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1.
Cell Biosci ; 12(1): 63, 2022 May 17.
Article in English | MEDLINE | ID: covidwho-1846866

ABSTRACT

BACKGROUND: Neutralizing antibodies are approved drugs to treat coronavirus disease-2019 (COVID-19) patients, yet mutations in severe acute respiratory syndrome coronavirus (SARS-CoV-2) variants may reduce the antibody neutralizing activity. New monoclonal antibodies (mAbs) and antibody remolding strategies are recalled in the battle with COVID-19 epidemic. RESULTS: We identified multiple mAbs from antibody phage display library made from COVID-19 patients and further characterized the R3P1-E4 clone, which effectively suppressed SARS-CoV-2 infection and rescued the lethal phenotype in mice infected with SARS-CoV-2. Crystal structural analysis not only explained why R3P1-E4 had selectively reduced binding and neutralizing activity to SARS-CoV-2 variants carrying K417 mutations, but also allowed us to engineer mutant antibodies with improved neutralizing activity against these variants. Thus, we screened out R3P1-E4 mAb which inhibits SARS-CoV-2 and related mutations in vitro and in vivo. Antibody engineering improved neutralizing activity of R3P1-E4 against K417 mutations. CONCLUSION: Our studies have outlined a strategy to identify and engineer neutralizing antibodies against SARS-CoV-2 variants.

2.
Metabolism ; 131: 155181, 2022 06.
Article in English | MEDLINE | ID: covidwho-1747686

ABSTRACT

OBJECTIVE: Obesity is an established risk factor for higher SARS-CoV-2 viral loads, severe COVID-19 pneumonia requiring hospitalization, and worse outcomes. However, the underlying mechanisms for the increased risk are not well understood. SARS-CoV-2 is a respiratory virus with the primary route of entry through the lungs, where the Spike protein of SARS-CoV-2 binds to the ACE2 receptor on pneumocytes. Lung surfactant produced by type II pneumocytes plays a major role in respiratory defense against infections. Surfactant predominantly contains lipids, especially phosphatidylcholines (PC), and obesity is characterized by aberrant lipid metabolism. We hypothesized that altered lipid composition in lung surfactant in obesity may promote SARS-CoV-2 infection, leading to severe COVID-19 disease. METHODS: Lipidomic analysis of lung tissue and bronchoalveolar lavage fluid (BALF) was performed using LC-MS/MS. The effects of PCs on SARS-CoV-2 pseudovirus infection were studied in HEK293T cells with ACE2 overexpression and in Vero-E6 cells with endogenous ACE2 expression. For the cell-cell fusion assay, HEK293T-ACE2 and HEK293T expressing SARS-CoV-2 Spike/eGFP were used as the target and effector cells, respectively. RESULTS: Lipidomic analysis revealed that myristic acid-containing dimyristoyl-PC (DMPC) and palmitoylmyristoyl-PC (PMPC) were reduced in lung tissue and BALF from high fat diet-induced obese mice. DMPC and PMPC markedly inhibited wild type and D614G mutant SARS-CoV-2 infection in HEK293T-ACE2 and Vero-E6 cells. Feeding obese mice with trimyristin, the triglycerides of myristic acid, increased DMPC and PMPC levels in lung surfactant. Lipid extract from BALF of trimyristin-treated obese mice mitigated the elevated wild type and D614G mutant SARS-CoV-2 infection. The inhibitory effects of DMPC and PMPC on SARS-CoV-2 infection were reversed by cholesterol. CONCLUSIONS: The reduced DMPC and PMPC in lung surfactant may promote SARS-CoV-2 infection. Increasing DMPC and PMPC in lung surfactant could be an innovative strategy for preventing and treating severe COVID-19 disease in obesity.


