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Cueto R, Harris AB, Root K, Sabharwal S, Raad M, Oni JK. Open Access Publication in Total Knee Arthroplasty Is Associated With Increased Social Media Attention, but Is Not Associated With Increased Citations. J Arthroplasty 2024; 39:285-289. [PMID: 37286049 DOI: 10.1016/j.arth.2023.05.085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 05/21/2023] [Accepted: 05/29/2023] [Indexed: 06/09/2023] Open
Abstract
BACKGROUND Open access (OA) publication is growing in total joint arthroplasty literature. While OA manuscripts are free to view, these publications require a fee from authors. This study aimed to compare social media attention and citation rates between OA and non-OA publications in the total knee arthroplasty (TKA) literature. METHODS There were 9,606 publications included, with 4,669 (48.61%) as OA articles. The TKA articles were identified from 2016 to 2022. Articles were grouped as OA or non-OA and Altmetric Attention Score (AAS), a weighted count of social media attention, and the Mendeley readership were analyzed using negative binomial regressions while adjusting for days since publication. RESULTS The OA articles had greater mean AAS (13.45 versus 8.42, P = .012) and Mendeley readership (43.91 versus 36.72, P < .001). OA was not an independent predictor of number of citations when compared to non-OA articles (13.98 versus 13.63, P = .914). Subgroup analysis of studies in the top 10 arthroplasty journals showed OA was not an independent predictor of AAS (13.51 versus 9.53, P = .084) or number of citations (19.51 versus 18.74, P = .495) but was an independent predictor of Mendeley readership (49.05 versus 40.25, P < .003). CONCLUSION The OA publications in the TKA literature were associated with increased social media attention, but not overall citations. This association was not observed among the top 10 journals. Authors may use these results to weigh the relative importance of readership, citations, and online engagement to the cost of OA publication.
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Affiliation(s)
- Robert Cueto
- College of Medicine, University of Florida, Gainesville, Florida
| | - Andrew B Harris
- Department of Orthopaedic Surgery, Johns Hopkins, Baltimore, Maryland
| | - Kevin Root
- College of Medicine, University of Florida, Gainesville, Florida
| | - Samir Sabharwal
- Department of Orthopaedic Surgery, Johns Hopkins, Baltimore, Maryland
| | - Micheal Raad
- Department of Orthopaedic Surgery, Johns Hopkins, Baltimore, Maryland
| | - Julius K Oni
- Department of Orthopaedic Surgery, Johns Hopkins, Baltimore, Maryland
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Pourret O, Ibarra DE. The rise of preprints in earth sciences. F1000Res 2023; 12:561. [PMID: 37448860 PMCID: PMC10336359 DOI: 10.12688/f1000research.133612.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
The rate of science information's spread has accelerated in recent years. In this context, it appears that many scientific disciplines are beginning to recognize the value and possibility of sharing open access (OA) online manuscripts in their preprint form. Preprints are academic papers that are published but have not yet been evaluated by peers. They have existed in research at least since the 1960s and the creation of ArXiv in physics and mathematics. Since then, preprint platforms-which can be publisher- or community-driven, profit or not for profit, and based on proprietary or free and open source software-have gained popularity in many fields (for example, bioRxiv for the biological sciences). Today, there are many platforms that are either disciplinary-specific or cross-domain, with exponential development over the past ten years. Preprints as a whole still make up a very small portion of scholarly publishing, but a large group of early adopters are testing out these value-adding tools across a much wider range of disciplines than in the past. In this opinion article, we provide perspective on the three main options available for earth scientists, namely EarthArXiv, ESSOAr/ESS Open Archive and EGUsphere.
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Affiliation(s)
| | - Daniel Enrique Ibarra
- Department of Earth, Environmental Sciences, and Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
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Glymour MM, Charpignon ML, Chen YH, Kiang MV. Counterpoint: Preprints and the Future of Scientific Publishing-In Favor of Relevance. Am J Epidemiol 2023; 192:1043-1046. [PMID: 36958814 DOI: 10.1093/aje/kwad052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 02/16/2023] [Accepted: 03/06/2023] [Indexed: 03/25/2023] Open
Abstract
Peer-reviewed journals provide an invaluable but inadequate vehicle for scientific communication. Preprints are now an essential complement to peer-reviewed publications. Eschewing preprints will slow scientific progress and reduce the public health impact of epidemiologic research. The coronavirus disease 2019 (COVID-19) pandemic highlighted long-standing limitations of the peer-review process. Preprint servers, such as bioRxiv and medRxiv, served as crucial venues to rapidly disseminate research and provide detailed backup to sound-bite science that is often communicated through the popular press or social media. The major criticisms of preprints arise from an unjustified optimism about peer review. Peer review provides highly imperfect sorting and curation of research and only modest improvements in research conduct or presentation for most individual papers. The advantages of peer review come at the expense of months to years of delay in sharing research methods or results. For time-sensitive evidence, these delays can lead to important missteps and ill-advised policies. Even with research that is not intrinsically urgent, preprints expedite debate, expand engagement, and accelerate progress. The risk that poor-quality papers will have undue influence because they are posted on a preprint server is low. If epidemiology aims to deliver evidence relevant for public health, we need to embrace strategic uses of preprint servers.
