DE-MHAIPs: Identification of SARS-CoV-2 phosphorylation sites based on differential evolution multi-feature learning and multi-head attention mechanism

The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) around the world affects the normal lives of people all over the world. The computational methods can be used to accurately identify SARS-CoV-2 phosphorylation sites. In this paper, a new prediction model of SARS-CoV-2 phosphorylation sites, called DE-MHAIPs, is proposed. First, we use six feature extraction methods to extract protein sequence information from different perspectives. For the first time, we use a differential evolution (DE) algorithm to learn individual feature weights and fuse multi-information in a weighted combination. Next, Group LASSO is used to select a subset of good features. Then, the important protein information is given higher weight through multi-head attention. After that, the processed data is fed into long short-term memory network (LSTM) to further enhance model's ability to learn features. Finally, the data from LSTM are input into fully connected neural network (FCN) to predict SARS-CoV-2 phosphorylation sites. The AUC values of the S/T and Y datasets under 5-fold cross-validation reach 91.98% and 98.32%, respectively. The AUC values of the two datasets on the independent test set reach 91.72% and 97.78%, respectively. The experimental results show that the DE-MHAIPs method exhibits excellent predictive ability compared with other methods.

[Effect of Shugan Tiaoshen acupuncture combined with western medication on depression-insomnia comorbidity due to COVID-19 quarantine: a multi-central randomized controlled trial].

OBJECTIVE: To observe the effect of Shugan Tiaoshen acupuncture (acupuncture for soothing the liver and regulating the mentality) combined with western medication on depression and sleep quality in the patients with depression-insomnia comorbidity due to COVID-19 quarantine, and investigate the potential mechanism from the perspective of cortical excitability. METHODS: Sixty patients with depression-insomnia comorbidity due to COVID-19 quarantine were randomly divided into an acupuncture group and a sham-acupuncture group, 30 cases in each one. The patients of both groups were treated with oral administration of sertraline hydrochloride tablets. In the acupuncture group, Shugan Tiaoshen acupuncture was supplemented. Body acupuncture was applied to Yintang (GV 24+), Baihui (GV 20), Hegu (LI 4), Zhaohai (KI 6), Qihai (CV 6), etc. The intradermal needling was used at Xin (CO15), Gan (CO12) and Shen (CO10). In the sham-acupuncture group, the sham-acupuncture was given at the same points as the acupuncture group. The compensatory treatment was provided at the end of follow-up for the patients in the sham-acupuncture group. In both groups, the treatment was given once every two days, 3 times a week, for consecutive 8 weeks. The self-rating depression scale (SDS) and insomnia severity index (ISI) scores were compared between the two groups before and after treatment and 1 month after the end of treatment (follow-up) separately. The cortical excitability indexes (resting motor threshold [rMT], motor evoked potential amplitude [MEP-A], cortical resting period [CSP]) and the level of serum 5-hydroxytryptamine (5-HT) were measured before and after treatment in the two groups. RESULTS: After treatment and in follow-up, SDS and ISI scores were decreased in both groups compared with those before treatment (P<0.05), and the scores in the acupuncture group were lower than those in the sham-acupuncture group (P<0.05), and the decrease range in the acupuncture group after treatment was larger than that in the sham-acupuncture group (P<0.05). After treatment, rMT was reduced (P<0.05), while MEP-A and CSP were increased (P<0.05) in the acupuncture group compared with that before treatment. The levels of serum 5-HT in both groups were increased compared with those before treatment (P<0.05). The rMT in the acupuncture group was lower than that in the sham-acupuncture group, while MEP-A and CSP, as well as the level of serum 5-HT were higher in the acupuncture group in comparison with the sham-acupuncture group (P<0.05). CONCLUSION: Shugan Tiaoshen acupuncture combined with western medication can relieve depression and improve sleep quality in the patients with depression-insomnia comorbidity due to COVID-19 quarantine, which is probably related to rectifying the imbalanced excitatory and inhibitory neuronal functions.

Does ambient air quality standard contribute to green innovation of enterprises in China? Implications for environmental protection and public health

In the post-COVID-19 era, environmental pollution has been a serious threat to public health. Enterprises are in urgent need of enhancing green technology innovation as the main source of pollutant emissions, and it is necessary for governments to support green innovation of enterprises to reduce pollutant emissions and promote public health. In this context, this paper investigates whether the Ambient Air Quality Standard (AAQS) implemented in 2012 in China contributes to green innovation of enterprises, to provide implications for environmental protection and public health. By using panel data of Chinese A-share listed companies from 2008 to 2020, this study adopts the difference-in-difference model to analyze the policy impact of environmental regulation on green innovation of enterprises and its internal mechanism. The results show that AAQS has significantly improved the green innovation of enterprises. Furthermore, AAQS affects the green innovation of enterprises by virtue of two mechanism paths: compliance cost effect and innovation offset effect. On the one hand, AAQS leads to an increase in production costs of enterprises, thus inhibiting green innovation activities of enterprises. On the other hand, AAQS encourages enterprises to increase R&D investment in green technology, thus enhancing their green innovation. In addition, the impact of AAQS on firms' green innovation has heterogeneous characteristics. Our findings not only enrich the studies of environmental regulation and green innovation of enterprises but also provide policymakers in China and other developing countries with implications for environmental protection and public health improvement.

