The Global Extinction of Languages Is Threatening a Vital Type of Human Knowledge

“As human languages are driven to extinction around the world, a verbal encyclopedia of medical knowledge is on the brink of being forgotten.

Among 12,495 medicinal uses for plants in indigenous communities, new research has found over 75 percent of those plants are each tied to just one local language. If these unique words trickle out of use, so too may the knowledge they contain….

Language extinction is a tragic phenomenon that’s been occurring worldwide, as languages spoken by precious few people are replaced by larger ones. Roughly one language ceases to be spoken every four months, and 3,054 languages are currently endangered around the world….

The vast majority of plant species in the study were found to have medical properties described in just one indigenous language, many of which are themselves endangered….

In North America, for instance, the authors found waning indigenous languages held 86 percent of all unique knowledge on plant medicine. In the northwest Amazon, on the other hand, 100 percent of medicinal plant knowledge is restricted to languages on the edge of extinction. …”

Abuse of ORCID’s weaknesses by authors who use paper mills | SpringerLink

Abstract:  In many countries around the world that use authorship and academic papers for career advancement and recognition, the accurate identity of participating authors is vital. ORCID (Open Researcher and Contributor ID), an author disambiguation tool that was created in 2012, is being vociferously implemented across a wide swathe of journals, including by many leading publishers. In some countries, authors who publish in indexed journals, particularly in journals that carry a Clarivate Analytics’ Journal Impact Factor, are rewarded, sometimes even monetarily. A strong incentive to cheat and abuse the publication ethos thus exists. There has been a recent spike in the detection of papers apparently derived from paper mills that have multiple issues with figures. The use of such figures across many papers compromises the integrity of the content in all those papers, with widespread ramifications for the integrity of the biomedical literature and of journals that may be gamed by academics. The use of ORCID does not guarantee the authenticity of authors associated with a paper mill-derived paper, nor does it fortify the paper’s integrity. These weaknesses of ORCID may dampen trust in this tool, especially if the ORCID platform is being populated by “ghost” (empty) ORCID accounts of academics whose identities cannot be clearly verified, or disposable accounts (perhaps created by paper mill operators) that are used only once, exclusively to pass the paper submission step. Open-source forensic tools to assist academics, editors and publishers to detect problematic figures, and more stringent measures by ORCID to ensure robust author identity verification, are urgently required to protect themselves, and the wider biomedical literature.

 

Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols | Nucleic Acids Research | Oxford Academic

Abstract:  Dockstore (https://dockstore.org/) is an open source platform for publishing, sharing, and finding bioinformatics tools and workflows. The platform has facilitated large-scale biomedical research collaborations by using cloud technologies to increase the Findability, Accessibility, Interoperability and Reusability (FAIR) of computational resources, thereby promoting the reproducibility of complex bioinformatics analyses. Dockstore supports a variety of source repositories, analysis frameworks, and language technologies to provide a seamless publishing platform for authors to create a centralized catalogue of scientific software. The ready-to-use packaging of hundreds of tools and workflows, combined with the implementation of interoperability standards, enables users to launch analyses across multiple environments. Dockstore is widely used, more than twenty-five high-profile organizations share analysis collections through the platform in a variety of workflow languages, including the Broad Institute’s GATK best practice and COVID-19 workflows (WDL), nf-core workflows (Nextflow), the Intergalactic Workflow Commission tools (Galaxy), and workflows from Seven Bridges (CWL) to highlight just a few. Here we describe the improvements made over the last four years, including the expansion of system integrations supporting authors, the addition of collaboration features and analysis platform integrations supporting users, and other enhancements that improve the overall scientific reproducibility of Dockstore content.

 

 

SORTEE (SOCIETY FOR OPEN, RELIABLE, AND TRANSPARENT ECOLOGY AND EVOLUTIONARY BIOLOGY)

“SORTEE is a service organization which brings together researchers working to improve reliability and transparency through cultural and institutional changes in ecology, evolutionary biology, and related fields broadly defined. Anyone interested in improving research in these disciplines is welcome to join, regardless of experience. The society is international in scope, membership, and objectives.is a service organization which brings together researchers working to improve reliability and transparency through cultural and institutional changes in ecology, evolutionary biology, and related fields broadly defined. Anyone interested in improving research in these disciplines is welcome to join, regardless of experience. The society is international in scope, membership, and objectives….”

 

Fee-free Open Access publishing in leading biological science journals now available to researchers in developing and transition economy countries

“From Albania to Zimbabwe, researchers in 30 developing and transition economy countries can benefit from immediate and fee-free Open Access publishing in The Company of Biologists’ subscription journals following a Read & Publish agreement with Electronic Information for Libraries (EIFL).

