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1.
Nature Machine Intelligence ; 2023.
Article in English | Scopus | ID: covidwho-2260047

ABSTRACT

The identification of the mechanisms by which T-cell receptors (TCRs) interact with human antigens provides a crucial opportunity to develop new vaccines, diagnostics and immunotherapies. However, the accurate prediction and recognition of TCR–antigen pairing represents a substantial computational challenge in immunology. Existing tools only learn the binding patterns of antigens from many known TCR binding repertoires and fail to recognize antigens that have never been presented to the immune system or for which only a few TCR binding repertoires are known. However, the binding specificity for neoantigens or exogenous peptides is crucial for immune studies and immunotherapy. Therefore, we developed Pan-Peptide Meta Learning (PanPep), a general and robust framework to recognize TCR–antigen binding, by combining the concepts of meta-learning and the neural Turing machine. The neural Turing machine adds external memory to avoid forgetting previously learned tasks, which is used here to accurately predict TCR binding specificity with any peptide, particularly unseen ones. We applied PanPep to various challenging clinical tasks, including (1) qualitatively measuring the clonal expansion of T cells;(2) efficiently sorting responsive T cells in tumour neoantigen therapy;and (3) accurately identifying immune-responsive TCRs in a large cohort from a COVID-19 study. Our comprehensive tests show that PanPep outperforms existing tools. PanPep also offers interpretability, revealing the nature of peptide and TCR interactions in 3D crystal structures. We believe PanPep can be a useful tool to decipher TCR–antigen interactions and that it has broad clinical applications. © 2023, The Author(s), under exclusive licence to Springer Nature Limited.

2.
Chinese Journal of Applied Clinical Pediatrics ; 37(12):893-896, 2022.
Article in Chinese | EMBASE | ID: covidwho-2256418

ABSTRACT

Objective To investigate drug resistance gene in Mycoplasma pneumoniae (MP) and the distribution of 13 respiratory pathogens in bronchoalveolar lavage fluid(BALF) of children with Mycoplasma pneumoniae pneumonia(MPP). Methods A total of 100 BALF of children with MPP in Peking University Third Hospital and Peking University First Hospital from January 2018 to January 2019 were collected. Fluorogenic quantitative PCR was used to detect nucleic acid and it's drug resistance gene of MP and multiple PCR method was adopted to detect influenza A virus, influenza A virus - H1 N1, influenza A virus - H3 N2, influenza B, human parainfluenza virus, adenovirus, human bocavirus, human rhino virus, Chlamydia pneumoniae, human metapneumovirus, MP, human corona virus, and respiratory syncytial virus gene, and the results were compared by using Chi square test. Results In 100 BALF samples, MP and drug resistance gene were detected by fluorogenic quantitative PCR. Totally, 83 cases (83. 00%) were MP positive and 78 cases (93. 98%) were drug resistant. All of them had the point mutations A2063G in V region of 23S rRNA domain. A total of 13 kinds of respiratory pathogens were detected by multiplex PCR method, and 89 cases (89. 00%) were positive. Totally, 79 cases (79. 00%) were MP positive, of which 74 cases (74. 00%) detected only MP, and 5 cases (5. 00%) detected MP combined with other pathogens. Other pathogens were detected in 10 cases (10. 00%). The virus detection rate of 0-4 years old group was higher than that of > 4-6 years old group (P - 0. 042) and > 6 years old group (P =0. 002), and the differences were statistically significant. Conclusions MP can be detected in most BALF samples of MPP children, the drug resistance phenomenon is serious, and the main point mutation is A2063G. There were other respiratory pathogens and 2 or 3 pathogens were detected in a small number of BALF samples.Copyright © 2022 Authors. All rights reserved.