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Hadad S, Aharony N. Researchers’ perceptions, patterns, motives, and challenges in self-archiving as a function of the discipline. JOURNAL OF LIBRARIANSHIP AND INFORMATION SCIENCE 2023. [DOI: 10.1177/09610006221146768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The green open access (OA) model, which offers the most economical approach to comply with open access policies, can increase researchers’ audience and scientific outputs impact by delivering wider and easier access. This study examined researchers’ perceptions from STEM (science, technology, engineering, math) and SSH (social sciences, art and humanities) disciplines in order to reveal the types, patterns, motives, and challenges underlying their articles’ self-archiving in the green route to open-access (repositories and institutional repositories) and ASNs (academic social networks). Interviews were conducted with 20 Israeli academic researchers. Half were from STEM and half from SSH disciplines. Interviews were mapped using a bottom-up thematic analysis and follow-up quantitative comparisons. According to the findings, STEM researchers self-archived pre/post-print versions of their articles to subject-based repositories as a part of their discipline norm resulting from their funding grant requirements and as a way to receive recognition and claim priority. SSH researchers post a link to the printed-published article at the publisher’s website in ASNs, and their goal is greater visibility. In addition, findings indicate a lack of awareness, mostly by SSH researchers, regarding copyright issues and OA repositories. The green OA model provides opportunities for researchers to self-archive their work. However, there are differences between the disciplines regarding where, when, why, and how to self-archive, and what is considered a legitimate mode of green OA. This indicates an urgent need to raise SSH researchers’ awareness of the existence of open subject-based repositories and of the terms of self-archiving from publishers.
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Affiliation(s)
- Shlomit Hadad
- The Open University of Israel, Israel
- Bar-Ilan University, Israel
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5
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SCICERO: A deep learning and NLP approach for generating scientific knowledge graphs in the computer science domain. Knowl Based Syst 2022. [DOI: 10.1016/j.knosys.2022.109945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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6
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Wuttke U, Claasen A, Michel A, Neuroth H, Euler E. Bibliothekswissenschaftliche Zukunftsfelder im Kontext der Neuausrichtung des Bachelorstudiengangs Bibliothekswissenschaft der Fachhochschule Potsdam. BIBLIOTHEK FORSCHUNG UND PRAXIS 2022. [DOI: 10.1515/bfp-2022-0039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Zusammenfassung
Im folgenden Beitrag werden bibliothekswissenschaftliche Zukunftsfelder skizziert, die maßgeblich die Überarbeitung des Curriculums des Bachelorstudiengangs Bibliothekswissenschaft an der Fachhochschule Potsdam geprägt haben. Besonders hervorgehoben werden dabei informationstechnologische sowie bibliotheks- und informationswissenschaftliche Trends, die für den kompetenten Umgang mit globalen Herausforderungen wie der nachhaltigen Digitalisierung maßgeblich sind und sich in den drei Studienschwerpunkten Bibliotheks- und Informationsdidaktik, Data Steward und Offenheit wiederfinden.
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Affiliation(s)
- Ulrike Wuttke
- Vertretungsprofessorin für Bibliotheks- und Informationstechnologien und Digitale Services, Fachhochschule Potsdam , Fachbereich Informationswissenschaften , Kiepenheuerallee 5 , Potsdam Germany
| | - Alexandra Claasen
- Akademische Mitarbeiterin, Fachhochschule Potsdam , Fachbereich Informationswissenschaften , Kiepenheuerallee 5 , Potsdam Germany
| | - Antje Michel
- Forschungsprofessorin, Fachhochschule Potsdam , Fachbereich Informationswissenschaften , Kiepenheuerallee 5 , Potsdam Germany
| | - Heike Neuroth
- Forschungsprofessorin, Fachhochschule Potsdam , Fachbereich Informationswissenschaften , Kiepenheuerallee 5 , Potsdam Germany
| | - Ellen Euler
- Dekanin, Fachbereich Informationswissenschaften , Fachhochschule Potsdam , Fachbereich Informationswissenschaften , Kiepenheuerallee 5 , Potsdam Germany
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7
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Factors influencing researchers to publish in open-access: Is it a self-decision or a self-reinforcing cycle? ONLINE INFORMATION REVIEW 2022. [DOI: 10.1108/oir-01-2022-0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
PurposeThe current study examined Israeli researchers from various disciplines concerning their perceptions, attitudes and awareness of scientific publications in open access (OA) journals and repositories.Design/methodology/approachA survey instrument was developed and distributed to 202 Israeli researchers from universities, colleges and research institutions. The study used the united theory of acceptance and use of technology (UTAUT) model as a tool for mapping the factors known to influence researchers to publish in OA journals and repositories.FindingsThe empirical model confirmed the mediating effect of the association between researchers’ perceptions and the actual publishing in OA, through their behavioral intentions (BI). Furthermore, the BI are mediated by researchers’ self-decision to publish in OA. More specifically, a researcher's publication level in OA depended not only on the positive attitudes (Atti), performance expectancy (PE) and social influence (SI) mediated by BI, but also on conditions that support researchers who publish in OA, and disciplinary affiliation to science, technology, engineering and math (STEM) which lead the researcher to voluntarily publish in both green and gold OA.Research limitations/implicationsThis study contributed to the cumulative understanding of OA publishing by formulating and validating an empirical research model of acceptance and use.Practical implicationsThe implications of the findings for scientific publication theory and practices are discussed.Originality/valueThe study suggests an effective framework to understand the researcher's final decision to publish in OA. This study's results are an essential step towards the cumulative understanding of OA publicity adoption and use by researchers as a global issue in general and in Israeli academic institutions in particular.
