A comparison study of topic modeling based literature analysis by using full texts and abstracts of scientific articles: a case of COVID-19 research

PurposeHow to extract useful information from a very large volume of literature is a great challenge for librarians. Topic modeling technique, which is a machine learning algorithm to uncover latent thematic structures from large collections of documents, is a widespread approach in literature analysis, especially with the rapid growth of academic literature. In this paper, a comparison of topic modeling based literature analysis has been done using full texts and s of articles.Design/methodology/approachThe authors conduct a comparison study of topic modeling on full-text paper and corresponding to assess the influence of the different types of documents been used as input for topic modeling. In particular, the authors use the large volumes of COVID-19 research literature as a case study for topic modeling based literature analysis. The authors illustrate the research topics, research trends and topic similarity of COVID-19 research by using Latent Dirichlet allocation (LDA) and topic visualization method.FindingsThe authors found 14 research topics for COVID-19 research. The authors also found that the topic similarity between using full-text paper and corresponding is higher when more documents are analyzed.Originality/valueFirst, this study contributes to the literature analysis approach. The comparison study can help us understand the influence of the different types of documents on the results of topic modeling analysis. Second, the authors present an overview of COVID-19 research by summarizing 14 research topics for it. This automated literature analysis can help specialists in the health and medical domain or other people to quickly grasp the structured morphology of the current studies for COVID-19.

Cathepsins in the extracellular space: Focusing on non-lysosomal proteolytic functions with clinical implications.

Cathepsins can be found in the extracellular space, cytoplasm, and nucleus. It was initially suspected that the primary physiological function of the cathepsins was to break down intracellular protein, and that they also had a role in pathological processes including inflammation and apoptosis. However, the many actions of cathepsins outside the cell and their complicated biological impacts have garnered much interest. Cathepsins play significant roles in a number of illnesses by regulating parenchymal cell proliferation, cell migration, viral invasion, inflammation, and immunological responses through extracellular matrix remodeling, signaling disruption, leukocyte recruitment, and cell adhesion. In this review, we outline the physiological roles of cathepsins in the extracellular space, the crucial pathological functions performed by cathepsins in illnesses, and the recent breakthroughs in the detection and therapy of specific inhibitors and fluorescent probes in associated dysfunction.

Roles of self-esteem and socioeconomic status in COVID-19 preventive behaviors: Research and Reviews

This study applied terror management theory to investigate whether self-esteem and socioeconomic status (i.e., income and education) predict coronavirus disease 2019 (COVID-19) prevention behavior. Data collection in this cross-sectional and analytical study was performed by an online survey of 1012 participants. In participants with high self-esteem, mortality salience was high when the perceived threat of COVID-19 was high whereas mortality salience was low when perceived efficacy was high. In contrast, mortality salience was not significantly associated with COVID-19 prevention behaviors in participants with high self-esteem. In people with low self-esteem, mortality salience was high when the perceived threat of COVID-19 was high, but mortality salience was not significantly associated with perceived efficacy. Moreover, mortality salience was significantly associated with COVID-19 prevention behaviors in people with low self-esteem. Both income and education had significant positive associations with COVID-19 prevention behaviors in all participants regardless of self-esteem level. The findings revealed that perceived threat and perceived efficacy mediate the effects of self-esteem on mortality salience and on COVID-19 prevention behaviors. We discuss how these findings improve understanding of COVID-19 prevention behaviors and how they can be used to encourage these behaviors during an outbreak.

The impact of COVID-19 on the tourism and hospitality Industry: Evidence from international stock markets

COVID-19 seriously affects the tourism and hospitality industry. In this study, we investigate the behavior of 40 tourism and hospitality stock market indices worldwide from two perspectives. First, empowered by the Granger causality test and network analysis, we test the spillover effects among these stock markets and find that the dynamics of interconnectedness network structures differ significantly in the pre-pandemic and in-pandemic periods. Second, we employ econometric models to explore how the influence of COVID-19 on these stock markets varies by considering the interconnectedness structure, the government response stringency index, and other country-level characteristics. We find that the interconnectedness structure significantly and robustly affects stock returns in the tourism and hospitality markets. Our investigation provides a better understanding of the impact of COVID-19 on tourism and hospitality industry.

Complex analysis of the personalized pharmacotherapy in the management of COVID-19 patients and suggestions for applications of predictive, preventive, and personalized medicine attitude.