6.
Chinese Journal of Applied Clinical Pediatrics ; 36(18):1361-1367, 2021.
Article in Chinese | EMBASE | ID: covidwho-2288886

ABSTRACT

At present, severe acute respiratory syndrome coronavirus-2(SARS-CoV-2)infection is still rampant worldwide.As of September 10, 2021, there were about 222 million confirmed cases of corona virus disease 2019(COVID-19)and more than 4.6 million deaths worldwide.With the development of COVID-19 vaccines and the gradual vaccination worldwide, the increasing number of cases in children and unvaccinated young people has drawn attention.According to World Health Organization surveillance data, the proportion of COVID-19 infection cases in children gradually increased, and the proportion of cases in the age groups of under 5 years and 5-14 years increased from 1.0% and 2.5% in January 2020 to 2.0% and 8.7% in July 2021, respectively.At present, billions of adults have been vaccinated with various COVID-19 vaccines worldwide, and their protective effects including reducing infection and transmission, reducing severe disease and hospitalization, and reducing death, as well as high safety have been confirmed.Canada, the United States, Europe and other countries have approved the emergency COVID-19 vaccination in children and adolescents aged 12 to 17 years, and China has also approved the phased vaccination of COVID-19 vaccination in children and adolescents aged 3 to 17 years. For smooth advancement and implementation of COVID-19 vaccination in children, academic institutions, including National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, and The Society of Pediatrics, Chinese Medical Association organized relevant experts to reach this consensus on COVID-19 vaccination in children.Copyright © 2021 by the Chinese Medical Association.

7.
Chinese Journal of Applied Clinical Pediatrics ; 36(18):1368-1372, 2021.
Article in Chinese | EMBASE | ID: covidwho-2287238

ABSTRACT

Severe acute respiratory syndrome coronavirus-2(SARS-CoV-2)infection is still worldwide.As a vulnerable group, severe and dead pediatric cases are also reported.Under this severe epidemic situation, children should be well protected.With the widespread vaccination of SARS-CoV-2 vaccine in adults, the infection rate have decreased.Therefore, SARS-CoV-2 vaccine inoculation for children groups step by step is of great significance to the protection of children and the prevention and control of corona virus disease 2019(COVID-19) as a whole.But the safety of children vaccinated with SARS-CoV-2 vaccine is a main concern of parents.Therefore, in order to ensure the safety of vaccination and the implementation of vaccination work, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health and the Society of Pediatrics, Chinese Medical Association organized experts to interpret the main issue of parents about SARS-CoV-2 vaccine for children, in order to answer the doubts of parents.Copyright © 2021 by the Chinese Medical Association.

8.
Chinese Journal of Microbiology and Immunology (China) ; 42(7):527-534, 2022.
Article in Chinese | EMBASE | ID: covidwho-2237331

ABSTRACT

The COVID-19 pandemic has become a serious global public health threat with more than 540 million infections and 6.32 million cases of death as of 25 June, 2022.Understanding whether COVID-19 patients can obtain persistent immune protection after recovery is crucial for vaccine development, disease control and epidemic forecast.The persistent immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is mainly derived from the immune memory.Thus, the generation and maintenance of immune memory specifically targeted to the virus were reviewed in this paper. Copyright © 2022 Society of Microbiology and Immunology. All rights reserved.

9.
3rd International Conference on Big Data, Artificial Intelligence and Internet of Things Engineering, ICBAIE 2022 ; : 66-69, 2022.
Article in English | Scopus | ID: covidwho-2213211

ABSTRACT

Since the outbreak of COVID-19, academia has published tens of thousands of new papers. Facing so much literature knowledge, how to realize the fine-grained classification of covid-19 literature and help researchers carry out research? This is an urgent problem to be solved. This paper makes COVID-19 text classification graph data set, designs covid-19 scientific literature fine-grained classification model LC-GAT based on graph attention network, adds attention mechanism at word level, sentence level and graph level, effectively retains the classification information contained in article title and key words, and significantly improves the performance of covid-19 scientific literature fine-grained classification. This paper has positive significance for the classification of COVID-19 scientific literature. © 2022 IEEE.