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8
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Pourret O, Irawan DE, Shaghaei N, van Rijsingen EM, Besançon L. Toward More Inclusive Metrics and Open Science to Measure Research Assessment in Earth and Natural Sciences. Front Res Metr Anal 2022; 7:850333. [PMID: 35419504 PMCID: PMC8996171 DOI: 10.3389/frma.2022.850333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Dasapta Erwin Irawan
- Applied Geology Research Group, Faculty of Earth Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | - Najmeh Shaghaei
- Central Administration, The University Library of Southern Denmark, Sønderborg, Denmark
| | | | - Lonni Besançon
- Faculty of Information and Technology, Monash University, Clayton, MO, Australia
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Dirnagl U, Duda GN, Grainger DW, Reinke P, Roubenoff R. Reproducibility, relevance and reliability as barriers to efficient and credible biomedical technology translation. Adv Drug Deliv Rev 2022; 182:114118. [PMID: 35066104 DOI: 10.1016/j.addr.2022.114118] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/14/2022] [Accepted: 01/15/2022] [Indexed: 12/23/2022]
Abstract
Biomedical research accuracy and relevance for improving healthcare are increasingly identified as costly problems. Basic research data quality, reporting and methodology, and reproducibility are common factors implicated in this challenge. Preclinical models of disease and therapy, largely conducted in rodents, have known deficiencies in replicating most human conditions. Their translation to human results is acknowledged to be poor for decades. Clinical data quality and quantity is also recognized as deficient; gold standard randomized clinical trials are expensive. Few solid conclusions from clinical studies are replicable and many remain unpublished. The translational pathway from fundamental biomedical research through to innovative solutions handed to clinical practitioners is therefore highly inefficient and costly in terms of wasted resources, early claims from fundamental discoveries never witnessed in humans, and few new, improved solutions available clinically for myriad diseases. Improving this biomedical research strategy and resourcing for reliability, translational relevance, reproducibility and clinical impact requires careful analysis and consistent enforcement at both funding and peer review levels.
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Affiliation(s)
- Ulrich Dirnagl
- Department of Experimental Neurology, Charité - Universitätsmedizin Berlin, Germany; QUEST Center for Responsible Research, Berlin Institute of Health, Germany
| | - Georg N Duda
- Berlin Institute of Health (BIH) Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Germany; Julius Wolff Institute for Biomechanics and Musculoskeletal Regeneration, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Germany
| | - David W Grainger
- Department of Pharmaceutics and Pharmaceutical Chemistry, Health Sciences, University of Utah, Salt Lake City, UT 84112 USA; Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112 USA.
| | - Petra Reinke
- Berlin Institute of Health (BIH) Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Germany; Berlin Center for Advanced Therapies (BeCAT), Charité - Universitaetsmedizin Berlin, 13353 Berlin, Germany
| | - Ronenn Roubenoff
- Novartis Institutes for Biomedical Research, Cambridge, Basel, Massachusetts, Switzerland
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Abstract
In this short communication, we discuss the latest advances regarding Open Access in the earth sciences and geochemistry community from preprints to findable, accessible, interoperable, and reusable data following the 14f session held at Goldschmidt conference (4–9 July 2021) dedicated to “Open Access in Earth Sciences”.
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11
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Are journal archiving and embargo policies impeding the success of India's open access policy? LEARNED PUBLISHING 2022. [DOI: 10.1002/leap.1441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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12
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Diong J, Kroeger CM, Reynolds KJ, Barnett A, Bero LA. Strengthening the incentives for responsible research practices in Australian health and medical research funding. Res Integr Peer Rev 2021; 6:11. [PMID: 34340719 PMCID: PMC8328133 DOI: 10.1186/s41073-021-00113-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/16/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Australian health and medical research funders support substantial research efforts, and incentives within grant funding schemes influence researcher behaviour. We aimed to determine to what extent Australian health and medical funders incentivise responsible research practices. METHODS We conducted an audit of instructions from research grant and fellowship schemes. Eight national research grants and fellowships were purposively sampled to select schemes that awarded the largest amount of funds. The funding scheme instructions were assessed against 9 criteria to determine to what extent they incentivised these responsible research and reporting practices: (1) publicly register study protocols before starting data collection, (2) register analysis protocols before starting data analysis, (3) make study data openly available, (4) make analysis code openly available, (5) make research materials openly available, (6) discourage use of publication metrics, (7) conduct quality research (e.g. adhere to reporting guidelines), (8) collaborate with a statistician, and (9) adhere to other responsible research practices. Each criterion was answered using one of the following responses: "Instructed", "Encouraged", or "No mention". RESULTS Across the 8 schemes from 5 funders, applicants were instructed or encouraged to address a median of 4 (range 0 to 5) of the 9 criteria. Three criteria received no mention in any scheme (register analysis protocols, make analysis code open, collaborate with a statistician). Importantly, most incentives did not seem strong as applicants were only instructed to register study protocols, discourage use of publication metrics and conduct quality research. Other criteria were encouraged but were not required. CONCLUSIONS Funders could strengthen the incentives for responsible research practices by requiring grant and fellowship applicants to implement these practices in their proposals. Administering institutions could be required to implement these practices to be eligible for funding. Strongly rewarding researchers for implementing robust research practices could lead to sustained improvements in the quality of health and medical research.
