitancy in the elderly population (OR=2.624,95%CI: 1.447-4.757, P＜0.001). Then the vaccination rate of the COVID-19 vaccine is far from reaching the requirements of herd immunity, and more flexible and comprehensive efforts are needed to increase the vaccination willingness of the frail elderly.

Early prediction of noninvasive ventilation failure after extubation: development and validation of a machine-learning model.

BACKGROUND: Noninvasive ventilation (NIV) has been widely used in critically ill patients after extubation. However, NIV failure is associated with poor outcomes. This study aimed to determine early predictors of NIV failure and to construct an accurate machine-learning model to identify patients at risks of NIV failure after extubation in intensive care units (ICUs). METHODS: Patients who underwent NIV after extubation in the eICU Collaborative Research Database (eICU-CRD) were included. NIV failure was defined as need for invasive ventilatory support (reintubation or tracheotomy) or death after NIV initiation. A total of 93 clinical and laboratory variables were assessed, and the recursive feature elimination algorithm was used to select key features. Hyperparameter optimization was conducted with an automated machine-learning toolkit called Neural Network Intelligence. A machine-learning model called Categorical Boosting (CatBoost) was developed and compared with nine other models. The model was then prospectively validated among patients enrolled in the Cardiac Surgical ICU of Zhongshan Hospital, Fudan University. RESULTS: Of 929 patients included in the eICU-CRD cohort, 248 (26.7%) had NIV failure. The time from extubation to NIV, age, Glasgow Coma Scale (GCS) score, heart rate, respiratory rate, mean blood pressure (MBP), saturation of pulse oxygen (SpO2), temperature, glucose, pH, pressure of oxygen in blood (PaO2), urine output, input volume, ventilation duration, and mean airway pressure were selected. After hyperparameter optimization, our model showed the greatest accuracy in predicting NIV failure (AUROC: 0.872 [95% CI 0.82-0.92]) among all predictive methods in an internal validation. In the prospective validation cohort, our model was also superior (AUROC: 0.846 [95% CI 0.80-0.89]). The sensitivity and specificity in the prediction group is 89% and 75%, while in the validation group they are 90% and 70%. MV duration and respiratory rate were the most important features. Additionally, we developed a web-based tool to help clinicians use our model. CONCLUSIONS: This study developed and prospectively validated the CatBoost model, which can be used to identify patients who are at risk of NIV failure. Thus, those patients might benefit from early triage and more intensive monitoring. TRIAL REGISTRATION: NCT03704324. Registered 1 September 2018, https://register. CLINICALTRIALS: gov .

Estimation of NO2 emission strengths over Riyadh and Madrid from space from a combination of wind-assigned anomalies and machine learning technique

Nitrogen dioxide (NO2) air pollution provides valuable information for quantifying NOx emissions and exposures. This study presents a comprehensive method to estimate average tropospheric NO2 emission strengths derived from three-year (April 2018 - March 2021) TROPOMI observations by combining a wind-assigned anomaly approach and a Machine Learning (ML) method, the so-called Gradient Descent. This combined approach is firstly applied to the Saudi Arabian capital city Riyadh, as a test site, and yields a total emission rate of 1.04×1026 molec./s. The ML-trained anomalies fit very well with the wind-assigned anomalies with an R2 value of 1.0 and a slope of 0.99. Hotspots of NO2 emissions are apparent at several sites where the cement plant and power plants are located and over areas along the highways. Using the same approach, an emission rate of 1.80×1025 molec./s is estimated in the Madrid metropolitan area, Spain. Both the estimate and spatial pattern are comparable to the CAMS inventory. Weekly variations of NO2 emission are highly related to anthropogenic activities, such as the transport sector. The NO2 emissions were reduced by 24% at weekends in Riyadh, and high reductions are found near the city center and the areas along the highway. An average weekend reduction estimate of 30% in Madrid is found. The regions with dominant sources are located in the east of Madrid, where the residential areas and the Madrid-Barajas airport are located. Additionally, the NO2 emissions decreased by 21% in March-June 2020 compared to the same period in 2019 induced by the COVID-19 lockdowns in Riyadh. A much higher reduction (60%) is estimated for Madrid where a very strict lockdown policy was implemented. The high emission strengths during lockdown only persist in the residential areas and cover smaller areas during weekdays than at weekends. The spatial patterns of NO2 emission strengths during lockdown are similar to those observed at weekends in both cities. Though our analysis is limited to two cities as testing examples, the method has proved to provide reliable and consistent results. Therefore, it is expected to be suitable for other trace gases and other target regions. [ FROM AUTHOR] Copyright of Atmospheric Measurement Techniques Discussions is the property of Copernicus Gesellschaft mbH and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