10.
Journal of Chinese medicinal materials ; 44(3):756-766, 2021.
Article in Chinese | EMBASE | ID: covidwho-2145398

ABSTRACT

Objective: To explore the material basis of potential effect and possible molecular mechanisms of Qingre huashi kangdu prescription proposed by Chinese medicine master Wu Bing-cai on the treatment of Corona Virus Disease 2019(COVID-19), and to provide reference for the treatment and scientific research of COVID-19 in traditional Chinese medicine. Method(s): TCMSP, Batman and other databases were used to search chemical components and action targets in traditional Chinese medicines of Qingre huashi kangdu prescription.The disease targets of COVID-19 were screened out by GeneCards, OMIM, GEO databases.Cytoscape software was used to construct the "drugs-components-targets-diseases" network and the interaction relationship between potential targets.Metascape enrichment analysis was used to predict the core modules and mechanism of action, and ACE2 was docking with the main components. Result(s): 202 kinds of chemical components and 301 drug targets in the Qingre huashi kangdu prescription were excavated, there were 360 COVID-19 related disease targets, and 64 intersections of the two.Nine main chemical components were found in the formula, and the key targets involved PTGS2, NOS2, PPARG, MAPK14, NOS3, RELA, etc.Three core modules were predicted, and the core terms mainly included infectious diseases, immune diseases and pathways, immune and inflammatory pathways.A total of 196 items were obtained by GO enrichment analysis, which mainly involved cytokine-mediated signaling pathway, response to oxidative stress, apoptosis signaling pathway, regulation of protein localization establishment, reactive oxygen metabolism, 147 signaling pathways were screened out by KEGG pathway enrichment, including AGE-RAGE signaling pathway in diabetes complications, toxoplasmosis, apoptosis, MAPK signaling pathway, amoebiasis, HIF-1 signaling pathway and RIG-I-like signaling pathway.Molecular docking showed that luteolin, quercetin, baicalein, kaempferol, robinin, wogonin and naringenin had good binding abilities with ACE2, and the combination of quercetin, baicalein and kaempferol with ACE2 was more stable. Conclusion(s): Qingre huashi kangdu prescription treats COVID-19 through multi-components, multi-targets and multi-pathways. Copyright © 2021, Central Station of Chinese Medicinal Materials Information, National Medical Products Administration. All right reserved.

11.
Chinese Journal of Applied Clinical Pediatrics ; 37(12):893-896, 2022.
Article in Chinese | Scopus | ID: covidwho-2143845

ABSTRACT

Objective To investigate drug resistance gene in Mycoplasma pneumoniae (MP) and the distribution of 13 respiratory pathogens in bronchoalveolar lavage fluid(BALF) of children with Mycoplasma pneumoniae pneumonia(MPP). Methods A total of 100 BALF of children with MPP in Peking University Third Hospital and Peking University First Hospital from January 2018 to January 2019 were collected. Fluorogenic quantitative PCR was used to detect nucleic acid and it's drug resistance gene of MP and multiple PCR method was adopted to detect influenza A virus, influenza A virus - H1 N1, influenza A virus - H3 N2, influenza B, human parainfluenza virus, adenovirus, human bocavirus, human rhino virus, Chlamydia pneumoniae, human metapneumovirus, MP, human corona virus, and respiratory syncytial virus gene, and the results were compared by using Chi square test. Results In 100 BALF samples, MP and drug resistance gene were detected by fluorogenic quantitative PCR. Totally, 83 cases (83. 00%) were MP positive and 78 cases (93. 98%) were drug resistant. All of them had the point mutations A2063G in V region of 23S rRNA domain. A total of 13 kinds of respiratory pathogens were detected by multiplex PCR method, and 89 cases (89. 00%) were positive. Totally, 79 cases (79. 00%) were MP positive, of which 74 cases (74. 00%) detected only MP, and 5 cases (5. 00%) detected MP combined with other pathogens. Other pathogens were detected in 10 cases (10. 00%). The virus detection rate of 0-4 years old group was higher than that of > 4-6 years old group (P - 0. 042) and > 6 years old group (P =0. 002), and the differences were statistically significant. Conclusions MP can be detected in most BALF samples of MPP children, the drug resistance phenomenon is serious, and the main point mutation is A2063G. There were other respiratory pathogens and 2 or 3 pathogens were detected in a small number of BALF samples. © 2022 Authors. All rights reserved.