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Affiliation(s)
- Joanna Diong
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, 2006, Australia.
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.
| | - Cynthia M Kroeger
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Central Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Katherine J Reynolds
- School of Public Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Adrian Barnett
- Australian Centre for Health Services Innovation and Centre for Healthcare Transformation, School of Public Health and Social Work, Faculty of Health, Queensland University of Technology, QLD, Brisbane, 4000, Australia
| | - Lisa A Bero
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, 2006, Australia
- Centre for Bioethics and Humanities, University of Colorado, Boulder, CO, 80309-0552, USA
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Ensuring Prevention Science Research is Synthesis-Ready for Immediate and Lasting Scientific Impact. PREVENTION SCIENCE : THE OFFICIAL JOURNAL OF THE SOCIETY FOR PREVENTION RESEARCH 2021; 23:809-820. [PMID: 34291384 DOI: 10.1007/s11121-021-01279-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2021] [Indexed: 12/24/2022]
Abstract
When seeking to inform and improve prevention efforts and policy, it is important to be able to robustly synthesize all available evidence. But evidence sources are often large and heterogeneous, so understanding what works, for whom, and in what contexts can only be achieved through a systematic and comprehensive synthesis of evidence. Many barriers impede comprehensive evidence synthesis, which leads to uncertainty about the generalizability of intervention effectiveness, including inaccurate titles/abstracts/keywords terminology (hampering literature search efforts), ambiguous reporting of study methods (resulting in inaccurate assessments of study rigor), and poorly reported participant characteristics, outcomes, and key variables (obstructing the calculation of an overall effect or the examination of effect modifiers). To address these issues and improve the reach of primary studies through their inclusion in evidence syntheses, we provide a set of practical guidelines to help prevention scientists prepare synthesis-ready research. We use a recent mindfulness trial as an empirical example to ground the discussion and demonstrate ways to ensure the following: (1) primary studies are discoverable; (2) the types of data needed for synthesis are present; and (3) these data are readily synthesizable. We highlight several tools and practices that can aid authors in these efforts, such as using a data-driven approach for crafting titles, abstracts, and keywords or by creating a repository for each project to host all study-related data files. We also provide step-by-step guidance and software suggestions for standardizing data design and public archiving to facilitate synthesis-ready research.
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14
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Xu F, Ou G, Ma T, Wang X. The consistency of impact of preprints and their journal publications. J Informetr 2021. [DOI: 10.1016/j.joi.2021.101153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Nüst D, Eglen SJ. CODECHECK: an Open Science initiative for the independent execution of computations underlying research articles during peer review to improve reproducibility. F1000Res 2021; 10:253. [PMID: 34367614 PMCID: PMC8311796 DOI: 10.12688/f1000research.51738.2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/15/2021] [Indexed: 11/20/2022] Open
Abstract
The traditional scientific paper falls short of effectively communicating computational research. To help improve this situation, we propose a system by which the computational workflows underlying research articles are checked. The CODECHECK system uses open infrastructure and tools and can be integrated into review and publication processes in multiple ways. We describe these integrations along multiple dimensions (importance, who, openness, when). In collaboration with academic publishers and conferences, we demonstrate CODECHECK with 25 reproductions of diverse scientific publications. These CODECHECKs show that asking for reproducible workflows during a collaborative review can effectively improve executability. While CODECHECK has clear limitations, it may represent a building block in Open Science and publishing ecosystems for improving the reproducibility, appreciation, and, potentially, the quality of non-textual research artefacts. The CODECHECK website can be accessed here: https://codecheck.org.uk/.
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Affiliation(s)
- Daniel Nüst
- Institute for Geoinformatics, University of Münster, Münster, Germany
| | - Stephen J. Eglen
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
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Nüst D, Eglen SJ. CODECHECK: an Open Science initiative for the independent execution of computations underlying research articles during peer review to improve reproducibility. F1000Res 2021; 10:253. [PMID: 34367614 PMCID: PMC8311796 DOI: 10.12688/f1000research.51738.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/22/2021] [Indexed: 11/08/2023] Open
Abstract
The traditional scientific paper falls short of effectively communicating computational research. To help improve this situation, we propose a system by which the computational workflows underlying research articles are checked. The CODECHECK system uses open infrastructure and tools and can be integrated into review and publication processes in multiple ways. We describe these integrations along multiple dimensions (importance, who, openness, when). In collaboration with academic publishers and conferences, we demonstrate CODECHECK with 25 reproductions of diverse scientific publications. These CODECHECKs show that asking for reproducible workflows during a collaborative review can effectively improve executability. While CODECHECK has clear limitations, it may represent a building block in Open Science and publishing ecosystems for improving the reproducibility, appreciation, and, potentially, the quality of non-textual research artefacts. The CODECHECK website can be accessed here: https://codecheck.org.uk/.
