Reviewers' Decision to Sign Reviews Is Related to Their Recommendation
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Do You Speak Open Science? Resources and Tips to Learn the Language
Do You Speak Open Science? Resources and Tips to Learn the Language. Paola Masuzzo1, 2 - ORCID: 0000-0003-3699-1195, Lennart Martens1,2 - ORCID: 0000- 0003-4277-658X Author Affiliation 1 Medical Biotechnology Center, VIB, Ghent, Belgium 2 Department of Biochemistry, Ghent University, Ghent, Belgium Abstract The internet era, large-scale computing and storage resources, mobile devices, social media, and their high uptake among different groups of people, have all deeply changed the way knowledge is created, communicated, and further deployed. These advances have enabled a radical transformation of the practice of science, which is now more open, more global and collaborative, and closer to society than ever. Open science has therefore become an increasingly important topic. Moreover, as open science is actively pursued by several high-profile funders and institutions, it has fast become a crucial matter to all researchers. However, because this widespread interest in open science has emerged relatively recently, its definition and implementation are constantly shifting and evolving, sometimes leaving researchers in doubt about how to adopt open science, and which are the best practices to follow. This article therefore aims to be a field guide for scientists who want to perform science in the open, offering resources and tips to make open science happen in the four key areas of data, code, publications and peer-review. The Rationale for Open Science: Standing on the Shoulders of Giants One of the most widely used definitions of open science originates from Michael Nielsen [1]: “Open science is the idea that scientific knowledge of all kinds should be openly shared as early as is practical in the discovery process”. -
Downloads Presented on the Abstract Page
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.27.063578; this version posted April 28, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. A systematic examination of preprint platforms for use in the medical and biomedical sciences setting Jamie J Kirkham1*, Naomi Penfold2, Fiona Murphy3, Isabelle Boutron4, John PA Ioannidis5, Jessica K Polka2, David Moher6,7 1Centre for Biostatistics, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom. 2ASAPbio, San Francisco, CA, USA. 3Murphy Mitchell Consulting Ltd. 4Université de Paris, Centre of Research in Epidemiology and Statistics (CRESS), Inserm, Paris, F-75004 France. 5Meta-Research Innovation Center at Stanford (METRICS) and Departments of Medicine, of Epidemiology and Population Health, of Biomedical Data Science, and of Statistics, Stanford University, Stanford, CA, USA. 6Centre for Journalology, Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, Canada. 7School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Canada. *Corresponding Author: Professor Jamie Kirkham Centre for Biostatistics Faculty of Biology, Medicine and Health The University of Manchester Jean McFarlane Building Oxford Road Manchester, M13 9PL, UK Email: [email protected] Tel: +44 (0)161 275 1135 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.27.063578; this version posted April 28, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
Peer Review Fails Equity Test Analysis of Submissions to Elife Reveals a Gender Gap in Whom Journals Invite to Do Reviews
IN FOCUS NEWS Micrograph of yttrium studied images of the The technique could eventually help barium copper oxide, pseudogap. Patterns physicists to understand high-temperature a high-temperature in the images, taken superconductivity, says Allan, although he superconductor. with a scanning cautions that the paper is far from definitive tunnelling micro- and that debate about what the pseudogap is scope, often seem disordered to the human eye will continue. because of the material’s naturally chaotic and The work is an impressive, original fluctuating nature, and noise in the measure- application of machine-learning algorithms to ments. The advantage of machine learning in this type of experimental data, says Tremblay. this situation is that algorithms can learn to But the algorithm can only distinguish recognize patterns that are invisible to