AIMS: Coronavirus disease 2019 (COVID-19) is rapidly spreading worldwide. Drug therapy is one of the major treatments, but contradictory results of clinical trials have been reported among different individuals. Furthermore, comprehensive analysis of personalized pharmacotherapy is still lacking. In this study, analyses were performed on 47 well-characterized COVID-19 drugs used in the personalized treatment of COVID-19. METHODS: Clinical trials with published results of drugs use for COVID-19 treatment were collected to evaluate drug efficacy. Drug-to-Drug Interactions (DDIs) were summarized and classified. Functional variations in actionable pharmacogenes were collected and systematically analysed. "Gene Score" and "Drug Score" were defined and calculated to systematically analyse ethnicity-based genetic differences, which are important for the safer use of COVID-19 drugs. RESULTS: Our results indicated that four antiviral agents (ritonavir, darunavir, daclatasvir and sofosbuvir) and three immune regulators (budesonide, colchicine and prednisone) as well as heparin and enalapril could generate the highest number of DDIs with common concomitantly utilized drugs. Eight drugs (ritonavir, daclatasvir, sofosbuvir, ribavirin, interferon alpha-2b, chloroquine, hydroxychloroquine (HCQ) and ceftriaxone had actionable pharmacogenomics (PGx) biomarkers among all ethnic groups. Fourteen drugs (ritonavir, daclatasvir, prednisone, dexamethasone, ribavirin, HCQ, ceftriaxone, zinc, interferon beta-1a, remdesivir, levofloxacin, lopinavir, human immunoglobulin G and losartan) showed significantly different pharmacogenomic characteristics in relation to the ethnic origin of the patient. CONCLUSION: We recommend that particularly for patients with comorbidities to avoid serious DDIs, the predictive, preventive, and personalized medicine (PPPM, 3 PM) strategies have to be applied for COVID-19 treatment, and genetic tests should be performed for drugs with actionable pharmacogenes, especially in some ethnic groups with a higher frequency of functional variations, as our analysis showed. We also suggest that drugs associated with higher ethnic genetic differences should be given priority in future pharmacogenetic studies for COVID-19 management. To facilitate translation of our results into clinical practice, an approach conform with PPPM/3 PM principles was suggested. In summary, the proposed PPPM/3 PM attitude should be obligatory considered for the overall COVID-19 management. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13167-021-00247-0.

Advances in treatment of COVID-19

The novel coronavirus pneumonia is an acute infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The global pandemic of this novel coronavirus pneumonia has greatly threatened human health and brought enormous economy losses. By the end of May 20, 2020, the pandemic of this disease had caused more than 2.70 million infections and more than 320 thousand deaths. This paper reviewed the recent advances in the treatment of the novel coronavirus pneumonia to provide basic references for disease control.

Epidemiological and clinical features of pediatric COVID-19.

BACKGROUND: COVID-19 is an extremely severe infectious disease. However, few studies have focused on the epidemiological and clinical characteristics of pediatric COVID-19. This study conducted a retrospective review of the epidemiological and clinical features of COVID-19 in children. METHODS: A retrospective study was conducted on children with a definite diagnosis of COVID-19 in mainland China using the web crawler technique to collect anonymous COVID-19 updates published by local health authorities. RESULTS: Three hundred forty-one children aged 4 days to 14 years with a median age of 7 years were included. Sixty-six percent of pediatric patients were infected via family members with COVID-19. The median incubation period was 9 days (interquartile range, 6 to 13). Asymptomatic cases accounted for 5.9%, of which 30% had abnormal chest radiologic findings. A majority of pediatric COVID-19 cases showed mild to moderate clinical features, and only a few developed severe or critical diseases (0.6% and 0.3%, respectively). Fever (77.9%) and cough (32.4%) were the predominant presenting symptoms of pediatric COVID-19. The pediatric patients had fewer underlying diseases and complications than adults. The treatment modalities for pediatric COVID-19 patients were not as complex as those of adult COVID-19 patients. The overall prognosis of pediatric COVID-19 was benign with a decent recovery. The median time from onset to cure was 16 days (interquartile range, 13 to 21). CONCLUSIONS: Compared to adults, COVID-19 in children has distinct features of epidemiology and clinical manifestations. The findings from this study might help to guide the development of measures to prevent and treat this ongoing global pandemic. TRIAL REGISTRATION: Chinese Clinical Trial Registry ( chictr.org.cn ) identifier: ChiCTR2000030464.