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Affiliation(s)
- Daniel Nüst
- Institute for Geoinformatics, University of Münster, Münster, Germany
| | - Stephen J. Eglen
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
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17
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Web of Science (WoS) and Scopus: The Titans of Bibliographic Information in Today’s Academic World. PUBLICATIONS 2021. [DOI: 10.3390/publications9010012] [Citation(s) in RCA: 133] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Nowadays, the importance of bibliographic databases (DBs) has increased enormously, as they are the main providers of publication metadata and bibliometric indicators universally used both for research assessment practices and for performing daily tasks. Because the reliability of these tasks firstly depends on the data source, all users of the DBs should be able to choose the most suitable one. Web of Science (WoS) and Scopus are the two main bibliographic DBs. The comprehensive evaluation of the DBs’ coverage is practically impossible without extensive bibliometric analyses or literature reviews, but most DBs users do not have bibliometric competence and/or are not willing to invest additional time for such evaluations. Apart from that, the convenience of the DB’s interface, performance, provided impact indicators and additional tools may also influence the users’ choice. The main goal of this work is to provide all of the potential users with an all-inclusive description of the two main bibliographic DBs by gathering the findings that are presented in the most recent literature and information provided by the owners of the DBs at one place. This overview should aid all stakeholders employing publication and citation data in selecting the most suitable DB.
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18
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Horbach SPJM. No time for that now! Qualitative changes in manuscript peer review during the Covid-19 pandemic. RESEARCH EVALUATION 2021. [PMCID: PMC7928627 DOI: 10.1093/reseval/rvaa037] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The global Covid-19 pandemic has had a considerable impact on the scientific enterprise, including scholarly publication and peer-review practices. Several studies have assessed these impacts, showing among others that medical journals have strongly accelerated their review processes for Covid-19-related content. This has raised questions and concerns regarding the quality of the review process and the standards to which manuscripts are held for publication. To address these questions, this study sets out to assess qualitative differences in review reports and editorial decision letters for Covid-19 related, articles not related to Covid-19 published during the 2020 pandemic, and articles published before the pandemic. It employs the open peer-review model at the British Medical Journal and eLife to study the content of review reports, editorial decisions, author responses, and open reader comments. It finds no clear differences between the review processes of articles not related to Covid-19 published during or before the pandemic. However, it does find notable diversity between Covid-19 and non-Covid-19-related articles, including fewer requests for additional experiments, more cooperative comments, and different suggestions to address too strong claims. In general, the findings suggest that both reviewers and journal editors implicitly and explicitly use different quality criteria to assess Covid-19-related manuscripts, hence transforming science’s main evaluation mechanism for their underlying studies and potentially affecting their public dissemination.
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Affiliation(s)
- Serge P J M Horbach
- Department of Political Sciences, Danish Centre for Studies in Research and Research Policy, Aarhus University, Bartholins Allé 7, Aarhus C, 8000, Denmark
- Faculty of Social Sciences, Centre for Science and Technology Studies (CWTS), Faculty of Social Sciences, Leiden University, Wassenaarseweg 62A, AL Leiden 2333, The Netherlands
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Abstract
Understanding the evolution of scientific literature is a critical and necessary step for the development and strengthening of a research field. However, an overview of global dinoflagellate research remains unavailable. Herein, global dinoflagellate research output was analyzed based on a scientometric approach using the Scopus data archive. The basic characteristics and worldwide interactions of dinoflagellate research output were analyzed to determine the temporal evolution and new emerging trends. The results confirm that dinoflagellate research output, reflected in the number of publications, is a fast-growing area since the mid-1990s. In total, five research subareas emerged using a bibliometric keywords analysis: (1) “symbiosis with coral reefs”, (2) “phylogeny”, (3) “palynology”, (4) “harmful algal blooms” and (5) “nutrition strategies”. Dinoflagellate publications were modeled by fish production (both aquaculture and fisheries) and economic and social indexes. Finally, directions for future research are proposed and discussed. The presented scientometric analysis confirms that dinoflagellate research is an active and important area with focus on mitigating economic impacts, especially in regard to fish production.