This landmark agreement runs until 31 December 2023 and institutional members of EIFL-partner library consortia in eligible countries can participate free of charge.

Researchers in eligible countries will be able to publish an uncapped number of Open Access research articles in Development, Journal of Cell Science and Journal of Experimental Biology without paying an article processing charge (APC). They will also benefit from free and unlimited access to the journals and their archives dating back to 1853….”

What Is BHL’s New Persistent Identifier Working Group DOI’ng? – Biodiversity Heritage Library

“In October 2020, BHL launched a new working group with a momentous goal: to make the content on BHL persistently discoverable, citable and trackable using DOIs (Digital Object Identifiers)….

BHL has been retrospectively minting DOIs for historic publications since 2011, but the focus has primarily been on monographs. BHL’s new Persistent Identifier Working Group (PIWG) is (at least initially) focusing on journal articles. Minting DOIs for articles on BHL is a far more complex and time-consuming task than minting DOIs for monographs. This is because article DOIs need article data: every journal volume uploaded onto BHL must be accompanied by journal and volume data, but there is no requirement that contributors provide article data….

COVID-19 provided an unexpected opportunity to make a considerable dent in this work. With no access to scanners or library materials, a number of BHL contributors, including Harvard University Libraries, Muséum National d’Histoire Naturelle and BHL Australia, pivoted from making new content accessible to making their existing content on BHL more discoverable. For example, BHL Australia’s digitisation volunteers gathered, gap filled and checked article-level metadata for over 30,000 articles in 2020….”

Analysis of single comments left for bioRxiv preprints till September 2019 – Biochemia Medica

Abstract:  Introduction

While early commenting on studies is seen as one of the advantages of preprints, the type of such comments, and the people who post them, have not been systematically explored.

Materials and methods

We analysed comments posted between 21 May 2015 and 9 September 2019 for 1983 bioRxiv preprints that received only one comment on the bioRxiv website. The comment types were classified by three coders independently, with all differences resolved by consensus.

Results

Our analysis showed that 69% of comments were posted by non-authors (N = 1366), and 31% by the preprints’ authors themselves (N = 617). Twelve percent of non-author comments (N = 168) were full review reports traditionally found during journal review, while the rest most commonly contained praises (N = 577, 42%), suggestions (N = 399, 29%), or criticisms (N = 226, 17%). Authors’ comments most commonly contained publication status updates (N = 354, 57%), additional study information (N = 158, 26%), or solicited feedback for the preprints (N = 65, 11%).

Conclusions

Our results indicate that comments posted for bioRxiv preprints may have potential benefits for both the public and the scholarly community. Further research is needed to measure the direct impact of these comments on comments made by journal peer reviewers, subsequent preprint versions or journal publications.

Data Sharing in Biomedical Sciences: A Systematic Review of Incentives | Biopreservation and Biobanking

Abstract:  Background: The lack of incentives has been described as the rate-limiting step for data sharing. Currently, the evaluation of scientific productivity by academic institutions and funders has been heavily reliant upon the number of publications and citations, raising questions about the adequacy of such mechanisms to reward data generation and sharing. This article provides a systematic review of the current and proposed incentive mechanisms for researchers in biomedical sciences and discusses their strengths and weaknesses.

Methods: PubMed, Web of Science, and Google Scholar were queried for original research articles, editorials, and opinion articles on incentives for data sharing. Articles were included if they discussed incentive mechanisms for data sharing, were applicable to biomedical sciences, and were written in English.

 

Results: Although coauthorship in return for the sharing of data is common, this might be incompatible with authorship guidelines and raise concerns over the ability of secondary analysts to contest the proposed research methods or conclusions that are drawn. Data publication, citation, and altmetrics have been proposed as alternative routes to credit data generators, which could address these disadvantages. Their primary downsides are that they are not well-established, it is difficult to acquire evidence to support their implementation, and that they could be gamed or give rise to novel forms of research misconduct.

Conclusions: Alternative recognition mechanisms need to be more commonly used to generate evidence on their power to stimulate data sharing, and to assess where they fall short. There is ample discussion in policy documents on alternative crediting systems to work toward Open Science, which indicates that that there is an interest in working out more elaborate metascience programs.

Post-publication peer review: another sort of quality control of the scientific record in biomedicine | Gaceta Médica de México

Abstract:  Traditional peer review is undergoing increasing questioning, given the increase in scientific fraud detected and the replication crisis biomedical research is currently going through. Researchers, academic institutions, and research funding agencies actively promote scientific record analysis, and multiple tools have been developed to achieve this. Different biomedical journals were founded with post-publication peer review as a feature, and there are several digital platforms that make this process possible. In addition, an increasing number biomedical journals allow commenting on articles published on their websites, which is also possible in preprint repositories. Moreover, publishing houses and researchers are largely using social networks for the dissemination and discussion of articles, which sometimes culminates in refutations and retractions.