Subject(s)
COVID-19 , Angiotensin-Converting Enzyme 2 , Animals , Chromatography, Liquid , Dimyristoylphosphatidylcholine/metabolism , HEK293 Cells , Humans , Lung , Mice , Myristic Acid/metabolism , Obesity/metabolism , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/metabolism , Surface-Active Agents/metabolism , Tandem Mass Spectrometry
3.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-318211

ABSTRACT

How to contain the spread of the COVID-19 virus is a major concern for most countries. As the situation continues to change, various countries are making efforts to reopen their economies by lifting some restrictions and enforcing new measures to prevent the spread. In this work, we review some approaches that have been adopted to contain the COVID-19 virus such as contact tracing, clusters identification, movement restrictions, and status validation. Specifically, we classify available techniques based on some characteristics such as technology, architecture, trade-offs (privacy vs utility), and the phase of adoption. We present a novel approach for evaluating privacy using both qualitative and quantitative measures of privacy-utility assessment of contact tracing applications. In this new method, we classify utility at three (3) distinct levels: no privacy, 100% privacy, and at k where k is set by the system providing the utility or privacy.

4.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-315333

ABSTRACT

Background: Since the first case of a coronavirus disease 2019 (COVID-19) infection pneumonia was detected in Wuhan, China, a series of confirmed cases of the COVID-19 were found in Southwest China. The aim of this study was to describe the imaging manifestations of hospitalized patients with confirmed COVID-19 infection in southwest China. Methods: In this retrospective study, data were collected from 131 patients with confirmed coronavirus disease 2019 (COVID-19) from 3 Chinese hospitals. Their common clinical manifestations, as well as characteristics and evolvement features of chest CT images, were analyzed. Results: A total of 100 (76%) patients had a history of close contact with people living in Wuhan , Hubei. The clinical manifestations of COVID-19 included cough, fever. Most of the lesions identified in chest CT images were multiple lesions of bilateral lungs, lesions were more localized in the peripheral lung, 109 (83%) patients had more than two lobes involved, 20 (15%) patients presented with patchy ground glass opacities, patchy ground glass opacities and consolidation of lesions co-existing in 61 (47%) cases. Complications such as pleural thickening, hydrothorax, pericardial effusion, and enlarged mediastinal lymph nodes were detected but only in rare cases. For the follow-up chest CT examinations (91 cases), We found 66 (73%) cases changed very quickly, with an average of 3.5 days, 25 cases (27%) presented absorbed lesions, progression was observed in 41 cases (46%), 25 (27%) cases showed no significant changes. Conclusion: Chest CT plays an important role in diagnosing COVID-19. The imaging pattern of multifocal peripheral ground glass or mixed consolidation is highly suspicious of COVID-19, that can quickly change over a short period of time.

5.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-313875

ABSTRACT

The COVID-19 pandemic has prompted technological measures to control the spread of the disease. Private contact tracing (PCT) is one of the promising techniques for the purpose. However, the recently proposed Bluetooth-based PCT has several limitations in terms of functionality and flexibility. The existing systems are only able to detect direct contact (i.e., human-human contact), but cannot detect indirect contact (i.e., human-object, such as the disease transmission through surface). Moreover, the rule of risky contact cannot be flexibly changed with the environmental situation and the nature of the virus. In this paper, we propose a secure and efficient trajectory-based PCT system using trusted hardware. We formalize trajectory-based PCT as a generalization of the well-studied Private Set Intersection (PSI), which is mostly based on cryptographic primitives and thus insufficient. We solve the problem by leveraging trusted hardware such as Intel SGX and designing a novel algorithm to achieve a secure, efficient and flexible PCT system. Our experiments on real-world data show that the proposed system can achieve high performance and scalability. Specifically, our system (one single machine with Intel SGX) can process thousands of queries on 100 million records of trajectory data in a few seconds.

