Compilation of E-Mailed Comments for Public Access Policy Forum Part 4
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What Is Peer Review?
What is Peer Review? Scholarly peer review is the process of evaluation of scientific, academic, or professional work by others working in the same field. The process is designed to ensure that academic publications make substantial contributions to the state of knowledge about a subject and meet minimum standards of reliability. Fundamentals Is it worth it to do the extra work to find peer reviewed sources? When researching, it is important to look at articles recently published in top tier peer Keep in Mind reviewed or refereed journals to understand the current issues and developments of a Many scholarly journals only peer review original topic. research. The standards of peer review for editorials, literature review/survey articles, and How can I tell if an article is peer book reviews may be less stringent (or non- reviewed? existent) even if they are published in refereed Follow these steps: journals. • Check the UlrichsWeb database for the journal (is it refereed, is the content type listed as academic/scholarly). • If the journal is not in UlrichsWeb, try googling it. On the publisher’s website, look for the About page or submission guidelines. These pages will usually explicitly say whether a journal is peer reviewed or refereed and often will describe the process. The Process What is “blind” peer review? Usually the refereeing process involves what is called “blind” peer review. This is when the reviewers do not know who wrote the article they are reviewing. This encourages reviewers to evaluate the sources according to the norms of their community rather than the reputation of the author. -
How Frequently Are Articles in Predatory Open Access Journals Cited
publications Article How Frequently Are Articles in Predatory Open Access Journals Cited Bo-Christer Björk 1,*, Sari Kanto-Karvonen 2 and J. Tuomas Harviainen 2 1 Hanken School of Economics, P.O. Box 479, FI-00101 Helsinki, Finland 2 Department of Information Studies and Interactive Media, Tampere University, FI-33014 Tampere, Finland; Sari.Kanto@ilmarinen.fi (S.K.-K.); tuomas.harviainen@tuni.fi (J.T.H.) * Correspondence: bo-christer.bjork@hanken.fi Received: 19 February 2020; Accepted: 24 March 2020; Published: 26 March 2020 Abstract: Predatory journals are Open Access journals of highly questionable scientific quality. Such journals pretend to use peer review for quality assurance, and spam academics with requests for submissions, in order to collect author payments. In recent years predatory journals have received a lot of negative media. While much has been said about the harm that such journals cause to academic publishing in general, an overlooked aspect is how much articles in such journals are actually read and in particular cited, that is if they have any significant impact on the research in their fields. Other studies have already demonstrated that only some of the articles in predatory journals contain faulty and directly harmful results, while a lot of the articles present mediocre and poorly reported studies. We studied citation statistics over a five-year period in Google Scholar for 250 random articles published in such journals in 2014 and found an average of 2.6 citations per article, and that 56% of the articles had no citations at all. For comparison, a random sample of articles published in the approximately 25,000 peer reviewed journals included in the Scopus index had an average of 18, 1 citations in the same period with only 9% receiving no citations. -
How to Review Papers 2 3 for Academic Meta-Jokes
How to Review Papers 2 3 For academic meta-jokes: https://www.facebook.com/groups/reviewer2/ 4 “How not to be Reviewer #2 (https://amlbrown.com/2015/11/10/how-not-to-be-reviewer-2/)” - Ashley Brown, U. of Utaha Who is the Reviewer #2? ✘ “Literally, Reviewer 2 is the anonymised moniker given to the second peer to review a research paper. In common parlance, Reviewer 2 can be summarised as possessing the following qualities: ○ Grumpy, aggressive ○ Vague, unhelpful, inflexible ○ Overbearingly committed to a pet discipline ○ Overly focused on a particular methodology ○ Unwilling to give the benefit of the doubt ○ Unwilling to view the authors of a submitted paper as peers” 5 6 What is peer review? ✘ Evaluation of work by one or more people of similar competence to the producers of the work (=peers) – Wikipedia ✘ Scholarly peer review helps editors and program chairs to decide whether to publish/accept specific work ✘ Reviewers work for free (also editors and chairs) – perhaps the weirdest part of any academic’s job to laymen’s eyes ✘ It has appeared 300 years ago (Philosophical Transactions of Royal Society, editor Henry Oldenburg 1618-1677) 7 Why should we do peer review? ✘ Ensures and even improves the quality, value, and integrity of scientific communication ✘ Only the experts in the same domain can provide sufficiently detailed yet impartial opinions ✘ If you do not care about quality of other’s work, eventually everyone will stop caring about your work as well 8 Why should we do peer review? ✘ Scientific ideals aside, certain events just -
Multi-Class Protein Classification Using Adaptive Codes