Targeting autophagy regulation in NLRP3 inflammasome-mediated lung inflammation in COVID-19.

Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Emerging evidence indicates that the NOD-, LRR- and pyrin domain-containing protein 3 (NLRP3) inflammasome is activated, which results in a cytokine storm at the late stage of COVID-19. Autophagy regulation is involved in the infection and replication of SARS-CoV-2 at the early stage and the inhibition of NLRP3 inflammasome-mediated lung inflammation at the late stage of COVID-19. Here, we discuss the autophagy regulation at different stages of COVID-19. Specifically, we highlight the therapeutic potential of autophagy activators in COVID-19 by inhibiting the NLRP3 inflammasome, thereby avoiding the cytokine storm. We hope this review provides enlightenment for the use of autophagy activators targeting the inhibition of the NLRP3 inflammasome, specifically the combinational therapy of autophagy modulators with the inhibitors of the NLRP3 inflammasome, antiviral drugs, or anti-inflammatory drugs in the fight against COVID-19.

Strategies for screening, occupational prevention, and management of COVID-19 in outpatient clinics in Shandong

Objective We hope to analyze the information of outpatients in a tertiary care hospital during the epidemic of COVID-19, so as to formulate effective regulations for the prevention and control of COVID-19. Methods We collected information from outpatients from January 28, 2020 to March 2, 2020 and performed the statistical analysis. Results During the study period, there were more than 60,000 outpatients. Among them, 404 patients with a body temperature above 37.3°C who had not been to Wuhan and had no contact with people from Wuhan. There were 8 people who had contact with people from Wuhan, such as 4 people with fever, 3 people with normal body temperature but cough symptoms, and 1 person with normal body temperature and no other discomfort. There were 2 patients with high body temperature from the epidemic area in Wuhan, and one novel Coronavirus patient was confirmed as the final result. Conclusion During the COVID-19 pandemic, outpatient medical staff should enhance their awareness of protection, hospitals should standardize the outpatient COVID-19 prevention and control system, improve the prevention and emergency system, and reduce occupational exposure hazards and the occurrence of post-exposure infections.

Traditional Chinese Medicine in Treating Children With Coronavirus Disease 2019: A Scoping Review

Coronavirus disease 2019 (COVID-19) is currently widely spread across the world. Traditional Chinese Medicine (TCM) plays an important role in the overall treatment process. As a special group of population, the treatment outcome of children with COVID-19 has attracted much attention. Our study summarizes the current situation of TCM treatment of children with COVID-19. The results showed that TCM displayed a positive role in the treatment process, and that no significant adverse reactions were found. Our findings provide analytical evidence for the efficacy and safety of TCM participation in the treatment of COVID-19 in children.

Developing and Testing the Validity and Reliability of the Brief Adolescent Respiratory System Health Assessment Scale-Student Version in a Chinese Sample.

Objectives: To develop a Brief Adolescent Respiratory System Health Assessment Scale-Student Version (BARSHAS-SV) and test the validity and reliability of the scale. Methods: Considering common respiratory system diseases and respiratory system symptoms as a theoretical basis, researchers developed a Brief Adolescent Respiratory System Health Assessment Scale-Student Version-I (BARSHAS-SV-I). After six medical experts reviewed the BARSHAS-SV-I, and six adolescents tested the BARSHAS-SV-I, researchers developed an updated BARSHAS-SV-II. Researchers randomly selected two middle schools in Baoding, China. Thousand twenty nine valid questionnaires were recovered. Researchers evaluated the validity and reliability of the scale and obtained the final version of the scale (BARSHAS-SV). The exploratory factor analysis (EFA) and the confirmatory factor analysis (CFA) were used to evaluate the construct validity of the scale. The content validity index (CVI) was used to evaluate the content validity of the scale. The Cronbach's α coefficient and the mean inter-item correlation coefficient (MIIC) were used to assess the reliability of the scale. Results: BARSHAS-SV Cronbach's α = 0.910, content validity = 0.941, and factor cumulative variance contribution rate = 64.047% conducting EFA. Conducting CFA, Chi square value (χ2) = 233.806, degrees of freedom (df) = 106, Chi square value/degree of freedom (χ2/df) = 2.206, root-mean-square error of approximation (RMSEA) = 0.063, normed fit index (NFI) = 0.922, goodness of fit index (GFI) = 0.917, Tueker-Lewis index (TLI) = 0.942, comparative fit index (CFI) = 0.955, incremental fit index (IFI) = 0.956. BARSHAS-SV consisted of 4 dimensions and 17 items. Four factors were as follows: Factor 1, mild respiratory system diseases (Cronbach's α coefficient = 0.781); Factor 2, severe respiratory system diseases (Cronbach's α coefficient = 0.829); Factor 3, respiratory system symptoms (Cronbach's α coefficient = 0.835); Factor 4, treatment and recovery of respiratory system diseases (Cronbach's α coefficient = 0.845). Conclusions: BARSHAS-SV is a valid and reliable method that can be applied to assess adolescent respiratory system health status. BARSHAS-SV may help teachers and medical staff in schools to quickly and conveniently evaluate the adolescent respiratory system health status and identify respiratory issues.