6.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-313874

ABSTRACT

Existing Bluetooth-based Private Contact Tracing (PCT) systems can privately detect whether people have come into direct contact with COVID-19 patients. However, we find that the existing systems lack functionality and flexibility, which may hurt the success of the contact tracing. Specifically, they cannot detect indirect contact (e.g., people may be exposed to coronavirus because of used the same elevator even without direct contact);they also cannot flexibly change the rules of "risky contact", such as how many hours of exposure or how close to a COVID-19 patient that is considered as risk exposure, which may be changed with the environmental situation. In this paper, we propose an efficient and secure contact tracing system that enables both direct contact and indirect contact. To address the above problems, we need to utilize users' trajectory data for private contact tracing, which we call trajectory-based PCT. We formalize this problem as Spatiotemporal Private Set Intersection. By analyzing different approaches such as homomorphic encryption that could be extended to solve this problem, we identify that Trusted Execution Environment (TEE) is a proposing method to achieve our requirements. The major challenge is how to design algorithms for spatiotemporal private set intersection under limited secure memory of TEE. To this end, we design a TEE-based system with flexible trajectory data encoding algorithms. Our experiments on real-world data show that the proposed system can process thousands of queries on tens of million records of trajectory data in a few seconds.

7.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-308312

ABSTRACT

Background: Coronavirus disease 2019 (COVID-19) has spread globally and resulted in the COVID-19 pandemic worldwide. To depict the psychological and behavioral responses, and knowledge of nursing interns who are facing the COVID-19 epidemic in China, we conducted a knowledge, attitude, and practice (KAP) survey using a convenience sample in the First People’s Hospital of Lianyungang, Kangda College of Nanjing Medical University, Jiangsu Province, China. Methods: : A combination of a face-to-face questionnaire survey and an online survey was used for nursing interns from 12 Chinese universities. The Symptom Checklist 90 was used to investigate anxiety and depression of the nursing interns during the COVID-19 epidemic. Self-designed questionnaires were used to investigate behavioral responses, COVID-19-related knowledge, and preventive measures. Results: : During the COVID-19 epidemic, the mean score of anxiety of 237 surveyed nursing interns were not statistically significantly different with that of the Chinese norm (1.42 vs. 1.39, P = 0.354). However, the mean score of depression of them were lower than that of the Chinese norm (1.22 vs. 1.50, P < 0.001). However, no statistically significant difference in the anxiety or depression was found between demographic subgroups. The most common way for the nursing interns to seek for help was asking for instructor or other medical professionals (89.45%). When the nursing interns had suspected symptoms, they will most likely go to the hospital for treatment (97.89%). The nursing interns have good knowledge regarding the origin and prevention of COVID-19 (correct percentage > 94%), however less knowledge regarding treatment and incubation (correct percentage < 10%). Conclusion: The nursing interns showed relative lower depression in the face of COVID-19 public health emergencies, and took proper preventive measures during the epidemic, however, were lack of certain epidemiology knowledge about COVID-19.

8.
EuropePMC;
Preprint in English | EuropePMC | ID: ppcovidwho-326084

ABSTRACT

Existing Bluetooth-based Private Contact Tracing (PCT) systems can privately detect whether people have come into direct contact with COVID-19 patients. However, we find that the existing systems lack functionality and flexibility, which may hurt the success of the contact tracing. Specifically, they cannot detect indirect contact (e.g., people may be exposed to coronavirus because of used the same elevator even without direct contact);they also cannot flexibly change the rules of "risky contact", such as how many hours of exposure or how close to a COVID-19 patient that is considered as risk exposure, which may be changed with the environmental situation. In this paper, we propose an efficient and secure contact tracing system that enables both direct contact and indirect contact. To address the above problems, we need to utilize users' trajectory data for private contact tracing, which we call trajectory-based PCT. We formalize this problem as Spatiotemporal Private Set Intersection. By analyzing different approaches such as homomorphic encryption that could be extended to solve this problem, we identify that Trusted Execution Environment (TEE) is a proposing method to achieve our requirements. The major challenge is how to design algorithms for spatiotemporal private set intersection under limited secure memory of TEE. To this end, we design a TEE-based system with flexible trajectory data encoding algorithms. Our experiments on real-world data show that the proposed system can process thousands of queries on tens of million records of trajectory data in a few seconds.

