McIntosh "Improving the quality of preprints with automated checks"
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The document discusses the enhancement of preprint quality through automated checks, highlighting the lack of standardized reporting and issues such as retractions in COVID-19-related studies. It also emphasizes the importance of data availability for improving citations and reproducibility of research, supported by examples of specific studies and their findings. Automation is presented as a potential solution to streamline the review process and improve the overall quality of research publications.
![Article DOI Study
Purpose
Author-
ship
Funding
Statement
Data
location
DAS Code
availability
10.1101/2020.01.30.927871 Yes 2 No None No No
Uncanny similarity of unique inserts in the 2019-nCoV spike
protein to HIV-1 gp120 and Gag
Methodology
Retrieval and alignment of nucleic acid and protein sequences
We retrieved all the available coronavirus sequences (n=55) from NCBI viral
genome database (https://www.ncbi.nlm.nih.gov/) and we used the GISAID (Elbe
& Buckland-Merrett, 2017)[https://www.gisaid.org/] to retrieve all available full-
length sequences (n=28) of 2019-nCoV as on 27 Jan 2020. Multiple sequence
alignment of all coronavirus genomes was performed by using MUSCLE
software (Edgar, 2004) based on neighbour joining method. Out of 55
coronavirus genome 32 representative genomes of all category were used for
phylogenetic tree development using MEGAX software (Kumar et al., 2018). The
closest relative was found to be SARS CoV.](https://image.slidesharecdn.com/final-mcintosh-5-apr21-210423133412/85/McIntosh-Improving-the-quality-of-preprints-with-automated-checks-23-320.jpg)
McIntosh "Improving the quality of preprints with automated checks"
- 1. Improving the quality of pre-prints with automated checks
- 2. Leslie McIntosh, PhD Ripeta, founder and CEO @ripetaReview
- 3. What’s Happening in Preprints?
- 4. What’s happening in preprints? No standard way of reporting or removing preprints 32 Retracted + 3 ‘Letters of Concern’ from Covid preprints Still exploring checks Automating checks
- 7. Ripeta, LLC. All rights reserved. This is not to be shared without official permission. ripetaReview
- 8. Ripeta, LLC. All rights reserved. This is not to be shared without official permission. ripetaReview Quality review of one paper ripetaReview
- 9. Ripeta, LLC. All rights reserved. This is not to be shared without official permission. ripetaReview Sample ripetaReview Research Quality Study Objective: Yes Professionalism ID: Confirmed with ORCID Funding Statement: Yes Reproducibility DAS: Yes Data Location: In paper Code Availability: No Data Location Result: Text found The data used to support the findings of this study are included within the article. Recommendations: Please consider depositing data and materials into an accessible repository. Having data easily accessible has shown to increase the number of citations to your article. This also assists in making your work reproducible. Relationship between the ABO Blood Group and the COVID-19 Susceptibility DOI: 10.1101/2020.03.11.20031096 Results Feedback
- 10. Will authors improve manuscripts? (ResearchSquare) 33% of authors corrected and re- uploaded their preprint
- 12. Ripeta, LLC. All rights reserved. This is not to be shared without official permission. ripetaReport
- 13. Ripeta, LLC. All rights reserved. This is not to be shared without official permission. ripetaReport Report of Portfolio of Publications Sample ripetaReport (Wellcome Trust)
- 14. ripetaReporting
- 15. Can quality papers be quickly identified? (Covid preprints)
- 18. Research Relationship between the ABO Blood Group and the COVID-19 Susceptibility DOI: 10.1101/2020.03.11.20031096 Here, we investigated the relationship between the ABO blood type and the susceptibility to COVID-19 in patients from three hospitals in Wuhan and Shenzhen, China to test if the former may be a biomarker for the latter. Study Objective Scientific Headings Abstracts, Background/Introduction, Methods
- 19. Professionalism
- 20. Reproducibility Relationship between the ABO Blood Group and the COVID-19 Susceptibility DOI: 10.1101/2020.03.11.20031096 Data Availability The data used to support the findings of this study are included within the article. Data Availability The data used to support the findings of this study are included within the article. {Not Found} Data Availability Statement Data Location Code Availability
- 22. Covid Preprint Analyses ripetaScore Outcome Citations Similarity nCoV spike protein 10.1101/2020.01.30.927871 Low Withdrawn 50 Hydroxychloroquine 10.1101/2020.03.16.20037135 Medium Questioned 3000 ABO Blood Group 10.1101/2020.03.11.20031096 Medium Overhyped 150 Potential vaccine targets 10.1101/2020.02.03.933226 High Published 450
- 23. Article DOI Study Purpose Author- ship Funding Statement Data location DAS Code availability 10.1101/2020.01.30.927871 Yes 2 No None No No Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag Methodology Retrieval and alignment of nucleic acid and protein sequences We retrieved all the available coronavirus sequences (n=55) from NCBI viral genome database (https://www.ncbi.nlm.nih.gov/) and we used the GISAID (Elbe & Buckland-Merrett, 2017)[https://www.gisaid.org/] to retrieve all available full- length sequences (n=28) of 2019-nCoV as on 27 Jan 2020. Multiple sequence alignment of all coronavirus genomes was performed by using MUSCLE software (Edgar, 2004) based on neighbour joining method. Out of 55 coronavirus genome 32 representative genomes of all category were used for phylogenetic tree development using MEGAX software (Kumar et al., 2018). The closest relative was found to be SARS CoV.
- 24. Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial Article DOI Study Purpose Author- ship Funding Statement Data location DAS Code availability 10.1016/j.ijantimicag.2020 .105949 Yes 1 Yes None No No Elisabeth Bik took a close look at the IJAA article and detailed a long list of serious problems with the study, including questions about its ethical underpinnings, messy confounding variables, missing patients, rushed and conflicted peer review, and confusing data.
- 25. Relationship between the ABO Blood Group and the COVID-19 Susceptibility Article DOI Study Purpose Author- ship Funding Statement Data location DAS Code availability 10.1101/2020.03.11.200310 96 Yes 4 Yes In paper Yes No
- 26. Preliminary identification of potential vaccine targets for the COVID-19 coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies Article DOI Study Purpose Author- ship Funding Statement Data location DAS Code availability 10.1101/2020.02.03.933226 Yes 4 Yes External repo Yes Yes
- 27. Can automation save time? (SpringerNature & bioRxiv/medRxiv Preprints) 4 minutes instead of 40 hours to check 400+ manuscripts
- 28. Does automation solve all problems?
- 29. Automated checks can make better science easier Follow us @RipetaReview for more memes
- 30. Follow us for weekly academic highlights, transparency tips, and more! @RipetaReview @Ripeta info@ripeta.com www.ripeta.com Stay Informed
- 31. Leslie McIntosh CEO Cynthia Hudson Vitale COO, co-founder Chris Westling Data Engineer Ruth Whittam Data Scientist, Lead Josh Sumner Data Scientist, Intern Leah Haynes Data Scientist, Intern ripetinis Paola Ortega Saborío Data Engineer August DeVore Editor
- 33. ripetaData Research Professionalism Reproducibility Open Access Ethical Approval Statement Data Availability Statements Abstract Ethical Approval Organization Data Locations - Repository Study Objective Author Contribution Statement Data Locations - PID Funding Statement Competing Interests Data Locations - Identifiers Funding Source Funding Source Data Locations - URL Funding Grant ID Funding Grant ID Analysis Software Count of Authors (single) Analysis Software Version Self-Citations Statistical Methods Author Identification Code Availability Statement