The clinical characteristics and mortal causes analysis of COVID-19 death patients (preprint)

Abstract Purpose: Currently, COVID-19 is causing a large number of deaths globally. However, few researches focused on the clinical features of death patients. This study conducted a retrospective analysis of clinical characteristics and mortal causes in Chinese COVID-19 death patients. Patients and methods: The clinical characteristics of death patients were collected from publicized by local health authorities in China. Expressions of virus targets in human organs were obtained from GTEx database. Results: 159 patients from 24 provinces in China were recruited in our study, including 26 young patients under 60 and 133 aged 60 or older. The median age was 71 years, which indicated that most death patients were elderly. More male patients died of COVID-19 than females (1.65 fold). Hypertension was the most common coexisting disorder and respiratory failure was the most common direct cause of death. Fever (71.19%) and cough (55.08%) were the predominant presenting symptoms. There was one asymptomatic patient. In addition, by comparing young and old patients, heart disease was identified as an important risk factor for death in the aged patients. ACE2 and TMPRSS2 were the targets of SARS-CoV-2, we analyzed their expression in different organs. TMPRSS2 and ACE2 had a high expression in the organs which had corresponding clinical features in death patients. Conclusion: Male, age and heart disease were the main risk factors of death. Beside, asymptomatic patients with serious coexisting disorders may also die of SARS-CoV-2. Thus, more attention should be paid to the old patients with heart disease and asymptomatic patients in the treatment . Keywords: COVID-19, SARS-Cov-2, death, coexisting disorder, cause of death

Genetic Profiles in Pharmacogenes Indicate Personalized Drug Therapy for COVID-19 (preprint)

Background: The coronavirus disease 2019 (COVID-19) has become a global pandemic currently. Many drugs showed potential for COVID-19 therapy. However, genetic factors which can lead to different drug efficiency and toxicity among populations are still undisclosed in COVID-19 therapy. Methods: We selected 67 potential drugs for COVID-19 therapy (DCTs) from clinical guideline and clinical trials databases. 313 pharmaco-genes related to these therapeutic drugs were included. Variation information in 125,748 exomes were collected for racial differences analyses. The expression level of pharmaco-genes in single cell resolution was evaluated from single-cell RNA sequencing (scRNA-seq) data of 17 healthy adults. Results: Pharmacogenes, including CYP3A4, ABCB1, SLCO1B1, ALB, CYP3A5, were involved in the process of more than multi DCTs. 224 potential drug-drug interactions (DDI) of DCTs were predicted, while 112 of them have been reported. Racial discrepancy of common nonsynonymous mutations was found in pharmacogenes including: VDR, ITPA, G6PD, CYP3A4 and ABCB1 which related to DCTs including ribavirin, -interferon, chloroquine and lopinavir. Moreover, ACE2, the target of 2019-nCoV, was only found in parts of lung cells, which makes drugs like chloroquine that prevent virus binding to ACE2 more specific than other targeted drugs such as camostat mesylate. Conclusions: At least 17 drugs for COVID-19 therapy with predictable pharmacogenes should be carefully utilized in risk races which are consisted of more risk allele carriers. At least 29 drugs with potential of DDIs are reported to be affected by other DDIs, they should be replaced by similar drugs without interaction if it is possible. Drugs which specifically targeted to infected cells with ACE2 such as chloroquine are preferred in COVID-19 therapy.

An overview of literature on COVID-19, MERS and SARS: Using text mining and latent Dirichlet allocation

The unprecedented outbreak of COVID-19 is one of the most serious global threats to public health in this century. During this crisis, specialists in information science could play key roles to support the efforts of scientists in the health and medical community for combatting COVID-19. In this article, we demonstrate that information specialists can support health and medical community by applying text mining technique with latent Dirichlet allocation procedure to perform an overview of a mass of coronavirus literature. This overview presents the generic research themes of the coronavirus diseases: COVID-19, MERS and SARS, reveals the representative literature per main research theme and displays a network visualisation to explore the overlapping, similarity and difference among these themes. The overview can help the health and medical communities to extract useful information and interrelationships from coronavirus-related studies.