12.
Ieee Access ; 10:114434-114454, 2022.
Article in English | Web of Science | ID: covidwho-2123158

ABSTRACT

Physicians facing the COVID-19 pandemic are likely to experience acute and chronic, and often unpredictable, occupational stressors that can incur post-traumatic stress symptoms (PTSS), prevention of which is of utmost importance to enhance healthcare workforce efficiency. Unlike previous studies, in this paper we developed a generalized data-driven framework to generate insights into the complex, nonlinear associations of cognitive/occupational factors with physicians' PTSS-risk. Data were collected from practicing physicians in the 18 states with the largest COVID-19 cases by deploying a cross-sectional, anonymous, web-based survey, following the second COVID-19 peak in the US. Analyses revealed that physicians directly treating COVID-19 patients (frontline) were at higher occupational risk of PTSS than those who didn't (secondline). We implemented a suite of eight statistical learning algorithms to evaluate the associations between cognitive/occupational factors and PTSS in frontline physicians. We found that random forest outperformed all other models, in particular the traditionally-used logistic regression by 6.4% (F1-score) and 9.6% (accuracy) in goodness-of-fit performance, and 4.8% (F1-score) and 4.6% (accuracy) in predictive performance, indicating existence of complex interactions and nonlinearity in associations between the cognitive/occupational factors and PTSS-risk. Our results show that depression, burnout, negative coping, fears of contracting/transmitting COVID-19, perceived stigma, and insufficient resources to treat COVID-19 patients are positively associated with PTSS-risk, while higher resilience and support from employer/friends/family/significant others are negatively associated with PTSS-risk. Insights obtained from this study will help to bring new attention to frontline physicians, allowing for more informed prioritization of their care during future pandemics/epidemics.

13.
Zhonghua Er Ke Za Zhi ; 60(11): 1168-1171, 2022 Nov 02.
Article in Chinese | MEDLINE | ID: covidwho-2099942

ABSTRACT

Objective: To summarize the application experience and the therapeutic effect of Nirmatrelvir-Ritonavir (trade name: Paxlovid) for COVID-19 in children. Methods: A retrospective analysis was performed on the clinical data, including collecting the clinical manifestations and clinical outcomes, dynamically monitoring the blood routine, hepatic and renal function and SARS-CoV-2 nucleic acid results, and observing the related side effects during the treatment, etc, of 3 cases with COVID-19 treated with Paxlovid admitted to Shanghai Children's Hospital (designated referral hospital for SARS-CoV-2 infection in Shanghai) from May 1st to June 1st, 2022. Results: The 3 cases were 12, 14, 17 years of age, among which 2 cases were males, 1 case was female. All 3 cases were mild cases with underlying diseases and risk of developing into severe COVID-19, with symptoms of high fever, sore throat and dry cough. The treatment of Paxlovid at 3rd day of symptom onset contributed to the symptom-free after 1-2 days and negative results of SARS-CoV-2 nucleic acid after 2-4 days. All patients had no adverse manifestations of gastrointestinal tract and nervous system but a case had little skin rashes, which recovered after the withdrawal of Paxlovid. Three cases had normal hepatic and renal function during the Paxlovid treatment. At 3 months after discharge, no clinical manifestations of post-COVID syndrome were found in all 3 cases. Conclusion: Paxlovid was effective and relatively safe in the treatment of 3 children with COVID-19.