Heating behavior using household air-conditioners during the COVID-19 lockdown in Wuhan: An exploratory and comparative study.

Wuhan is located in China's hot summer and cold winter (HSCW) zone, where the average temperature of the city from January to February 2020 is only 6.6 °C. This study aimed to explore and compare the air conditioner (AC) heating behavior of Wuhan residents before and after the COVID-19 lockdown. The date of commencement of the Wuhan lockdown (January 23, 2020) was considered the demarcation point to divide the AC monitoring data from the Internet of Things cloud platform into two groups; before and after Wuhan lockdown. Statistical methods were applied to analyze AC heating behavior of Wuhan residents from a total of 378 air conditioners during these two periods. The daily AC usage rate and average daily AC usage duration following the lockdown had a stronger correlation with daily outdoor temperature than that before the lockdown. AC heating behavior continued to demonstrate a part-time intermittent operation during the lockdown period, despite residents staying at home for a longer period. Trigger temperatures for occupants to turn on or adjust their AC during the lockdown period were overall 1-2 °C higher than before the lockdown. The AC heating demand in the HSCW zone has been increasing in recent years. These research results inform research on household energy demand and thermal comfort in China's HSCW zone, and provide a reference on the household behavioral changes in the occupants in the context of a lockdown as a result of the global COVID-19 pandemic.

Beneficial effect of Indigo Naturalis on acute lung injury induced by influenza A virus (preprint)

Background: Infections induced by influenza viruses, as well as coronavirus disease 19 (COVID-19) pandemic induced by severe acute respiratory coronavirus 2 (SARS-CoV-2) led to acute lung injury (ALI) and multi organ failure, during which traditional Chinese medicine (TCM) played an important role in treatment of the pandemic. The study aimed to investigate the effect of Indigo Naturalis on ALI induced by influenza A virus (IAV) in mice. Method: The anti-influenza and anti-inflammatory properties of aqueous extract of Indigo Naturalis (INAE) were evaluated in vitro . BALB/c mice inoculated intranasally with IAV (H1N1) were treated intragastrically with INAE (40, 80 and 160 mg·kg -1 /d) 2 h later for 4 or 7 days. Animal lifespan and mortality were recorded. Expression of high mobility group box-1 protein (HMGB-1) and toll-like receptor 4 (TLR4) were evaluated through immunohistological staining. Inflammatory cytokines were also monitored by ELISA. Result: INAE inhibited virus replication on Madin-Darby canine kidney (MDCK) cells and decreased nitric oxide (NO) production from lipopolysaccharide (LPS)-stimulated peritoneal macrophages in vitro . The results showed that oral administration of 160 mg/kg of INAE significantly improved the lifespan ( P < 0.01) and survival rate of IAV infected mice, improved lung injury and lowered viral replication in lung tissue ( P < 0.01). Treatment with INAE (40, 80 and 160 mg/kg) significantly increased liver weight and liver index ( P < 0.05), as well as weight and organ index of thymus and spleen at 160 mg/kg ( P < 0.05). Serum alanine transaminase (ALT) and aspartate aminotransferase (AST) levels were reduced by INAE administration ( P < 0.05). The expression of HMGB-1 and TLR4 in lung tissue were also suppressed. The increased production of myeloperoxidase (MPO) and methylene dioxyamphetamine (MDA) in lung tissue were inhibited by INAE treatment ( P < 0.05). Treatment with INAE reduced the high levels of interferon α (IFN-α), interferon β (IFN-β), monocyte chemoattractant protein-1 (MCP-1), regulated upon activation normal T cell expressed and secreted factor (RANTES), interferon induced protein-10 (IP-10), tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) ( P < 0.05), with increased production of interferon γ (IFN-γ) and interleukin-10 (IL-10) ( P < 0.05). Conclusion: The results showed that INAE alleviated IAV induced ALI in mice. The mechanisms of INAE were associated with its anti-influenza, anti-inflammatory and anti-oxidation properties. Indigo Naturalis might have clinical potential to treat ALI induced by IAV.

Household transmission of COVID-19, Shenzhen, January-February 2020 (preprint)

Coronavirus disease 2019 has led to more than three million cases globally. Since the first family cluster of COVID-19 cases identified in Shenzhen in early January, most of the local transmission occurred within household contacts. Identifying the factors associated with household transmission is of great importance to guide preventive measures.