people. between the various hypotheses it is given, he says, rather than find entirely new patterns. PATTERN RECOGNITION During her talk, Kim said that work is under To train the algorithms, the team fed neural way to apply the technique to rapidly make networks examples of rippled patterns that sense of data from the X-ray diffraction of corresponded to different theoretical predic- quantum materials — a technique that uses the tions. Having learnt to recognize these exam- scattering of electromagnetic waves to reveal ples, each algorithm applied this learning to a mater ial’s 3D physical structure, but which real data from cuprates in the pseudogap. Over creates patterns so rich that they can take 81 iterations, the algorithms repeatedly identi- months to unravel by conventional means. In fied one modulating pattern that corresponded this case, the AI must draw out similarities and to the particle-like description of electrons, classifications itself, rather than be given pre- which dates back to the 1990s. -
Badges for Sharing Data and Code at an Biostatistics
F1000Research 2018, 7:90 Last updated: 09 MAR 2018 RESEARCH ARTICLE Badges for sharing data and code at Biostatistics: an observational study [version 2; referees: 2 approved] Anisa Rowhani-Farid , Adrian G. Barnett Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, 4001, Australia v2 First published: 19 Jan 2018, 7:90 (doi: 10.12688/f1000research.13477.1) Open Peer Review Latest published: 07 Mar 2018, 7:90 (doi: 10.12688/f1000research.13477.2) Referee Status: Abstract Background: The reproducibility policy at the journal Biostatistics rewards articles with badges for data and code sharing. This study investigates the Invited Referees effect of badges at increasing reproducible research. 1 2 Methods: The setting of this observational study is the Biostatistics and Statistics in Medicine (control journal) online research archives. The data consisted of 240 randomly sampled articles from 2006 to 2013 (30 articles per version 2 report report year) per journal. Data analyses included: plotting probability of data and code published sharing by article submission date, and Bayesian logistic regression modelling. 07 Mar 2018 Results: The probability of data sharing was higher at Biostatistics than the control journal but the probability of code sharing was comparable for both version 1 journals. The probability of data sharing increased by 3.9 times (95% credible published report report 19 Jan 2018 interval: 1.5 to 8.44 times, p-value probability that sharing increased: 0.998) after badges were introduced at Biostatistics. On an absolute scale, this difference was only a 7.6% increase in data sharing (95% CI: 2 to 15%, 1 Gustav Nilsonne , Stockholm p-value: 0.998). -
SCIENCE CITATION INDEX EXPANDED - JOURNAL LIST Total Journals: 8631
SCIENCE CITATION INDEX EXPANDED - JOURNAL LIST Total journals: 8631 1. 4OR-A QUARTERLY JOURNAL OF OPERATIONS RESEARCH 2. AAPG BULLETIN 3. AAPS JOURNAL 4. AAPS PHARMSCITECH 5. AATCC REVIEW 6. ABDOMINAL IMAGING 7. ABHANDLUNGEN AUS DEM MATHEMATISCHEN SEMINAR DER UNIVERSITAT HAMBURG 8. ABSTRACT AND APPLIED ANALYSIS 9. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 10. ACADEMIC EMERGENCY MEDICINE 11. ACADEMIC MEDICINE 12. ACADEMIC PEDIATRICS 13. ACADEMIC RADIOLOGY 14. ACCOUNTABILITY IN RESEARCH-POLICIES AND QUALITY ASSURANCE 15. ACCOUNTS OF CHEMICAL RESEARCH 16. ACCREDITATION AND QUALITY ASSURANCE 17. ACI MATERIALS JOURNAL 18. ACI STRUCTURAL JOURNAL 19. ACM COMPUTING SURVEYS 20. ACM JOURNAL ON EMERGING TECHNOLOGIES IN COMPUTING SYSTEMS 21. ACM SIGCOMM COMPUTER COMMUNICATION REVIEW 22. ACM SIGPLAN NOTICES 23. ACM TRANSACTIONS ON ALGORITHMS 24. ACM TRANSACTIONS ON APPLIED PERCEPTION 25. ACM TRANSACTIONS ON ARCHITECTURE AND CODE OPTIMIZATION 26. ACM TRANSACTIONS ON AUTONOMOUS AND ADAPTIVE SYSTEMS 27. ACM TRANSACTIONS ON COMPUTATIONAL LOGIC 28. ACM TRANSACTIONS ON COMPUTER SYSTEMS 29. ACM TRANSACTIONS ON COMPUTER-HUMAN INTERACTION 30. ACM TRANSACTIONS ON DATABASE SYSTEMS 31. ACM TRANSACTIONS ON DESIGN AUTOMATION OF ELECTRONIC SYSTEMS 32. ACM TRANSACTIONS ON EMBEDDED COMPUTING SYSTEMS 33. ACM TRANSACTIONS ON GRAPHICS 34. ACM TRANSACTIONS ON INFORMATION AND SYSTEM SECURITY 35. ACM TRANSACTIONS ON INFORMATION SYSTEMS 36. ACM TRANSACTIONS ON INTELLIGENT SYSTEMS AND TECHNOLOGY 37. ACM TRANSACTIONS ON INTERNET TECHNOLOGY 38. ACM TRANSACTIONS ON KNOWLEDGE DISCOVERY FROM DATA 39. ACM TRANSACTIONS ON MATHEMATICAL SOFTWARE 40. ACM TRANSACTIONS ON MODELING AND COMPUTER SIMULATION 41. ACM TRANSACTIONS ON MULTIMEDIA COMPUTING COMMUNICATIONS AND APPLICATIONS 42. ACM TRANSACTIONS ON PROGRAMMING LANGUAGES AND SYSTEMS 43. ACM TRANSACTIONS ON RECONFIGURABLE TECHNOLOGY AND SYSTEMS 44. -