9.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-325193

ABSTRACT

Objectives: To investigated the relationship between the neutrophil-to-lymphocyte ratio (NLR) and the severity of lung injury in corona virus disease 2019 (COVID-19) patients.Methods The clinical data, laboratory examination, and chest computed tomography (CT) findings of 167 patients with confirmed COVID-19 admitted to 5 hospitals in Chongqing, China from January 2020 to February 2020 were retrospectively reviewed. According to the diagnostic criteria sixth edition of the “Diagnosis and Treatment of New Coronavirus Pneumonitis” published by the China National Health Commission, the patients were stratified by the severity of their illness to 3 groups: mild (n = 17), moderate (n = 119), or severe (n = 31).Results Differences of the NLR among the three groups and between each of the groups were significant (all p < 0.001). The NLR and CT severity score were positively correlated (r = 0.823, p < 0.001). Receiver operating characteristic (ROC) curve analysis found that NLR had diagnostic and prognostic value in COVID-19 patients with either negative or positive CT results. The area under curve (AUC) was 0.819 (95% CI: 0.729-0.910, p < 0.001), the sensitivity was 61.3%, specificity was 94.1%, and the optimal NLR cutoff value was 3.634.Conclusion NLR reflected the degree of lung injury and predicted the progression of COVID-19. NLR is a low-cost, convenient, bedside alternative to chest CT scanning to indicate the severity of lung injury in patients with COVID-19, especially in relatively underdeveloped areas.

10.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-323878

ABSTRACT

Background: Many of severe COVID-19 patients are admitted to the hospital or even to the Intensive Care Unit(ICU). The present study was aimed to investigated the risk factors in death from COVID-19. Methods: In this retrospective study, all inpatients confirmed severe or critical COVID-19 from two tertiary hospital in Huangshi were included, who had been discharged or died by March19,2020. Demographic,clinical,treatment,laboratory data and information were extracted from electronic medical records and compared between survivors group and non-survivors group. The univariable and multivariable logistic regression analysis was used to analyze the risk factors associated with in-hospital death. Results: 81 patients were included in this study, of whom 55 were discharged and 26 died in hospital. In all patients, 36(44.4%) patients had comorbidity, including hypertension(27[33.3%]), diabetes(11[13.6%]) and coronary heart disease (CHD)(11[13.6%]), and 16(19.8%) patients accompanied with more than 2 kinds of underlying diseases. The proportion of CHD in non-survivors group was significantly higher than that in survivors group(26.9% vs 7.3%, P=0.032), but there were no differences in hypertension, diabetes and COPD between the non-survivors group and the survivors group. Multivariable logistic regression analysis showed increasing odds of in-hospital death associated with aspartate aminotransferase(AST) and invasive mechanical ventilation (IMV) (P<0.001)(P=0.017). Conclusions: : Invasive Mechanical Ventilation may contribute to mortality of severe/critical COVID-19 pneumonia, and with higher AST at admission was one of the indicators of poor prognosis. Trial registration: Chinese Clinical Trial Registration;ChiCTR2000031494;Registered 02 April 2020;http:// www.medresman.org

11.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-322402

ABSTRACT

Recently, differential privacy (DP) is getting attention as a privacy definition when publishing statistics of a dataset. However, when answering a decision problem with a DP mechanism, it causes a two-sided error. This characteristic of DP is not desirable when publishing risk information such as concerning COVID-19. This paper proposes relaxing DP to mitigate the limitation and improve the utility of published information. First, we define a policy that separates information into sensitive and non-sensitive. Then, we define asymmetric differential privacy (ADP) that provides the same privacy guarantee as DP to sensitive information. This partial protection induces asymmetricity in privacy protection to improve utility and allow a one-sided error mechanism. Following ADP, we propose two mechanisms for two tasks based on counting query with utilizing these characteristics: top-$k$ query and publishing risk information of viruses with an accuracy guarantee. Finally, we conducted experiments to evaluate proposed algorithms using real-world datasets and show their practicality and improvement of the utility, comparing state-of-the-art algorithms.