Usage of compromised lung volume in monitoring steroid therapy on severe COVID-19.

BACKGROUND: Quantitative computed tomography (QCT) analysis may serve as a tool for assessing the severity of coronavirus disease 2019 (COVID-19) and for monitoring its progress. The present study aimed to assess the association between steroid therapy and quantitative CT parameters in a longitudinal cohort with COVID-19. METHODS: Between February 7 and February 17, 2020, 72 patients with severe COVID-19 were retrospectively enrolled. All 300 chest CT scans from these patients were collected and classified into five stages according to the interval between hospital admission and follow-up CT scans: Stage 1 (at admission); Stage 2 (3-7 days); Stage 3 (8-14 days); Stage 4 (15-21 days); and Stage 5 (22-31 days). QCT was performed using a threshold-based quantitative analysis to segment the lung according to different Hounsfield unit (HU) intervals. The primary outcomes were changes in percentage of compromised lung volume (%CL, - 500 to 100 HU) at different stages. Multivariate Generalized Estimating Equations were performed after adjusting for potential confounders. RESULTS: Of 72 patients, 31 patients (43.1%) received steroid therapy. Steroid therapy was associated with a decrease in %CL (- 3.27% [95% CI, - 5.86 to - 0.68, P = 0.01]) after adjusting for duration and baseline %CL. Associations between steroid therapy and changes in %CL varied between different stages or baseline %CL (all interactions, P < 0.01). Steroid therapy was associated with decrease in %CL after stage 3 (all P < 0.05), but not at stage 2. Similarly, steroid therapy was associated with a more significant decrease in %CL in the high CL group (P < 0.05), but not in the low CL group. CONCLUSIONS: Steroid administration was independently associated with a decrease in %CL, with interaction by duration or disease severity in a longitudinal cohort. The quantitative CT parameters, particularly compromised lung volume, may provide a useful tool to monitor COVID-19 progression during the treatment process. Trial registration Clinicaltrials.gov, NCT04953247. Registered July 7, 2021, https://clinicaltrials.gov/ct2/show/NCT04953247.

Spatiotemporal Characteristics and Patterns of the COVID-19 Pandemic in China: An Empirical Study Based on 413 Cities or Regions.

The global economy was stagnant and even regressed since the outbreak of COVID-19. Exploring the spatiotemporal characteristics and patterns of COVID-19 pandemic spread may contribute to more scientific and effective pandemic prevention and control. This paper attempts to investigate the spatiotemporal characteristics in cumulative confirmed COVID-19 cases, mortality, and cure rate in 413 Chinese cities or regions using the data officially disclosed by the government. The results showed that: (1) The pandemic development can be divided into five stages: early stage (sustained growth), early mid-stage (accelerated growth), mid-stage (rapid growth), late mid-stage (slow growth), and late-stage (stable disappearance); (2) the cumulative number of confirmed COVID-19 cases remained constant in Wuhan, whilst the mortality tended to rise faster from the early stage to the late-stage and the cure rate moved from the southeast to the northwest; (3) the three indicators mentioned above showed significant and positive spatial correlation. Moran's I curve demonstrated an inverted "V" trend in cumulative confirmed COVID-19 cases; the mortality curve was generally flat; the cure rate curve tended to rise. There are apparent differences in the local spatial autocorrelation pattern of the three primary indicators.