Subject(s)
COVID-19 , Nucleic Acids , Child , Male , Humans , Female , SARS-CoV-2 , Ritonavir/therapeutic use , Retrospective Studies , China , COVID-19 Drug Treatment
14.
Ieee Access ; 10:104156-104168, 2022.
Article in English | Web of Science | ID: covidwho-2070271

ABSTRACT

The named entity recognition based on the epidemiological investigation of information on COVID-19 can help analyze the source and route of transmission of the epidemic to control the spread of the epidemic better. Therefore, this paper proposes a Chinese named entity recognition model BERT-BiLSTM-IDCNN-ELU-CRF (BBIEC) based on the epidemiological investigation of information on COVID-19 of the BERT pre-training model. The model first processes the unlabeled epidemiological investigation of information on COVID-19 into the character-level corpus and annotates it with artificial entities according to the BIOES character-level labeling system and then uses the BERT pre-training model to obtain the word vector with position information;then, through the bidirectional long-short term memory neural network (BiLSTM) and the improved iterated dilated convolutional neural network (IDCNN) extract global context and local features from the generated word vectors and concatenate them serially;output all possible label sequences to the conditional random field (CRF);finally pass the condition random The airport decodes and generates the entity tag sequence. The experimental results show that the model is better than other traditional models in recognizing the entity of the epidemiological investigation of information on COVID-19.

15.
Journal of Medical Pest Control ; 38(2):160-163, 2022.
Article in Chinese | Scopus | ID: covidwho-2056260

ABSTRACT

Objective To analyze the transmission characteristics of family clustering of Corona Virus Disease 2019 (COVID-19) in a town in Tianjin, and to study new epidemiological investigation method applied for the epidemic. Methods The field epidemiological method was applied to investigate confirmed, suspected cases and close contacts of COVID-19, and this clustering epidemic was analyze;and real-time fluorescence PCR (RT-PCR) assay was used for 2019-nCoV nucleic acid testing. Results A total of 11 confirmed cases and 1 suspected case, with three generations of transmission and median generation interval of 6 (2-26) days were involved in current clustering epidemic, the confirmed cases were infectious at the end of the incubation period, the recurrence rate within the families was 33. 33% (19/57), and the epidemiological investigation information acquired through case narration were deviated compared with the trace investigated by police force and the information provided by close contacts. Conclusion The COVID-19 can cause the family clustering spread, and it may infectious at the end of the incubation period. It is necessary to strengthen the trace and management of close contacts during clustering epidemics, and multiple methods adopted making for acquiring epidemiological investigation information. © 2022, Editorial Department of Medical Pest Control. All rights reserved.

16.
Chinese Journal of Microbiology and Immunology (China) ; 42(7):527-534, 2022.
Article in Chinese | Scopus | ID: covidwho-2055467

ABSTRACT

The COVID-19 pandemic has become a serious global public health threat with more than 540 million infections and 6.32 million cases of death as of 25 June, 2022.Understanding whether COVID-19 patients can obtain persistent immune protection after recovery is crucial for vaccine development, disease control and epidemic forecast.The persistent immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is mainly derived from the immune memory.Thus, the generation and maintenance of immune memory specifically targeted to the virus were reviewed in this paper. © 2022 Society of Microbiology and Immunology. All rights reserved.

17.
Zhonghua Liu Xing Bing Xue Za Zhi ; 43(9): 1370-1375, 2022 Sep 10.
Article in Chinese | MEDLINE | ID: covidwho-2040007

ABSTRACT

Objective: To understand the transmission characteristics and risk factors of household COVID-19 clusters caused by 2019-nCoV Omicron variant in Tianjin and provide evidence for COVID-19 prevention and control. Methods: Field epidemiological method was used to investigate the epidemiological characteristics of COVID-19 cases, and descriptive analysis was used to describe the epidemiological information. Results: A total of 430 cases were reported in this epidemic in Tianjin, in which 409 cases were included in this study. Among these cases, 70.90% (290/409) occurred in families. The family secondary attack rate was 33.64% The family secondary attack rate in age group 12-17 years (13.79%) was significantly lower than that in age group 18-49 years (36.48%), the OR was 0.378 (95%CI: 0.170-0.840). The logistic regression analysis showed that compared with centralized quarantine, the OR of the index cases found in closed-off/controlled areas and in home quarantine were 2.951 (95%CI:1.322-6.586) and 2.287 (95%CI:1.164-4.495), respectively, compared with the cases without sore throat, the OR of the index cases with sore throat was 3.003 (95%CI: 1.576-5.720), and compared with cases in families without completed COVID-19 vaccinations in all members, the OR of the cases in families with completed COVID-19 vaccinations in all members was 0.268 (95%CI: 0.132-0.552). Conclusions: The risk of household transmission of infection with Omicron variant was high. Detecting the index case in closed-off/controlled areas or in home quarantine and sore throat in index cases were the risk factors of the household transmission, completed COVID-19 vaccination was the protective factor.