Journal of Machine Learning Research 8 (2007) 1557-1581 Submitted 8/06; Revised 4/07; Published 7/07 Multi-class Protein Classification Using Adaptive Codes Iain Melvin∗ [email protected] NEC Laboratories of America Princeton, NJ 08540, USA Eugene Ie∗ [email protected] Department of Computer Science and Engineering University of California San Diego, CA 92093-0404, USA Jason Weston [email protected] NEC Laboratories of America Princeton, NJ 08540, USA William Stafford Noble [email protected] Department of Genome Sciences Department of Computer Science and Engineering University of Washington Seattle, WA 98195, USA Christina Leslie [email protected] Center for Computational Learning Systems Columbia University New York, NY 10115, USA Editor: Nello Cristianini Abstract Predicting a protein’s structural class from its amino acid sequence is a fundamental problem in computational biology. Recent machine learning work in this domain has focused on develop- ing new input space representations for protein sequences, that is, string kernels, some of which give state-of-the-art performance for the binary prediction task of discriminating between one class and all the others. However, the underlying protein classification problem is in fact a huge multi- class problem, with over 1000 protein folds and even more structural subcategories organized into a hierarchy. To handle this challenging many-class problem while taking advantage of progress on the binary problem, we introduce an adaptive code approach in the output space of one-vs- the-rest prediction scores. Specifically, we use a ranking perceptron algorithm to learn a weight- ing of binary classifiers that improves multi-class prediction with respect to a fixed set of out- put codes. -
Establishing Incentives and Changing Cultures to Support Data Access
EXPERT ADVISORY GROUP ON DATA ACCESS ESTABLISHING INCENTIVES AND CHANGING CULTURES TO SUPPORT DATA ACCESS May 2014 ACKNOWLEDGEMENT This is a report of the Expert Advisory Group on Data Access (EAGDA). EAGDA was established by the MRC, ESRC, Cancer Research UK and the Wellcome Trust in 2012 to provide strategic advice on emerging scientific, ethical and legal issues in relation to data access for cohort and longitudinal studies. The report is based on work undertaken by the EAGDA secretariat at the Group’s request. The contributions of David Carr, Natalie Banner, Grace Gottlieb, Joanna Scott and Katherine Littler at the Wellcome Trust are gratefully acknowledged. EAGDA would also like to thank the representatives of the MRC, ESRC and Cancer Research UK for their support and input throughout the project. Most importantly, EAGDA owes a considerable debt of gratitude to the many individuals from the research community who contributed to this study through feeding in their expert views via surveys, interviews and focus groups. The Expert Advisory Group on Data Access Martin Bobrow (Chair) Bartha Maria Knoppers James Banks Mark McCarthy Paul Burton Andrew Morris George Davey Smith Onora O'Neill Rosalind Eeles Nigel Shadbolt Paul Flicek Chris Skinner Mark Guyer Melanie Wright Tim Hubbard 1 EXECUTIVE SUMMARY This project was developed as a key component of the workplan of the Expert Advisory Group on Data Access (EAGDA). EAGDA wished to understand the factors that help and hinder individual researchers in making their data (both published and unpublished) available to other researchers, and to examine the potential need for new types of incentives to enable data access and sharing. -
A History and Development of Peer-Review Process
Annals of Library and Information Studies Vol. 66, December 2019, pp. 152-162 A history and development of peer-review process Siladitya Jana Assistant Librarian, Indian Institute of Science Education and Research Kolkata, Mohanpur 741 246, India, Email: [email protected] Received: 24 July 2019; accepted 28 November 2019 The paper shows the importance of peer review process in the scholarly communication system and discusses both the closed and the newly emerging open peer review models. It also examines the peer review system at the scholarly academies or societies in their nomination systems for prizes, rewards, etc. It also discusses the various facets of the newly developed open peer review models now prevalent in various journals. The paper may help to understand and appreciate the role played by peer review in the scholarly communication system and the efforts being made to make it more transparent. Keywords : Double-blind peer review; Open access; Open peer review; Peer review; Scholarly communication; Single-blind peer review Introduction learned organisations to publish any material submitted by its members, etc. These factors resulted Peer review is the quality control mechanism in the in the uneven growth of peer review as a means of entire ecology of the scholarly communication 3 system. International Committee of Medical Journal controlling the quality of the publishable materials . Recent reports of peer review fraud also raise Editors (ICMJE) defines peer review as the critical 4,5,6 assessment of manuscripts submitted to journals by concerns about its efficacy and future . 1 experts who are usually not part of the editorial staff . -
Gender Bias in Research Teams and the Underrepresentation of Women in Science 2 Roslyn Dakin1* and T