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Pourret O, Irawan DE, Tennant JP, Hursthouse A, van Hullebusch ED. The growth of open access publishing in geochemistry. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.ringeo.2020.100001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Yang C, Hawwash D, De Baets B, Bouwman J, Lachat C. Perspective: Towards Automated Tracking of Content and Evidence Appraisal of Nutrition Research. Adv Nutr 2020; 11:1079-1088. [PMID: 32504536 PMCID: PMC7490154 DOI: 10.1093/advances/nmaa057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/10/2020] [Accepted: 04/24/2020] [Indexed: 11/13/2022] Open
Abstract
Robust recommendations for healthy diets and nutrition require careful synthesis of available evidence. Given the increasing volume of research articles generated, the retrieval and synthesis of evidence are increasingly becoming laborious and time-consuming. Information technology could help to reduce workload for humans. To guide supervised learning however, human identification of key study characteristics is necessary. Reporting guidelines recommend that authors include essential content in articles and could generate manually labeled training data for automated evidence retrieval and synthesis. Here, we present a semiautomated approach to annotate, link, and track the content of nutrition research manuscripts. We used the STROBE extension for nutritional epidemiology (STROBE-nut) reporting guidelines to manually annotate a sample of 15 articles and converted the semantic information into linked data in a Neo4j graph database through an automated process. Six summary statistics were computed to estimate the reporting completeness of the articles. The content structure, presence of essential study characteristics as well as the reporting completeness of the articles are visualized automatically from the graph database. The archived linked data are interoperable through their annotations and relations. A graph database with linked data on essential study characteristics can enable Natural Language Processing in nutrition.
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Affiliation(s)
- Chen Yang
- Department of Food Technology, Safety and Health, Ghent University, Ghent, Belgium
| | - Dana Hawwash
- Department of Food Technology, Safety and Health, Ghent University, Ghent, Belgium
| | - Bernard De Baets
- KERMIT (Research Unit of Knowledge-based Systems), Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Jildau Bouwman
- Netherlands Organization for Applied Scientific Research, Zeist, The Netherlands
| | - Carl Lachat
- Department of Food Technology, Safety and Health, Ghent University, Ghent, Belgium
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Pourret O, Irawan DE, Tennant JP, Wien C, Dorch BF. Comments on "Factors affecting global flow of scientific knowledge in environmental sciences" by Sonne et al. (2020). THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 721:136454. [PMID: 31924309 DOI: 10.1016/j.scitotenv.2019.136454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/29/2019] [Accepted: 12/29/2019] [Indexed: 06/10/2023]
Abstract
There are major challenges that need to be addressed in the world of scholarly communication, especially in the field of environmental studies and in the context of the United Nations Sustainable Development Goals. Recently, Sonne et al. (2020) published an article in Science of the Total Environment discussing some of these challenges. However, we feel that many of the arguments misrepresent critical elements of Open Access (OA), Plan S, and broader issues in scholarly publishing. In our response, we focus on addressing key elements of their discussion on (i) OA and Plan S, as well as (ii) Open Access Predatory Journals (OAPJ). The authors describe OA and Plan S as restricting author choice, especially through the payment of article-processing charges. The reality is that 'green OA' self-archiving options alleviate virtually all of the risks they mention, and are even the preferred 'routes' to OA as stated by both institutional and national policies in Denmark. In alignment with this, Plan S is also taking a progressive stance on reforming research evaluation. The assumptions these authors make about OA in the "global south" also largely fail to acknowledge some of the progressive work being done in regions like Indonesia and Latin America. Finally, Sonne et al. (2020) highlight the threat that OAPJs face to our scholarly knowledge production system. While we agree generally that OAPJs are problematic, the authors simultaneously fail to mention many of the excellent initiatives helping to combat this threat (e.g., the Directory of Open Access Journals). We call for researchers to more effectively equip themselves with sufficient knowledge of relevant systems before making public statements about them, in order to prevent misinformation from polluting the debate about the future of scholarly communication.
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Affiliation(s)
- Olivier Pourret
- UniLaSalle, AGHYLE, 19 rue Pierre Waguet, 60026 Beauvais cedex, France.
| | - Dasapta Erwin Irawan
- Faculty of Earth Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | | | - Charlotte Wien
- SDU, Faculty of Health, Clinical Department/The University Library of Southern Denmark, Odense, Denmark
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Southan C. Opening up connectivity between documents, structures and bioactivity. Beilstein J Org Chem 2020; 16:596-606. [PMID: 32280387 PMCID: PMC7136548 DOI: 10.3762/bjoc.16.54] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/12/2020] [Indexed: 12/17/2022] Open
Abstract
Bioscientists reading papers or patents strive to discern the key relationships reported within a document "D" where a bioactivity "A" with a quantitative result "R" (e.g., an IC50) is reported for chemical structure "C" that modulates (e.g., inhibits) a protein target "P". A useful shorthand for this connectivity thus becomes DARCP. The problem at the core of this article is that the community has spent millions effectively burying these relationships in PDFs over many decades but must now spend millions more trying to get them back out. The key imperative for this is to increase the flow into structured open databases. The positive impacts will include expanded data mining opportunities for drug discovery and chemical biology. Over the last decade commercial sources have manually extracted DARCP from ≈300,000 documents encompassing ≈7 million compounds interacting with ≈10,000 targets. Over a similar time, the Guide to Pharmacology, BindingDB and ChEMBL have carried out analogues DARCP extractions. Although their expert-curated numbers are lower (i.e., ≈2 million compounds against ≈3700 human proteins), these open sources have the great advantage of being merged within PubChem. Parallel efforts have focused on the extraction of document-to-compound (D-C-only) connectivity. In the absence of molecular mechanism of action (mmoa) annotation, this is of less value but can be automatically extracted. This has been significantly accomplished for patents, (e.g., by IBM, SureChEMBL and WIPO) for over 30 million compounds in PubChem. These have recently been joined by 1.4 million D-C submissions from three major chemistry publishers. In addition, both the European and US PubMed Central portals now add chemistry look-ups from abstracts and full-text papers. However, the fully automated extraction of DARCLP has not yet been achieved. This stands in contrast to the ability of biocurators to discern these relationships in minutes. Unfortunately, no journals have yet instigated a flow of author-specified DARCP directly into open databases. Progress may come from trends such as open science, open access (OA), findable, accessible, interoperable and reusable (FAIR), resource description framework (RDF) and WikiData. However, we will need to await the technical applicability in respect to DARCP capture to see if this opens up connectivity.