Peerj – a Case Study in Improving Research Collaboration at the Journal Level
Information Services & Use 33 (2013) 251–255 251 DOI 10.3233/ISU-130714 IOS Press PeerJ – A case study in improving research collaboration at the journal level Peter Binfield PeerJ, P.O. Box 614, Corte Madera, CA 94976, USA E-mail: PeterBinfi[email protected] Abstract. PeerJ Inc. is the Open Access publisher of PeerJ (a peer-reviewed, Open Access journal) and PeerJ PrePrints (an un-peer-reviewed or collaboratively reviewed preprint server), both serving the biological, medical and health sciences. The Editorial Criteria of PeerJ (the journal) are similar to those of PLOS ONE in that all submissions are judged only on their scientific and methodological soundness (not on subjective determinations of impact, or degree of advance). PeerJ’s peer-review process is managed by an Editorial Board of 800 and an Advisory Board of 20 (including 5 Nobel Laureates). Editor listings by subject area are at: https://peerj.com/academic-boards/subjects/ and the Advisory Board is at: https://peerj.com/academic- boards/advisors/. In the context of Understanding Research Collaboration, there are several unique aspects of the PeerJ set-up which will be of interest to readers of this special issue. Keywords: Open access, peer reviewed 1. Introduction PeerJ is based in San Francisco and London, and was launched in 2012 by Co-Founders Jason Hoyt (previously of Mendeley) and Peter Binfield (previously of PLOS ONE). PeerJ Inc. has been financed by Venture Capital investment from O’Reilly Media and OATV and Tim O’Reilly is on the Governing Board. PeerJ is a full member of CrossRef, OASPA (the Open Access Scholarly Publishers Association) and COPE (the Committee on Publication Ethics). -
Security Implications of Emerging Biotechnologies: Workshop Summary, Analysis, and Recommendations
Security Implications of Emerging Biotechnologies: Workshop Summary, Analysis, and Recommendations Diane DiEuliis and Charles Lutes June 2016 Security Implications of Emerging Biotechnologies Workshop Summary, Analysis, and Recommendations Diane DiEuliis and Charles Lutes On April 26th, 2016, the Center for the Study of Weapons of Mass Destruction (CSWMD) at National Defense University held a workshop to explore “Security Implications of Emerging Biotechnologies.” Participants from government, NGOs and academia discussed opportunities and challenges of a new era of biotechnology, one highlighted by the advancing ease with which the genomes of organisms can be engineered for specific purposes, potentially more rapidly than we are prepared to assess and deal responsibly with its ramifications. Synthetic biology and associated genome editing tools will be essential for addressing the global challenge of resource scarcity, provide unprecedented advances in public health and medicine, and create innovative products that can support national defense, as well as commodities that stimulate the US economy. At the same time, new dual-use technologies will present significant challenges to biosecurity, biosafety, and have already begun to generate ethical and moral dilemmas. Participants stressed the need to address these issues in ways that do not stifle the technology’s advancement nor America’s competitiveness in the global bioeconomy. The workshop was convened to consider the potential biosecurity concerns of emerging biotechnologies and their impact on national security. The dual use problem was discussed in the context of “biosecurity by design,” a concept conceived specifically in preparation for the workshop in which government, industry, academia, national laboratories, and individual users should be mindful of developing potential security solutions at each step of technology development. -
The Royal Society Moves to Continuous Publication
