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Examining linguistic shifts between preprints and publications

Authors : David N. Nicholson, Vincent Rubinetti, Dongbo Hu, Marvin Thielk, Lawrence E. Hunter, Casey S. Greene

Preprints allow researchers to make their findings available to the scientific community before they have undergone peer review. Studies on preprints within bioRxiv have been largely focused on article metadata and how often these preprints are downloaded, cited, published, and discussed online.

A missing element that has yet to be examined is the language contained within the bioRxiv preprint repository. We sought to compare and contrast linguistic features within bioRxiv preprints to published biomedical text as a whole as this is an excellent opportunity to examine how peer review changes these documents.

The most prevalent features that changed appear to be associated with typesetting and mentions of supporting information sections or additional files. In addition to text comparison, we created document embeddings derived from a preprint-trained word2vec model.

We found that these embeddings are able to parse out different scientific approaches and concepts, link unannotated preprint–peer-reviewed article pairs, and identify journals that publish linguistically similar papers to a given preprint.

We also used these embeddings to examine factors associated with the time elapsed between the posting of a first preprint and the appearance of a peer-reviewed publication. We found that preprints with more versions posted and more textual changes took longer to publish.

Lastly, we constructed a web application (https://greenelab.github.io/preprint-similarity-search/) that allows users to identify which journals and articles that are most linguistically similar to a bioRxiv or medRxiv preprint as well as observe where the preprint would be positioned within a published article landscape.

URL : Examining linguistic shifts between preprints and publications

DOI : https://doi.org/10.1371/journal.pbio.3001470

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More journal articles and fewer books: Publication practices in the social sciences in the 2010’s

Authors : William E. Savage, Anthony J. Olejniczak

The number of scholarly journal articles published each year is growing, but little is known about the relationship between journal article growth and other forms of scholarly dissemination (e.g., books and monographs).

Journal articles are the de facto currency of evaluation and prestige in STEM fields, but social scientists routinely publish books as well as articles, representing a unique opportunity to study increased article publications in disciplines with other dissemination options.

We studied the publishing activity of social science faculty members in 12 disciplines at 290 Ph.D. granting institutions in the United States between 2011 and 2019, asking: 1) have publication practices changed such that more or fewer books and articles are written now than in the recent past?; 2) has the percentage of scholars actively participating in a particular publishing type changed over time?; and 3) do different age cohorts evince different publication strategies?

In all disciplines, journal articles per person increased between 3% and 64% between 2011 and 2019, while books per person decreased by at least 31% and as much as 54%. All age cohorts show increased article authorship over the study period, and early career scholars author more articles per person than the other cohorts in eight disciplines.

The article-dominated literatures of the social sciences are becoming increasingly similar to those of STEM disciplines.

URL : More journal articles and fewer books: Publication practices in the social sciences in the 2010’s

DOI : https://doi.org/10.1371/journal.pone.0263410

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Integrative data reuse at scientifically significant sites: Case studies at Yellowstone National Park and the La Brea Tar Pits

Author : Andrea K. Thomer

Scientifically significant sites are the source of, and long-term repository for, considerable amounts of data—particularly in the natural sciences. However, the unique data practices of the researchers and resource managers at these sites have been relatively understudied.

Through case studies of two scientifically significant sites (the hot springs at Yellowstone National Park and the fossil deposits at the La Brea Tar Pits), I developed rich descriptions of site-based research and data curation, and high-level data models of information classes needed to support integrative data reuse.

Each framework treats the geospatial site and its changing natural characteristics as a distinct class of information; more commonly considered information classes such as observational and sampling data, and project metadata, are defined in relation to the site itself.

This work contributes (a) case studies of the values and data needs for researchers and resource managers at scientifically significant sites, (b) an information framework to support integrative reuse at these sites, and (c) a discussion of data practices at scientifically significant sites.

URL : Integrative data reuse at scientifically significant sites: Case studies at Yellowstone National Park and the La Brea Tar Pits

DOI : https://doi.org/10.1002/asi.24620

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Gender disparity in publication records: a qualitative study of women researchers in computing and engineering

Authors : Mohammad Hosseini, Shiva Sharifzad

Background

The current paper follows up on the results of an exploratory quantitative analysis that compared the publication and citation records of men and women researchers affiliated with the Faculty of Computing and Engineering at Dublin City University (DCU) in Ireland.

Quantitative analysis of publications between 2013 and 2018 showed that women researchers had fewer publications, received fewer citations per person, and participated less often in international collaborations.

Given the significance of publications for pursuing an academic career, we used qualitative methods to understand these differences and explore factors that, according to women researchers, have contributed to this disparity.

Methods

Sixteen women researchers from DCU’s Faculty of Computing and Engineering were interviewed using a semi-structured questionnaire. Once interviews were transcribed and anonymised, they were coded by both authors in two rounds using an inductive approach.

Results

Interviewed women believed that their opportunities for research engagement and research funding, collaborations, publications and promotions are negatively impacted by gender roles, implicit gender biases, their own high professional standards, family responsibilities, nationality and negative perceptions of their expertise and accomplishments.