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Affiliation(s)
- Christopher Southan
- Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
- TW2Informatics Ltd, Västra Frölunda, Gothenburg, 42166, Sweden
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Abstract
Preprints are gaining visibility in many fields. Thanks to the exponential growth in submissions to bioRxiv, an online server for preprints in biology, versions of manuscripts prior to the completion of journal-organized peer review are poised to become a standard component of the publishing experience in the life sciences. Here, we provide an overview of current challenges facing preprints, both technical and social, and a vision for their future development.
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Open Access publishing practice in geochemistry: overview of current state and look to the future. Heliyon 2020; 6:e03551. [PMID: 32181407 PMCID: PMC7063138 DOI: 10.1016/j.heliyon.2020.e03551] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/23/2020] [Accepted: 03/03/2020] [Indexed: 11/21/2022] Open
Abstract
Open Access (OA) describes the free, unrestricted access to and re-use of research articles. Recently, a new wave of interest, debate, and practice surrounding OA publishing has emerged. In this paper, we provide a simple overview of the trends in OA practice in the broad field of geochemistry. Characteristics of the approach such as whether or not an article processing charge (APC) exists, what embargo periods or restrictions on self-archiving' policies are in place, and whether or not the sharing of preprints is permitted are described. The majority of journals have self-archiving policies that allow authors to share their peer reviewed work via green OA without charge. There is no clear relationship between journal impact and APC. The journals with the highest APC are typically those of the major commercial publishers, rather than the geochemistry community themselves. The rise in OA publishing has potential impacts on the profiles of researchers and tends to devolve costs from organizations to individuals. Until the geochemistry community makes the decision to move away from journal-based evaluation criteria, it is likely that such high costs will continue to impose financial inequities upon research community. However, geochemists could more widely choose legal self-archiving as an equitable and sustainable way to disseminate their research.
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Wang K, Shen Z, Huang C, Wu CH, Dong Y, Kanakia A. Microsoft Academic Graph: When experts are not enough. QUANTITATIVE SCIENCE STUDIES 2020. [DOI: 10.1162/qss_a_00021] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
An ongoing project explores the extent to which artificial intelligence (AI), specifically in the areas of natural language processing and semantic reasoning, can be exploited to facilitate the studies of science by deploying software agents equipped with natural language understanding capabilities to read scholarly publications on the web. The knowledge extracted by these AI agents is organized into a heterogeneous graph, called Microsoft Academic Graph (MAG), where the nodes and the edges represent the entities engaging in scholarly communications and the relationships among them, respectively. The frequently updated data set and a few software tools central to the underlying AI components are distributed under an open data license for research and commercial applications. This paper describes the design, schema, and technical and business motivations behind MAG and elaborates how MAG can be used in analytics, search, and recommendation scenarios. How AI plays an important role in avoiding various biases and human induced errors in other data sets and how the technologies can be further improved in the future are also discussed.
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Abstract
Open science refers to both the practices and norms of more open and transparent communication and research in scientific disciplines and the discourse on these practices and norms. There is no such discourse dedicated to the humanities. Though the humanities appear to be less coherent as a cluster of scholarship than the sciences are, they do share unique characteristics which lead to distinct scholarly communication and research practices. A discourse on making these practices more open and transparent needs to take account of these characteristics. The prevalent scientific perspective in the discourse on more open practices does not do so, which confirms that the discourse’s name, open science, indeed excludes the humanities so that talking about open science in the humanities is incoherent. In this paper, I argue that there needs to be a dedicated discourse for more open research and communication practices in the humanities, one that integrates several elements currently fragmented into smaller, unconnected discourses (such as on open access, preprints, or peer review). I discuss three essential elements of open science—preprints, open peer review practices, and liberal open licences—in the realm of the humanities to demonstrate why a dedicated open humanities discourse is required.
