1
|
An X, Zhang M, Xu S. An active learning-based approach for screening scholarly articles about the origins of SARS-CoV-2. PLoS One 2022; 17:e0273725. [PMID: 36112646 PMCID: PMC9480989 DOI: 10.1371/journal.pone.0273725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 08/13/2022] [Indexed: 11/17/2022] Open
Abstract
To build a full picture of previous studies on the origins of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), this paper exploits an active learning-based approach to screen scholarly articles about the origins of SARS-CoV-2 from many scientific publications. In more detail, six seed articles were utilized to manually curate 170 relevant articles and 300 nonrelevant articles. Then, an active learning-based approach with three query strategies and three base classifiers is trained to screen the articles about the origins of SARS-CoV-2. Extensive experimental results show that our active learning-based approach outperforms traditional counterparts, and the uncertain sampling query strategy performs best among the three strategies. By manually checking the top 1,000 articles of each base classifier, we ultimately screened 715 unique scholarly articles to create a publicly available peer-reviewed literature corpus, COVID-Origin. This indicates that our approach for screening articles about the origins of SARS-CoV-2 is feasible.
Collapse
Affiliation(s)
- Xin An
- School of Economics & Management, Beijing Forestry University, Beijing, P.R. China
| | - Mengmeng Zhang
- School of Economics & Management, Beijing Forestry University, Beijing, P.R. China
| | - Shuo Xu
- College of Economics and Management, Beijing University of Technology, Beijing, P.R. China
- * E-mail:
| |
Collapse
|
2
|
Winkley K, Banerjee D, Bradley T, Koseva B, Cheung WA, Selvarangan R, Pastinen T, Grundberg E. Immune cell residency in the nasal mucosa may partially explain respiratory disease severity across the age range. Sci Rep 2021; 11:15927. [PMID: 34354210 PMCID: PMC8342554 DOI: 10.1038/s41598-021-95532-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/20/2021] [Indexed: 12/26/2022] Open
Abstract
Previous studies focusing on the age disparity in COVID-19 severity have suggested that younger individuals mount a more robust innate immune response in the nasal mucosa after infection with SARS-CoV-2. However, it is unclear if this reflects increased immune activation or increased immune residence in the nasal mucosa. We hypothesized that immune residency in the nasal mucosa of healthy individuals may differ across the age range. We applied single-cell RNA-sequencing and measured the cellular composition and transcriptional profile of the nasal mucosa in 35 SARS-CoV-2 negative children and adults, ranging in age from 4 months to 65 years. We analyzed in total of ~ 30,000 immune and epithelial cells and found that age and immune cell proportion in the nasal mucosa are inversely correlated, with little evidence for structural changes in the transcriptional state of a given cell type across the age range. Orthogonal validation by epigenome sequencing indicate that it is especially cells of the innate immune system that underlie the age-association. Additionally, we characterize the predominate immune cell type in the nasal mucosa: a resident T cell like population with potent antiviral properties. These results demonstrate fundamental changes in the immune cell makeup of the uninfected nasal mucosa over the lifespan. The resource we generate here is an asset for future studies focusing on respiratory infection and immunization strategies.
Collapse
Affiliation(s)
- Konner Winkley
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Dithi Banerjee
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Todd Bradley
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Boryana Koseva
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Warren A Cheung
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.
| |
Collapse
|
3
|
Eigenmann P. Risk factors for bronchiolitis and asthma, and COVID-19 symptoms in young children. Pediatr Allergy Immunol 2021; 32:215-218. [PMID: 33522012 PMCID: PMC8014648 DOI: 10.1111/pai.13436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 12/04/2022]
Affiliation(s)
- Philippe Eigenmann
- Department of Women-Children-Teenagers, University Hospital of Geneva, Geneva, Switzerland
| |
Collapse
|
4
|
Giacomet V, Stracuzzi M, Paradiso L, Di Cosimo ME, Rubinacci V, Zuccotti G. Defining the clinical phenotype of COVID-19 in children. Pediatr Allergy Immunol 2020; 31 Suppl 26:82-84. [PMID: 33236440 PMCID: PMC7753524 DOI: 10.1111/pai.13355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 08/04/2020] [Indexed: 01/10/2023]
Abstract
On January 7, 2020, a novel coronavirus (SARS-CoV-2) was identified as the causative agent of a cluster of pneumonia of unknown origin detected in Wuhan City by Chinese authorities. Since SARS-CoV-2 discovery, the corresponding disease (COVID-19) has rapidly expanded throughout the globe, making as a consequence the World Health Organization (WHO) declaring a pandemic. As of May 19, 2020, over 4.806.299 cases of COVID-19 had been confirmed worldwide, with more than 318.599 deaths.
Collapse
Affiliation(s)
- Vania Giacomet
- Paediatric Infectious Disease UnitDepartment of PediatricsLuigi Sacco HospitalUniversity of MilanMilanItaly
| | - Marta Stracuzzi
- Paediatric Infectious Disease UnitDepartment of PediatricsLuigi Sacco HospitalUniversity of MilanMilanItaly
| | - Laura Paradiso
- Department of Pediatrics, V. Buzzi Children's HospitalUniversity of MilanMilanItaly
| | - Maria Elisabetta Di Cosimo
- Paediatric Infectious Disease UnitDepartment of PediatricsLuigi Sacco HospitalUniversity of MilanMilanItaly
| | - Valeria Rubinacci
- Paediatric Infectious Disease UnitDepartment of PediatricsLuigi Sacco HospitalUniversity of MilanMilanItaly
| | - GianVincenzo Zuccotti
- Paediatric Infectious Disease UnitDepartment of PediatricsLuigi Sacco HospitalUniversity of MilanMilanItaly
- Department of Pediatrics, V. Buzzi Children's HospitalUniversity of MilanMilanItaly
| |
Collapse
|