Using mobile phone big data to discover the spatial patterns of rural migrant workers’ return to work in China’s three urban agglomerations in the post-COVID-19 era

Knowing how workers return to work is a key policymaking issue for economic recovery in the post-COVID-19 era. This paper uses country-wide time-series mobile phone big data (comparing monthly and annual figures), obtained between February 2019 and October 2019 and between February 2020 and October 2020, to discover the spatial patterns of rural migrant workers? (RMWs?) return to work in China?s three urban agglomerations (UAs): the Beijing?Tianjin?Hebei Region, the Yangtze River Delta and the Pearl River Delta. Spatial patterns of RMWs? return to work and how these patterns vary with location, city level and human attribute were investigated using the fine-scale social sensing related to post-pandemic human mobility. The results confirmed the multidimensional spatiotemporal differentiations, interaction effects between variable pairs and effects of the actual situation on the changing patterns of RMWs? return to work. The spatial patterns of RMWs? return to work in China?s major three UAs can be regarded as a comprehensive and complex interaction result accompanying the nationwide population redistribution, which was affected by various hidden factors. Our findings provide crucial implications and suggestions for data-informed policy decisions for a harmonious society in the post-COVID-19 era.

Sensing of C-Reactive Protein Using an Extended-Gate Field-Effect Transistor with a Tungsten Disulfide-Doped Peptide-Imprinted Conductive Polymer Coating.

C-reactive protein (CRP) is a non-specific biomarker of inflammation and may be associated with cardiovascular disease. In recent studies, systemic inflammatory responses have also been observed in cases of coronavirus disease 2019 (COVID-19). Molecularly imprinted polymers (MIPs) have been developed to replace natural antibodies with polymeric materials that have low cost and high stability and could thus be suitable for use in a home-care system. In this work, a MIP-based electrochemical sensing system for measuring CRP was developed. Such a system can be integrated with microfluidics and electronics for lab-on-a-chip technology. MIP composition was optimized using various imprinting template (CRP peptide) concentrations. Tungsten disulfide (WS2) was doped into the MIPs. Doping not only enhances the electrochemical response accompanying the recognition of the template molecules but also raises the top of the sensing range from 1.0 pg/mL to 1.0 ng/mL of the imprinted peptide. The calibration curve of the WS2-doped peptide-imprinted polymer-coated electrodes in the extended-gate field-effect transistor platform was obtained and used for the measurement of CRP concentration in real human serum.

Mechanistic Studies of an Automated Lipid Nanoparticle Reveal Critical Pharmaceutical Properties Associated with Enhanced mRNA Functional Delivery In Vitro and In Vivo.

Recently, lipid nanoparticles (LNPs) have attracted attention due to their emergent use for COVID-19 mRNA vaccines. The success of LNPs can be attributed to ionizable lipids, which enable functional intracellular delivery. Previously, the authors established an automated high-throughput platform to screen ionizable lipids and identified that the LNPs generated using this automated technique show comparable or increased mRNA functional delivery in vitro as compared to LNPs prepared using traditional microfluidics techniques. In this study, the authors choose one benchmark lipid, DLin-MC3-DMA (MC3), and investigate whether the automated formulation technique can enhance mRNA functional delivery in vivo. Interestingly, a 4.5-fold improvement in mRNA functional delivery in vivo by automated LNPs as compared to LNPs formulated by conventional microfluidics techniques, is observed. Mechanistic studies reveal that particles with large size accommodate more mRNA per LNP, possess more hydrophobic surface, are more hemolytic, bind a larger protein corona, and tend to accumulate more in macropinocytosomes, which may quantitatively benefit mRNA cytosolic delivery. These data suggest that mRNA loading per particle is a critical factor that accounts for the enhanced mRNA functional delivery of automated LNPs. These mechanistic findings provide valuable insight underlying the enhanced mRNA functional delivery to accelerate future mRNA LNP product development.

Mesenchymal stem cell therapy for severe COVID-19.