bioRxiv preprint doi: https://doi.org/10.1101/741694; this version posted August 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Gender bias in research teams and the underrepresentation of women in science 2 Roslyn Dakin1* and T. Brandt Ryder2,3 4 1 Department of Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada 6 2 Bird Conservancy of the Rockies, Fort Collins, Colorado, 80525, USA 3 Migratory Bird Center, Smithsonian Conservation Biology Institute, National Zoological Park, 8 Washington, DC 20013, USA 10 * Correspondence to: [email protected] 12 Abstract Why are females still underrepresented in science? The social factors that affect career choices 14 and trajectories are thought to be important but are poorly understood. We analyzed author gender in a sample of >61,000 scientific articles in the biological sciences to evaluate the factors 16 that shape the formation of research teams. We find that authorship teams are more gender- assorted than expected by chance, with excess homotypic assortment accounting for up to 7% of 18 published articles. One possible mechanism that could explain gender assortment and broader patterns of female representation is that women may focus on different research topics than men 20 (i.e., the “topic preference” hypothesis). An alternative hypothesis is that researchers may consciously or unconsciously prefer to work within same-gender teams (the “gender homophily” 22 hypothesis). Using network analysis, we find no evidence to support the topic preference hypothesis, because the topics of female-authored articles are no more similar to each other than 24 expected within the broader research landscape. -
Transformative Models to Promote Prescription Drug Innovation and Access: a Landscape Analysis
Yale Journal of Health Policy, Law, and Ethics Volume 19 Issue 2 Article 2 2020 Transformative Models to Promote Prescription Drug Innovation and Access: A Landscape Analysis Phebe Hong Harvard Law School Aaron S. Kesselheim Professor of medicine at Harvard Medical School/Brigham and Women’s Hospital. Ameet Sarpatwari Assistant professor of medicine at Harvard Medical School/Brigham and Women’s Hospital. Follow this and additional works at: https://digitalcommons.law.yale.edu/yjhple Part of the Health Law and Policy Commons, and the Legal Ethics and Professional Responsibility Commons Recommended Citation Phebe Hong, Aaron S. Kesselheim & Ameet Sarpatwari, Transformative Models to Promote Prescription Drug Innovation and Access: A Landscape Analysis, 19 YALE J. HEALTH POL'Y L. & ETHICS (2020). Available at: https://digitalcommons.law.yale.edu/yjhple/vol19/iss2/2 This Article is brought to you for free and open access by Yale Law School Legal Scholarship Repository. It has been accepted for inclusion in Yale Journal of Health Policy, Law, and Ethics by an authorized editor of Yale Law School Legal Scholarship Repository. For more information, please contact [email protected]. Hong et al.: Transformative Models to Promote Prescription Drug Innovation and Transformative Models to Promote Prescription Drug Innovation and Access: A Landscape Analysis Phebe Hong, Aaron S. Kesselheim & Ameet Sarpatwari* Abstract: The patent-based pharmaceutical innovation system in the US does not incentivize the development of drugs with the greatest impact on patient or public health. It has also led to drug prices that patients and health care systems cannot afford. Three alternate approaches to promoting pharmaceutical innovation have been proposed to address these shortcomings. -
A Database of Globular Protein Structural Domains: Clustering of Representative Family Members Into Similar Folds R Sowdhamini, Stephen D Rufino and Tom L Blundell
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Research Paper 209 A database of globular protein structural domains: clustering of representative family members into similar folds R Sowdhamini, Stephen D Rufino and Tom L Blundell Background: A database of globular domains, derived from a non-redundant set Address: Imperial Cancer Research Fund Unit of of proteins, is useful for the sequence analysis of aligned domains, for structural Structural Molecular Biology, Department of Crystallography, Birkbeck College, Malet Street, comparisons, for understanding domain stability and flexibility and for fold London WC1E 7HX, UK. recognition procedures. Domains are defined by the program DIAL and classified structurally using the procedure SEA. Correspondence: Tom L Blundell e-mail: [email protected] Results: The DIAL-derived domain database (DDBASE) consists of 436 protein Key words: clustering, comparison, chains involving 695 protein domains. Of these, 206 are ␣-class, 191 are - protein domains, protein folds, structural similarity, class and 294 ␣ and  class. The domains, 63% from multidomain proteins and superfamilies 73% less than 150 residues in length, were clustered automatically using both Received: 19 Jan 1996 single-link cluster analysis and hierarchical clustering to give a quantitative Revisions requested: 13 Feb 1996 estimate of similarity in the domain-fold space. Revisions received: 01 Mar 1996 Accepted: 01 Mar 1996 ␣  Conclusions: Highly populated and well described folds (doubly wound / , Published: 13 May 1996 singly wound ␣/ barrels, globins ␣, large Greek-key  and flavin-binding ␣/) Electronic identifier: 1359-0278-001-00209 are recognized at a SEA cut-off score of 0.55 in single-link clustering and at 0.65 Folding & Design 13 May 1996, 1:209–220 in hierarchical clustering, although functionally related families are usually clearly distinguished at more stringent values. -
A New Method and Metric to Evaluate the Peer Review Process of Scholarly Journals