Insights – 26(2), July 2013 Royal Society moves to continuous publication | Helen Duriez 350 years at the cutting edge of scientific publishing – the Royal Society moves to continuous publication ‘Continuous publication’ is a digital-friendly concept that does exactly what it says on the tin. It is the idea that individual journal articles are published online, in their final format, as soon as they are ready. Collectively, they form a continuous feed of published articles. These articles are no longer constrained by the traditional print schedule, which means that citation details are available straight away and the reader has confidence that they are reading the version of record. A number of newly launched journals have experimented with a continuous format over the past few years, although to see established journals making the switch to a different publication model is still rare. So when the Royal Society, publisher of the world’s first science journal, decided to transition its titles to a continuous publication model, it was a bold move. This case study examines the reasons behind the move and the lessons that were learned. Introduction The Royal Society publishes nine peer-reviewed journals across the physical and biological sciences, including the world’s first science journal: Philosophical Transactions (now published in two parts, A1 and B2). In recent years, digital usage of its suite of journals has steadily overtaken print, to the point where the journals are now primarily found and downloaded from the internet. With the introduction of systematic digital archiving and curation, it has become clear that the future of published research will almost exclusively HELEN DURIEZ be online, and therefore steps are being taken towards removing the constraints that print ePublishing Manager production places upon online publication. -
Editorial to My Article in Open Biology Journal Richard H W Funk* Institute of Anatomy and Center for Regenerative Therapies, Dresden, Germany
tems: ys Op Funk, Biol Syst 2013, 2:2 l S e a n A ic c g c DOI: 10.4172/bso.1000e105 o l e s o i s B Biological Systems: Open Access ISSN: 2329-6577 Editorial Open Access Editorial to my Article in Open Biology Journal Richard H W Funk* Institute of Anatomy and Center for Regenerative Therapies, Dresden, Germany It is hard to believe, but it is true: some facts in modern cell biology The review by FUNK in this issue demonstrates by many well are ignored and disregarded, still. One example is the driving forces published studies that such ion gradients generate electric fields and in the early embryonic development and morphogenesis in general. direct currents, which are able to form patterns within cell membranes Recently, a very well compiled commentary summed up the history (e.g. in the early embryo), cell arrays (e.g. in the developing lens) and of the physical (mostly mechanical) forces in early embryogenesis [1] tissues (e.g. neural tube formation). Furthermore, not only small ions but one physical force was left out completely: the electric force or the like sodium or potassium can be involved in this field patterning but charges of molecules and ions and their gradients. Another example also larger biomolecules (which possess nearly all electrical charges) like is left – right pattern formation in early embryogenesis where most tissue factors, growth hormones, transmitters and signaling molecules theories set the starting point at the asymmetric beat of cilia moving the like serotonin and others. By the activity of ion pumps and channels as flow of growth factors or other signaling molecules into one preferred well as via charged transmitter molecules these electric phenomena are direction [2]. -
Working Together to Maximize Efficiency During the COVID-19 Pandemic
Working together to maximize efficiency during the COVID-19 pandemic A cross-publisher initiative #C19RapidReview Last updated: May 2020 This cross-publisher collaboration endorsed by the Open Access Scholarly Publishers Association (OASPA) aims to ensure research related to COVID-19 is reviewed and published as quickly as possible. We have come together across the open publishing industry to support academics; peer reviewers, editors and authors, and to ensure the widest and quickest dissemination of relevant quality content. To this end, we encourage academics to sign up to a reviewer database. Please, consider signing up as a rapid reviewer by filling in this