The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has placed a global public burden on health authorities. Although the virological characteristics and pathogenesis of COVID-19 has been largely clarified, there is currently no specific therapeutic measure. In severe cases, acute SARS-CoV-2 infection leads to immune disorders and damage to both the adaptive and innate immune responses. Having roles in immune regulation and regeneration, mesenchymal stem cells (MSCs) serving as a therapeutic option may regulate the over-activated inflammatory response and promote recovery of lung damage. Since the outbreak of the COVID-19 pandemic, a series of MSC-therapy clinical trials has been conducted. The findings indicate that MSC treatment not only significantly reduces lung damage, but also improves patient recovery with safety and good immune tolerance. Herein, we summarize the recent progress in MSC therapy for COVID-19 and highlight the challenges in the field.

Tailoring glucocorticoids in patients with severe COVID-19: a narrative review.

OBJECTIVE: To discuss the pathogenesis of severe coronavirus disease 2019 (COVID-19) infection and the pharmacological effects of glucocorticoids (GCs) toward this infection. To review randomized controlled trials (RCTs) using GCs to treat patients with severe COVID-19, and investigate whether GC timing, dosage, or duration affect clinical outcomes. Finally. to discuss the use of biological markers, respiratory parameters, and radiological evidence to select patients for improved GC therapeutic precision. BACKGROUND: COVID-19 has become an unprecedented global challenge. As GCs have been used as key immunomodulators to treat inflammation-related diseases, they may play key roles in limiting disease progression by modulating immune responses, cytokine production, and endothelial function in patients with severe COVID-19, who often experience excessive cytokine production and endothelial and renin-angiotensin system (RAS) dysfunction. Current clinical trials have partially proven this efficacy, but GC timing, dosage, and duration vary greatly, with no unifying consensus, thereby creating confusion. METHODS: Publications through March 2021 were retrieved from the Web of Science and PubMed. Results from cited references in published articles were also included. CONCLUSIONS: GCs play key roles in treating severe COVID-19 infections. Pharmacologically, GCs could modulate immune cells, reduce cytokine and chemokine, and improve endothelial functions in patients with severe COVID-19. Benefits of GCs have been observed in multiple clinical trials, but the timing, dosage and duration vary across studies. Tapering as an option is not widely accepted. However, early initiation of treatment, a tailored dosage with appropriate tapering may be of particular importance, but evidence is inconclusive and more investigations are needed. Biological markers, respiratory parameters, and radiological evidence could also help select patients for specific tailored treatments.

Real-Time Task Allocation of Heterogeneous Unmanned Aerial Vehicles for Search and Prosecute Mission

In recent years, the Internet of Things (IoT) has developed rapidly after the era of computers and smart phones, which is expected to be applied to cities to improve the quality of life and realize the intelligence of smart cities. In particular, with the outbreak of coronavirus disease 2019 (COVID-19) last year, in order to reduce contact, some IoT devices, such as robots, unmanned aerial vehicles (UAVs), and unmanned vehicles, have played a great role in temperature monitoring, goods delivery, and so on. In this paper, we study the real-time task allocation problem of heterogeneous UAVs searching and delivering goods in the city. Considering the resource requirement of task and resource constraints of the UAV, when the resource of a single UAV cannot meet the requirement of the task, we propose a method of forming a UAV coalition based on contract net protocol. We analyze the coalition formation problem from two aspects: mission completion time and UAV’s energy consumption. Firstly, the mathematical model is established according to the optimization objective and condition constraints. Then, according to the established mathematical model, different coalition formation algorithms are proposed. To minimize the mission completion time, we propose a two-stage coalition formation algorithm. Aiming at minimizing the UAV’s energy consumption, it is transformed into a zero-one integer programming problem, which can be solved by the existing solver. Then, considering both mission completion time and energy consumption, we propose a coalition formation algorithm based on a resource tree. Finally, we design some simulation experiments and compare with the task allocation algorithm based on resource welfare. The simulation results show that our proposed algorithms are feasible and effective.