Pub Res Q (2014) 30:23–38 DOI 10.1007/s12109-013-9339-y A New Method and Metric to Evaluate the Peer Review Process of Scholarly Journals Adam Etkin Published online: 6 December 2013 Ó The Author(s) 2013. This article is published with open access at Springerlink.com Abstract This paper will propose a new system that produces a metric that is an indicator of the level of peer review conducted prior to the publication of scholarly material. A mathematical algorithm which incorporates weighted values of the roles within the peer review process is created. The h-index, which is a value that ‘‘measures the productivity and impact of a scientist or scholar,’’ is also incorporated. Each round of review is weighted using the square root as later rounds of peer review are often less rigorous than earlier rounds. Once a paper is accepted the calculation is conducted and a ‘‘peer review evaluation’’ metric, or ‘‘Peer Review Evaluation Score’’ (pre-SCORE) is available. It is clear that such a metric would prove beneficial to all engaged parties (authors, publishers, readers, libraries). Authors will know that their work is being evaluated by a trustworthy publication and by experts in their field. Legitimate, ethical publishers will be recognized as such. Readers would have the ability to filter out material which was not properly vetted, and libraries/consortia would have further assurance that their limited funds are spent wisely. Future studies to see if there is a correlation between the pre-SCORE and Impact Factor or highly cited material is possible. -
Ad Hominem Arguments in the Service of Boundary Work Among Climate Scientists
SISSA – International School for Advanced Studies Journal of Science Communication ISSN 1824 – 2049 http://jcom.sissa.it/ RECEIVED: October 12, 2011 PUBLISHED: February 15, 2012 Article Ad hominem arguments in the service of boundary work among climate scientists Lawrence Souder, Furrah Qureshi ABSTRACT: Most accounts of an ideal scientific discourse proscribe ad hominem appeals as one way to distinguish it from public discourse. Because of their frequent use of ad hominem attacks, the Climategate email messages provoked strong criticisms of climate scientists and climate science. This study asks whether the distinction between public and scientific discourse holds in this case and thus whether the exclusion of ad hominem arguments from scientific discourse is valid. The method of analysis comes from the field of informal logic in which argument fallacies like the ad hominem are classified and assessed. The approach in this study focuses on a functional analysis of ad hominem—their uses rather than their classification. The analysis suggests three distinct functional uses of ad hominem remarks among the Climategate emails: (1) indirect, (2) tactical, and (3) meta-. Consistent with previous research on ad hominem arguments in both public and scientific discourse, these results reinforce the common opinion of their fallacious character. Only the remarks of the last type, the meta- ad hominem, seemed to be non-fallacious in that they might help to preempt the very use of ad hominem attacks in scientific discourse. “In this case, de Freitas is such a poor scientist that he may simply disappear.” (Tom Wigley, Climategate email, 1051230500.txt)1 “Pielke wouldn't understand independence if it hit him in the face.” (Phil Jones, Climategate email, 1233249393.txt) Introduction2 As scientists-in-training, Chris de Freitas and Roger Pielke, Sr., may have suffered appropriately the sting of such remarks from an overbearing advisor on their dissertation committees in a moment of impatience. -
Governance of Data Access
EXPERT ADVISORY GROUP ON DATA ACCESS GOVERNANCE OF DATA ACCESS June 2015 EAGDA Report: Governance of Data Access EXECUTIVE SUMMARY Whilst it is widely accepted that data should be shared for secondary research uses where these can be balanced with the maintenance of participant privacy, there has thus far been little oversight or coordination of policies, resources and infrastructure across research funders to ensure data access is efficient, effective and proportionate. Funders have different policies and processes for maximizing the value from the datasets generated by their researchers, and EAGDA wished to identify whether and how improvements to governance for data access and the dissemination of good practice across the funders could enhance this value. We identified several good practice exemplars for funders and the research community, but also evidence of significant variability between studies that, in practice, lead to inefficiencies in access to and use of data for secondary purposes. We suggest that an approach that is more transparent and coordinated among research funders would provide benefits, both in terms of increasing the efficiency of data access and in ensuring that good governance approaches can get on with the job of ensuring the right balance between protecting research participants’ interests and enabling access to data for further research. This report makes several recommendations to funders, many of which are interlinked. These focus on areas in which specific funder action could improve the governance of data access for human cohort studies: RECOMMENDATIONS 1. Research funders should require explicit data sharing and management plans as part of grant applications (even if these plans conclude that data sharing is not appropriate); and should ensure that these issues are adjudicated before funding for new studies, or renewal of existing studies, is agreed.