12.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-321462

ABSTRACT

Background: COVID-19 is a highly infectious respiratory disease. No therapeutics have yet been proven effective for treating severe COVID-19. Objectives: To determine whether human umbilical cord mesenchymal stem cell infusion may be effective and safe for the treatment of severe COVID-19. Methods: Patients with severe COVID-19 were randomly divided into 2 groups: the standard treatment group and the standard treatment plus hUC-MSC infusion group. The incidence of progression from severe to critical illness, 28-day mortality, clinical symptom improvement, time to clinical symptom improvement, hematologic indicators including C-reactive protein, lymphocyte number, and interleukin 6, and imaging changes were observed and compared between the two groups. Measurements and Main Results: The incidence of progression from severe to critical illness and the 28-day mortality rate were 0 in the hUC-MSC treatment group, while 4 patients in the control group deteriorated to critical condition and received invasive ventilation;3 of them died, and the 28-day mortality rate was 10.34% . In the hUC-MSC treatment group, the time to clinical improvement was shorter than that in the control group. Clinical symptoms of weakness and fatigue, shortness of breath, and low oxygen saturation obviously improved beginning on the third day of stem cell infusion and reached a significant difference on day 7. CRP and IL-6 levels were significantly lower from day 3 of infusion, the time for the lymphocyte count to return to the normal range was significantly faster, and lung inflammation absorption was significantly shorter on CT imaging in the hUC-MSC group than in the control group. Conclusions: Intravenous transplantation of hUC-MSCs is a safe and effective method that can be considered a salvage and priority treatment option for severe COVID-19.

13.
Molecules ; 27(3)2022 Jan 21.
Article in English | MEDLINE | ID: covidwho-1649047

ABSTRACT

Since the outbreak of SARS-CoV-2, numerous compounds against COVID-19 have been derived by computer-aided drug design (CADD) studies. They are valuable resources for the development of COVID-19 therapeutics. In this work, we reviewed these studies and analyzed 779 compounds against 16 target proteins from 181 CADD publications. We performed unified docking simulations and neck-to-neck comparison with the solved co-crystal structures. We computed their chemical features and classified these compounds, aiming to provide insights for subsequent drug design. Through detailed analyses, we recommended a batch of compounds that are worth further study. Moreover, we organized all the abundant data and constructed a freely available database, DrugDevCovid19, to facilitate the development of COVID-19 therapeutics.


Subject(s)
Antiviral Agents/chemistry , COVID-19/drug therapy , Drug Design , Antiviral Agents/therapeutic use , Databases, Pharmaceutical , Drug Development , Humans , Models, Molecular , Molecular Docking Simulation
14.
Social Behavior & Personality: an international journal ; 50(1):1-13, 2022.
Article in English | Academic Search Complete | ID: covidwho-1630811

ABSTRACT

We studied the prediction mechanism of the effects of the crowding perception, risk awareness, and safety perception of subway passengers on their behavioral decision making in the context of COVID-19 as a public health safety crisis. We conducted a survey of 305 subway passengers in Zhejiang Province, China, and used structural equation modeling for data analysis. The results show that the crowding perception of the passengers did not directly predict their behavioral decision making. Rather, risk awareness and safety perception played a chain mediating role between the crowding perception and behavioral decision making of passengers. We further explored the theoretical and practical implications of our findings. [ FROM AUTHOR] Copyright of Social Behavior & Personality: an international journal is the property of Society for Personality Research 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.)