Subject(s)
COVID-19 , Influenza, Human , Pharyngitis , Adolescent , Adult , COVID-19/epidemiology , COVID-19 Vaccines , Child , Humans , Influenza, Human/epidemiology , Middle Aged , Risk Factors , SARS-CoV-2 , Young Adult
18.
Prog Urol ; 32(16): 1431-1439, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-2031645

ABSTRACT

BACKGROUND: Impaired semen quality and reproductive hormone levels were observed in patients during and after recovery from coronavirus disease 2019 (COVID-19), which raised concerns about negative effects on male fertility. Therefore, this study systematically reviews available data on semen parameters and sex hormones in patients with COVID-19. METHODS: Systematic search was performed on PubMed and Google Scholar until July 18th, 2022. We identified relevant articles that discussed the effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on male fertility. RESULTS: A total number of 1,684 articles were identified by using a suitable keyword search strategy. After screening, 26 articles were considered eligible for inclusion in this study. These articles included a total of 1,960 controls and 2,106 patients. When all studies were considered, the results showed that the semen parameters and sex hormone levels of patients infected with SARS-CoV-2 exhibited some significant differences compared with controls. Fortunately, these differences gradually disappear as patients recover from COVID-19. CONCLUSION: While present data show the negative effects of SARS-CoV-2 infection on male fertility, this does not appear to be long-term. Semen quality and hormone levels will gradually increase to normal as patients recover.


Subject(s)
COVID-19 , Humans , Male , SARS-CoV-2 , Semen , Semen Analysis , Gonadal Steroid Hormones , Hormones
19.
IISE Annual Conference and Expo 2022 ; 2022.
Article in English | Scopus | ID: covidwho-2012849

ABSTRACT

Wearing a mask as one of the crucial non-pharmaceutical interventions has demonstrated to be effective in the battle against the COVID-19 pandemic. The implementation of face coverings for the public remains controversial and still faces some challenges. Whether or not to wear the mask could be a complex decision-making processing, involving the trade-offs between self-interest and collective interest among multiple stakeholders. In the literature, there is a lack of quantitative analysis for strategic mask-wearing decisions during the pandemic. This paper fills the gap by studying a game-theoretic model on wearing the mask considering conflicting interests. Using a susceptible-infected-susceptible (SIS) model, we consider the players as either susceptible or infectious, characterized by homogeneous preferences within the group but heterogeneous preferences between groups. Then we propose a game-theoretic framework to model how both susceptible and infectious players make their decisions. We implement one-way sensitivity analyses to examine how the equilibrium solutions are sensitive to changes in the model parameters. The proposed game model shows that susceptible player is more likely to wear face masks compared to infectious player, when the likelihood or the cost of infection is large. Decreasing the cost of wearing masks or increasing the mask efficacy could help mitigate the reluctance of mask wearing. This paper provides insights on population mask-wearing behaviors, which can support policy makers to design regulations and incentives. © 2022 IISE Annual Conference and Expo 2022. All rights reserved.

20.
4th International Conference on Frontiers of Biological Sciences and Engineering, FBSE 2021 ; 2511, 2022.
Article in English | Scopus | ID: covidwho-1991752

ABSTRACT

Among the coronaviruses that cause pneumonia, Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) are highly infectious and harmful to human beings, which have attracted wide attention. In this paper, the above two coronaviruses were taken as examples to explore the etiology, infection route and molecular basis of the disease, to provide a reference for the prevention and control of coronavirus-related diseases. © 2022 Author(s).

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