form. We also encourage authors to use preprint servers and call on other publishers to action with a focus on open data. Read the formal Letter of Intent for more information and help us spread the word on social media using #C19RapidReview. List of organizations and journal titles participating in the #C19RapidReview initiative Royal Society Proceedings A Proceedings B Open Biology Biology Letters Interface Royal Society Open Science Hindawi Advances in Public Health Analytical Cellular Pathology BioMed Research International Canadian Journal of Infectious Diseases and Medical Microbiology Canadian Respiratory Journal Cardiology Research and Practice Case Reports in Critical Care Case Reports in Emergency Medicine Case Reports in Immunology Case Reports in Infectious Diseases Case Reports in Medicine Case Reports in Otolaryngology Case Reports in Pulmonology Complexity -
Download the Copyright Letter
The Open Biology Journal Copyright letter Date: [_________] To: Director Publications BENTHAM SCIENCE PUBLISHERS LTD Executive Suite Y-2 PO Box 7917, Saif Zone Sharjah UNITED ARAB EMIRATES Fax: +971-6-557-1134 (UAE) Email: [email protected] Dear Sir Re: BENTHAM OPEN - Open Access Publishing Agreement Please find attached a copy of the Bentham Science Publishers Ltd (“Bentham Open”) terms and conditions (“Open Access Publication Terms & Conditions”) for open access publishing via Bentham Open, along with related Schedules including a schedule setting out details of the subject copyright work (the “Work”), namely: TITLE OF WORK: [INSERT] I am the Principal / Corresponding Author of the Work, and my contact details are found in the signature block below. In order to submit the Work for publication on an open access basis via Bentham Open, I understand that: it is necessary to complete and submit this Copyright Letter, along with the Open Access Publication Terms & Conditions and the attached Schedules; the Copyright Letter, along with the Open Access Publication Terms & Conditions and the attached Schedules, together comprise the agreement between myself and Bentham Open relating to the publication of the Work; and the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), along with the other terms and conditions found in the Copyright Letter, the Open Access Publication Terms & Conditions and Schedules, apply to the publication of the Work via Bentham Open. I have signed and dated this Copyright Letter, the Open Access Publication Terms & Conditions, and the Schedules. Please have these documents countersigned on behalf of Bentham Open, and return a copy to me by email at your nearest opportunity. -
Extending Arxiv. Org to Achieve Open Peer Review and Publishing
EXTENDING ARXIV.ORG TO ACHIEVE OPEN PEER REVIEW AND PUBLISHING AXEL BOLDT Abstract. Today’s peer review process for scientific articles is unnecessarily opaque and offers few incentives to referees. Likewise, the publishing process is unnecessarily inefficient and its results are only rarely made freely available to the public. In this article we outline a comparatively simple extension of arXiv.org, an online preprint archive widely used in the mathematical and physical sciences, that addresses both of these problems. Under the proposal, editors invite referees to write public and signed reviews to be attached to the posted preprints, and then elevate selected articles to “published” status. 1. The status quo In the system of peer review that is currently used in the sciences, an editor invites one or more referees to review an article submitted to a scientific journal. Based on the referees’ recommendations, the editor will accept the article, demand modifications, or reject it. Referee reports are generally made available to the article’s author in anonymized form only and are not otherwise published. (Some journals also anonymize the article to be refereed, even though ascertaining the arXiv:1011.6590v1 [cs.OH] 23 Nov 2010 true author of a submission is usually a simple matter of using an internet search engine.) The system as described is completely opaque to outside observers. Neither the quality and timeliness of reviews, nor the standards of a journal’s editors, nor the extent of modifications made after initial review, nor the number of times an article has been rejected by other journals are publicly available.