15.
Infect Drug Resist ; 14: 5395-5401, 2021.
Article in English | MEDLINE | ID: covidwho-1581593

ABSTRACT

PURPOSE: This study detects SARS-CoV-2 in the ocular surface through one-step reverse-transcription droplet digital PCR (one-step RT-ddPCR) and evaluates the possibility of the ocular surface as a possible transmission route. METHODS: A single-center prospective observational study was designed to investigate the viral loads in ocular surface. Specimens including the conjunctival swabs, nasopharyngeal swabs and blood were synchronously collected at a single time point for all COVID-19 patients. SARS-CoV-2 loads in nasopharyngeal swabs were tested by real-time polymerase chain reaction (PCR); the blood samples and conjunctival swabs were tested by real-time PCR and one-step RT-ddPCR. RESULTS: Sixty-eight COVID-19 patients confirmed by nasopharyngeal real-time PCR were recruited. In the single time point test, 40 cases showed positive SARS-CoV-2 detection in either the blood, tears, or nasopharynx, of which four cases were triple-positive, 10 were dual-positive, and 26 were single-positive. The positive rate of nasopharyngeal swab real-time PCR test was 22.1% (15/68). The positive rate of blood and conjunctival swabs by one-step RT-ddPCR was 38.2% (26/68) and 25% (17/68), respectively, whereas real-time PCR was all negative. Positive conjunctival swabs were significantly correlated with positive nasopharyngeal swabs (P = 0.028). The sampling lags from illness onset to sampling day in 3 out of 4 triple-positive patients and in 9 out of 10 dual-positive patients were respectively less than 9 days and less than 20 days. CONCLUSION: Our results indicate that the positive rate of SARS-CoV-2 on the ocular surface is much higher than expected. Transmission possibility through the ocular surface may be greatly underestimated.

16.
Curr Med Imaging ; 17(11): 1316-1323, 2021.
Article in English | MEDLINE | ID: covidwho-1574962

ABSTRACT

BACKGROUND: Though imaging manifestations of COVID-19 and other types of viral pneumonia are similar, their clinical treatment methods differ. Accurate, non-invasive diagnostic methods using CT imaging can help develop an optimal therapeutic regimen for both conditions. OBJECTIVE: To compare the initial CT imaging features in COVID-19 with those in other types of viral pneumonia. METHODS: Clinical and imaging data of 51 patients with COVID-19 and 69 with other types of viral pneumonia were retrospectively studied. All significant imaging features (Youden index >0.3) were included for constituting the combined criteria for COVID-19 diagnosis, composed of two or more imaging features with a parallel model. McNemar's chi-square test or Fisher's exact test was used to compare the validity indices (sensitivity and specificity) among various criteria. RESULTS: Ground glass opacities (GGO) dominated density, peripheral distribution, unilateral lung, clear margin of lesion, rounded morphology, long axis parallel to the pleura, vascular thickening, and crazy-paving pattern were more common in COVID-19 (p <0.05). Consolidation-dominated density, both central and peripheral distributions, bilateral lung, indistinct margin of lesion, tree-inbud pattern, mediastinal or hilar lymphadenectasis, pleural effusion, and pleural thickening were more common in other types of viral pneumonia (p < 0.05). GGO-dominated density or long axis parallel to the pleura (with the highest sensitivity), and GGO-dominated density or long axis parallel to the pleura or vascular thickening (with the highest specificity) are well combined criteria of COVID-19. CONCLUSION: The initial CT imaging features are helpful for the differential diagnosis of COVID-19 and other types of viral pneumonia.


Subject(s)
COVID-19 , COVID-19 Testing , Humans , Retrospective Studies , SARS-CoV-2 , Tomography, X-Ray Computed
17.
Front Psychiatry ; 12: 720722, 2021.
Article in English | MEDLINE | ID: covidwho-1560797

ABSTRACT

Nature exposure is known to promote life satisfaction and well-being, and indirect exposure through windows is likely to benefit isolated populations. However, whether such type of exposure can benefit prisoners, the extremely isolated population, is unknown. In the current study, we investigated 326 male prisoners from three prisons in southwest China. Psychological variables including depression, anxiety, loneliness, distress tolerance, life satisfaction, and well-being were measured using the Patient Health Questionnaire-9 (PHQ-9), Generalized Anxiety Disorder Scale (GAD-7), short-form UCLA Loneliness Scale (ULS-6), Distress Tolerance Scale (DTS), Satisfaction with Life Scale (SWLS), and 5-item World Health Organization Well-Being Index (WHO-5), respectively. Structural equation modeling was employed to identify the pathways from the visibility of nature through windows to prisoners' life satisfaction and well-being. Our results demonstrated that visibility of nature promoted the frequency and duration of viewing nature through windows. The frequency directly affected well-being, but the duration did not effectively affect any measured variables. The visibility of nature enhanced life satisfaction mainly via direct effects but enhanced well-being mainly via indirect effects. Regarding the indirect pathways, the visibility of nature increased distress tolerance and thus reduced loneliness and mental health problems. The reduced mental health problem, in turn, promoted life satisfaction and well-being. Our findings suggest that nature exposure through windows is effective in enhancing prisoners' life satisfaction and well-being. The policymaker may need to consider nature-based solutions such as indirect nature exposure in prions to benefit isolated populations.