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Müller UK. Editorial: Science Needs an Inclusive and Transparent Publication Process—How Integrative and Comparative Biology Works Toward This Aim. Integr Comp Biol 2019; 59:1445-1450. [DOI: 10.1093/icb/icz148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Ulrike K Müller
- Department of Biology, California State University—Fresno, 2555 E San Ramon Avenue, Fresno, CA, USA
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Which Are the Tools Available for Scholars? A Review of Assisting Software for Authors during Peer Reviewing Process. PUBLICATIONS 2019. [DOI: 10.3390/publications7030059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
There is a large amount of Information Technology and Communication (ITC) tools that surround scholar activity. The prominent place of the peer-review process upon publication has promoted a crowded market of technological tools in several formats. Despite this abundance, many tools are unexploited or underused because they are not known by the academic community. In this study, we explored the availability and characteristics of the assisting tools for the peer-reviewing process. The aim was to provide a more comprehensive understanding of the tools available at this time, and to hint at new trends for further developments. The result of an examination of literature assisted the creation of a novel taxonomy of types of software available in the market. This new classification is divided into nine categories as follows: (I) Identification and social media, (II) Academic search engines, (III) Journal-abstract matchmakers, (IV) Collaborative text editors, (V) Data visualization and analysis tools, (VI) Reference management, (VII) Proofreading and plagiarism detection, (VIII) Data archiving, and (IX) Scientometrics and Altmetrics. Considering these categories and their defining traits, a curated list of 220 software tools was completed using a crowdfunded database (AlternativeTo) to identify relevant programs and ongoing trends and perspectives of tools developed and used by scholars.
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Madsen RR. Scientific impact and the quest for visibility. FEBS J 2019; 286:3968-3974. [DOI: 10.1111/febs.15043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 08/16/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Ralitsa R. Madsen
- Centre for Cardiovascular Science Queen's Medical Research Institute University of Edinburgh UK
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Decomposing the Complexity of Value: Integration of Digital Transformation of Education with Circular Economy Transition. SOCIAL SCIENCES 2019. [DOI: 10.3390/socsci8080243] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In this article, we highlight the pressing need for integrating the windows of opportunities that digital transformation of education opens up with circular economy education to accelerate the achievements of sustainability outcomes. Circular economy transition, as a multi-scalar process, relates to several contexts, e.g., product, firm, industry-level transformations ranging from designing local socio-technical solutions to greening global value chains, with multi-level policy and business implications for finance, production, distribution, consumption that are fundamentally consequential to everyday life, work and learning. Drawing on theories of neo-capital, multi-level perspective and structuration, and as methodology, using content analysis and qualitative meta-synthesis of scientific publications in digital education for sustainability, we blended our findings into multi-level, multi-domain structuration blueprints, which capture the complexity of value emanating from the interactions among external structures, internal structures of agents, active agencies and outcomes, for circular economy open online education and massive open online course instructional designs. We conclude that learning and creating multiple values to increase social–ecological value, complementarily to economic value, necessitate activating the complexity of value embedded in digital education and circular economy transitions with cu2005mizable niches of learning preferences and journeys of individuals and groups, within broader (and evolving) technological, organizational and institutional structures.
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Vuong Q. The harsh world of publishing in emerging regions and implications for editors and publishers: The case of Vietnam. LEARNED PUBLISHING 2019. [DOI: 10.1002/leap.1255] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Quan‐Hoang Vuong
- Centre for Interdisciplinary Social ResearchPhenikaa University Hanoi Vietnam
- The European Association of Science Editors – Vietnam Regional Chapter Hanoi Vietnam
- NAFOSTED Scientific Council on Basic Research in the Social Sciences and Humanities Hanoi Vietnam
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Chiarelli A, Johnson R, Pinfield S, Richens E. Preprints and Scholarly Communication: Adoption, Practices, Drivers and Barriers. F1000Res 2019; 8:971. [PMID: 32055396 PMCID: PMC6961415 DOI: 10.12688/f1000research.19619.2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/11/2019] [Indexed: 11/20/2022] Open
Abstract
Background: Since 2013, there has been a dramatic increase in the number of preprint servers available online. To date, little is known about the position of researchers, funders, research performing organisations and other stakeholders with respect to this fast-paced landscape. In this article, we explore the benefits and challenges of preprint posting, along with issues such as infrastructure and financial sustainability. We also discuss the definition of a 'preprint' in different communities, and the impact this has on further uptake. Methods: This study is based on 38 detailed semi-structured interviews of key stakeholders based on a purposive heterogeneous sampling approach. Interviews were undertaken between October 2018 and January 2019. These were recorded, transcribed and subjected to thematic analysis to identify trends. Interview questions were designed based on Innovation Diffusion Theory, which is also used to interpret the results of this study. Results: Our study is the first using empirical data to understand the new wave of preprint servers and found that early and fast dissemination is the most appealing feature of the practice. The main concerns are related to the lack of quality assurance and the 'Ingelfinger rule'. We identified trust as an essential enabler of preprint posting and stress the enabling role of Twitter in showcasing preprints and enabling comments on these. Conclusions: The preprints landscape is evolving fast and disciplinary communities are at different stages in the innovation diffusion process. The landscape is characterised by significant experimentation, which leads to the conclusion that a one-size-fits-all approach to preprints is not feasible. Cooperation and active engagement between the stakeholders involved will play an important role in the future. In our paper, we share questions for the further development of the preprints landscape, with the most important being whether preprint posting will develop as a publisher- or researcher-centric practice.
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Affiliation(s)
| | - Rob Johnson
- Research Consulting Limited, Nottingham, NG7 2TU, UK
| | - Stephen Pinfield
- Information School, University of Sheffield, Sheffield, S1 4DP, UK
| | - Emma Richens
- Research Consulting Limited, Nottingham, NG7 2TU, UK
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