 

COVID-19 and the research scholarship ecosystem: help! – Journal of Clinical Epidemiology

Highlights

Data sharing is not common as part of biomedical publications
To increase data sharing biomedical journals, funders and academic institutions should introduce policies that will enhance data sharing and other open science practices
As part of research assessments incentives and rewards need to be introduced

Abstract

Objectives

Data sharing practices remain elusive in biomedicine. The COVID-19 pandemic has highlighted the problems associated with the lack of data sharing. The objective of this article is to draw attention to the problem and possible ways to address it.

Study Design and Setting

This article examines some of the current open access and data sharing practices at biomedical journals and funders. In the context of COVID-19 the consequences of these practices is also examined.

Results

Despite the best of intentions on the part of funders and journals, COVID-19 biomedical research is not open. Academic institutions need to incentivize and reward data sharing practices as part of researcher assessment. Journals and funders need to implement strong polices to ensure that data sharing becomes a reality. Patients support sharing of their data.

Conclusion

Biomedical journals, funders and academic institutions should act to require stronger adherence to data sharing policies.

Actives from MMV Open Access Boxes? A suggested way forward

Abstract:  It is estimated that more than 1 billion people across the world are affected by a neglected tropical disease (NTD) that requires medical intervention. These diseases tend to afflict people in areas with high rates of poverty and cost economies billions of dollars every year. Collaborative drug discovery efforts are required to reduce the burden of these diseases in endemic regions. The release of “Open Access Boxes” is an initiative launched by Medicines for Malaria Venture (MMV) in collaboration with its partners to catalyze new drug discovery in neglected diseases. These boxes are mainly requested by biology researchers across the globe who may not otherwise have access to compounds to screen nor knowledge of the workflow that needs to be followed after identification of actives from their screening campaigns. Here, we present guidelines on how to move such actives beyond the hit identification stage, to help in capacity strengthening and enable a greater impact of the initiative.

 

 

Increasing transparency through open science badges

“Authors who adopt transparent practices for an article in Conservation Biology are now able to select from 3 open science badges: open data, open materials, and preregistration. Badges appear on published articles as visible recognition and highlight these efforts to the research community. There is an emerging body of literature regarding the influences of badges, for example, an increased number of articles with open data (Kidwell et al 2016) and increased rate of data sharing (Rowhani?Farid et al. 2018). However, in another study, Rowhani?Farid et al. (2020) found that badges did not “noticeably motivate” researchers to share data. Badges, as far as we know, are the only data?sharing incentive that has been tested empirically (Rowhani?Farid et al. 2017).

Rates of data and code sharing are typically low (Herold 2015; Roche et al 2015; Archmiller et al 2020; Culina et al 2020). Since 2016, we have asked authors of contributed papers, reviews, method papers, practice and policy papers, and research notes to tell us whether they “provided complete machine and human?readable data and computer code in Supporting Information or on a public archive.” Authors of 31% of these articles published in Conservation Biology said they shared their data or code, and all authors provide human?survey instruments in Supporting Information or via a citation or online link (i.e., shared materials)….”

Webinar ‘Preprints – Accelerating plant sciences and agriculture’

“The use of preprints has accelerated in the last few years with many researchers now sharing their latest work with the scientific community before or in parallel to publication with a journal. After a slower start compared to other research fields, adoption of preprints in the plant sciences and agriculture is growing well.

Why are researchers in plant and agricultural sciences posting preprints? What should you consider before you post a preprint? How does a preprint relate to a journal publication? In this webinar, we will discuss the outlook of preprints in plant sciences and agriculture, explore what can be learned from fields with a longer tradition of preprint use and hear from researchers who have successfully used preprints for the communication of their research.”

Blog – Europe PMC: Five stories showing how Europe PMC is used by the life sciences community

“Europe PMC is a searchable database that allows access to life sciences publications worldwide including preprints and micropublications. Europe PMC offers cutting-edge tools to improve the discovery of articles around a topic of interest and provides links to the data behind the articles. In a commitment to open science, Europe PMC flags articles that are free to read and even better, free to re-use. Additionally, it offers powerful APIs and easy documentation for programmatic access to the knowledgebase in Europe PMC.

 

Europe PMC is used by both experienced and early career researchers, policy makers, biocurators and innovators seeking to enhance scholarly publishing and more. What could be better than letting Europe PMC users talk about their experiences? Watch the video below to see how Europe PMC helps different users in the life sciences community to do their everyday jobs….”