18.
Nat Methods ; 18(6): 627-630, 2021 06.
Article in English | MEDLINE | ID: covidwho-1550331

ABSTRACT

We introduce the TRUST4 open-source algorithm for reconstruction of immune receptor repertoires in αß/γδ T cells and B cells from RNA-sequencing (RNA-seq) data. Compared with competing methods, TRUST4 supports both FASTQ and BAM format and is faster and more sensitive in assembling longer-even full-length-receptor repertoires. TRUST4 can also call repertoire sequences from single-cell RNA-seq (scRNA-seq) data without V(D)J enrichment, and is compatible with both SMART-seq and 5' 10x Genomics platforms.


Subject(s)
Algorithms , Receptors, Immunologic/genetics , Sequence Analysis, RNA/methods , Single-Cell Analysis/methods , Receptors, Antigen, B-Cell/genetics , Receptors, Antigen, T-Cell/genetics , V(D)J Recombination
19.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-292390

ABSTRACT

Since the outbreak of SARS-CoV-2, numerous compounds against COVID-19 have been derived by computer-aided drug design (CADD) studies. They are valuable resources for the development of COVID-19 therapeutics. In this work, we reviewed these studies and analyzed 779 compounds against 16 target proteins from 181 CADD publications. We performed unified docking simulations and neck-to-neck comparison with the solved co-crystal structures. We computed their chemical features and classified these compounds aiming to provide insights for subsequent drug design. Through detailed analyses, we recommended a batch of compounds that are worth further study. Moreover, we organized all the abundant data and constructed a freely available database, DrugDevCovid19 (http://clab.labshare.cn/covid/php/index.php), to facilitate the development of COVID-19 therapeutics.

20.
Community Dent Oral Epidemiol ; 49(6): 557-564, 2021 12.
Article in English | MEDLINE | ID: covidwho-1494632

ABSTRACT

OBJECTIVE: The impact of the worldwide COVID-19 pandemic on the dental community is evident. Dental education programmes and academic activities have suffered from the ramifications of the pandemic. This study aimed to depict the impacts of the COVID-19 epidemic on the clinical services and academic activities in the department of stomatology of a tertiary hospital in Wuhan, China. METHODS: We obtained historical data of the Department of Stomatology from the Health Information System of the General Hospital of Central Theater Command, Wuhan, China between January 2018 and June 2020. Mean, standard deviation and median with interquartile range were used to summarize the variables. Line plots were used to illustrate the temporal trend. The Kruskal-Wallis equality-of-populations rank test was used to compare the difference between groups. RESULTS: A significant decrease was noted in the monthly average number of patients seeking outpatient services for the year 2020, which were decreased by two-thirds from 2018 to 2020. The number of emergency cases also decreased significantly by 57.6% in 2020. The monthly number of teaching hours decreased from 3.8 ± 1.5 in 2018 and 4.7 ± 1.4 in 2019 to 1.7 ± 1.9 in 2020. The number of interns also decreased by more than 77.0% in 2020. CONCLUSIONS: The impacts of COVID-19 in the stomatology clinic were significant with notable decreases in clinical services and education offered to the stomatology students. There is a need to find solutions to keep as many dental professionals as needed remaining on the frontline of oral health care.


Subject(s)
COVID-19 , Oral Medicine , China/epidemiology , Hospitals, General , Humans , Pandemics , SARS-CoV-2 , Tertiary Care Centers
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