Conclusions

Our study has found that women in DCU’s Faculty of Computing and Engineering face challenges that, according to those interviewed, negatively affect their engagement in various research activities, and, therefore, have contributed to their lower publication record.

We suggest that while affirmative programmes aiming to correct disparities are necessary, they are more likely to  improve organisational culture if they are implemented in parallel with bottom-up initiatives that engage all parties, including men researchers and non-academic partners, to inform and sensitise them about the significance of gender equity.

URL : Gender disparity in publication records: a qualitative study of women researchers in computing and engineering

DOI : https://doi.org/10.1186/s41073-021-00117-3

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Research data management systems and the organization of universities and research institutes: A systematic literature review

Author : Eva Katharina Donner

New technological developments, the availability of big data, and the creation of research platforms open a variety of opportunities to generate, store, and analyze research data. To ensure the sustainable handling of research data, the European Commission as well as scientific commissions have recently highlighted the importance of implementing a research data management system (RDMS) in higher education institutes (HEI) which combines technical as well as organizational solutions.

A deep understanding of the requirements of research data management (RDM), as well as an overview of the different stakeholders, is a key prerequisite for the implementation of an RDMS.

Based on a scientific literature review, the aim of this study is to answer the following research questions: “What organizational factors need to be considered when implementing an RDMS? How do these organizational factors interact with each other and how do they constrain or facilitate the implementation of an RDMS?”

The structure of the analysis is built on the four components of Leavitt’s classical model of organizational change: task, structure, technology, and people. The findings reveal that the implementation of RDMS is strongly impacted by the organizational structure, infrastructure, labor culture as well as strategic considerations.

Overall, this literature review summarizes different approaches for the implementation of an RDMS. It also identifies areas for future research.

URL : Research data management systems and the organization of universities and research institutes: A systematic literature review

DOI : https://doi.org/10.1177%2F09610006211070282

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EN

Academic social networks metrics: an effective indicator for university performance?

Authors : Łukasz Wiechetek, Zbigniew Pastuszak

Social networks have become popular among researchers and scientists. Specialized platforms for researchers offer many metrics and indicators which are used to evaluate various scientists and assess the strength of their impact. In this article the authors perform systematic comparison between the main university level ResearchGate (RG) metrics: total RG Score, number of publications, number of affiliated profiles and ARWU.

A tool for acquiring the RG metrics of research units and a framework for calculating alternative university ranks was implemented and tested. As a point of reference the ranking system of the Academic Ranking of World Universities (ARWU, 2019) was used. The authors used a web scraping technique to acquire data. Data analysis was based on Spearman’s rho and multiple linear regression (MLR).

Ten additional ranks were developed and compared with the benchmark ranking. The k-means clustering method was used to identify the groups of ARWU universities. The research results show that the metrics provided by specialized social networks can be used for the assessment of universities, however, an in-depth evaluation requires a more advanced procedure and indicators to measure many areas of scholarly activity like research, integration, application, teaching, and co-creation.

Clustering method showed also that the distance between the ARWU universities measured in values of RG metrics are bigger for the top of the ranking. The university authorities should encourage researchers to use specialized social networks, and train them how to do it, to promote not only their own achievements, but also to increase the impact and recognition of their respective research units.

At the end of the article some limitations of the method used and some practical recommendations for the university authorities were formulated.

URL : Academic social networks metrics: an effective indicator for university performance?

DOI : https://doi.org/10.1007/s11192-021-04258-6

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EN

Publishing of COVID-19 preprints in peer-reviewed journals, preprinting trends, public discussion and quality issues

Authors : Ivan Kodvanj, Jan Homolak, Vladimir Trkulja

COVID-19-related (vs. non-related) articles appear to be more expeditiously processed and published in peer-reviewed journals.

We aimed to evaluate: (i) whether COVID-19-related preprints were favored for publication, (ii) preprinting trends and public discussion of the preprints, and (iii) the relationship between the publication topic (COVID-19-related or not) and quality issues.

Manuscripts deposited at bioRxiv and medRxiv between January 1 and September 27 2020 were assessed for the probability of publishing in peer-reviewed journals, and those published were evaluated for submission-to-acceptance time. The extent of public discussion was assessed based on Altmetric and Disqus data.

The Retraction Watch Database and PubMed were used to explore the retraction of COVID-19 and non-COVID-19 articles and preprints. With adjustment for the preprinting server and number of deposited versions, COVID-19-related preprints were more likely to be published within 120 days since the deposition of the first version (OR = 1.96, 95% CI: 1.80–2.14) as well as over the entire observed period (OR = 1.39, 95% CI: 1.31–1.48). Submission-to-acceptance was by 35.85 days (95% CI: 32.25–39.45) shorter for COVID-19 articles.

Public discussion of preprints was modest and COVID-19 articles were overrepresented in the pool of retracted articles in 2020. Current data suggest a preference for publication of COVID-19-related preprints over the observed period.

URL : https://doi.org/10.1007/s11192-021-04249-7