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      The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles

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          Despite growing interest in Open Access (OA) to scholarly literature, there is an unmet need for large-scale, up-to-date, and reproducible studies assessing the prevalence and characteristics of OA. We address this need using oaDOI, an open online service that determines OA status for 67 million articles. We use three samples, each of 100,000 articles, to investigate OA in three populations: (1) all journal articles assigned a Crossref DOI, (2) recent journal articles indexed in Web of Science, and (3) articles viewed by users of Unpaywall, an open-source browser extension that lets users find OA articles using oaDOI. We estimate that at least 28% of the scholarly literature is OA (19M in total) and that this proportion is growing, driven particularly by growth in Gold and Hybrid. The most recent year analyzed (2015) also has the highest percentage of OA (45%). Because of this growth, and the fact that readers disproportionately access newer articles, we find that Unpaywall users encounter OA quite frequently: 47% of articles they view are OA. Notably, the most common mechanism for OA is not Gold, Green, or Hybrid OA, but rather an under-discussed category we dub Bronze: articles made free-to-read on the publisher website, without an explicit Open license. We also examine the citation impact of OA articles, corroborating the so-called open-access citation advantage: accounting for age and discipline, OA articles receive 18% more citations than average, an effect driven primarily by Green and Hybrid OA. We encourage further research using the free oaDOI service, as a way to inform OA policy and practice.

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          The mission of The Journal of General Physiology is to publish articles that elucidate basic biological, chemical, and physical principles of broad physiological significance. Physiological significance usually means mechanistic insights, which often are obtained only after extensive analysis of the experimental results. The significance of the mechanistic insights therefore can be no better than the validity of the theoretical framework used for the analysis—and it is usually better to be vaguely right than precisely wrong. The uncertainties associated with data analysis are well illustrated in the Perspectives on Ion Permeation through membrane-spanning channels (J. Gen. Physiol. 113:761–794) and the related Letters-to-the-Editor in this issue. This exchange moreover identified a particular problem that can be resolved by a change in editorial policy. The problem is the graphic representation of the results of kinetic analyses of ion permeation based on discrete-state rate models—and similar kinetic analyses of other physiological processes. It seems to have become de rigueur to summarize such results in a so-called energy profile (see Fig. 1), where the rate constants (k) deduced from the kinetic analysis are converted into free energies (ΔG ‡)—almost invariably using Eyring's transition state theory (TST): 1 \documentclass[10pt]{article} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{pmc} \usepackage[Euler]{upgreek} \pagestyle{empty} \oddsidemargin -1.0in \begin{document} \begin{equation*}{\mathrm{{\Delta}}}G^{{\mathrm{{\ddagger}}}}=-k_{{\mathrm{B}}}T{\cdot}{\mathrm{ln}} \left \left[k{\cdot} \left \left({h}/{k}_{{\mathrm{B}}}T\right) \right \right] \right {\mathrm{,}}\end{equation*}\end{document} where k B is Boltzmann's constant, T the temperature in kelvin, and h Planck's constant. The problems arise because will be valid only for elementary transitions; e.g., transitions over distances less than the mean free path in aqueous solutions, ∼0.1 Å. Whether or not one can use a discrete-state rate model to analyze a permeation process, for example, the (in)validity of depends primarily on the distances ions have to traverse in the transitions between the different kinetic states. The limitations inherent in the use of are well known, but energy profiles have taken on a life of their own because they provide a convenient graphic representation of the results, as opposed to the more tedious (albeit more correct) tabulation of the rate constants. Assuming the experimental results justify the use of a discrete-state model, which would entail a demonstration that the model and the deduced rate constants satisfactorily describe the results, the problem becomes, how can one represent the results graphically in a manner that avoids the errors associated with the use of ? One such representation of linear kinetic schemes can be implemented by noting that free energy profiles based on the Eyring TST (i.e., on the use of ) formally can be expressed as: 2 \documentclass[10pt]{article} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{pmc} \usepackage[Euler]{upgreek} \pagestyle{empty} \oddsidemargin -1.0in \begin{document} \begin{equation*}{\mathrm{{\Delta}}}G \left \left(p\right) \right =-k_{{\mathrm{B}}}T{\cdot}{\mathrm{ln}} \left \frac{{\prod_{{\mathrm{i}}=1,3,{\mathrm{{\ldots}}}}^{p}} \left \left[{k_{{\mathrm{i}}}}/{ \left \left({k_{{\mathrm{B}}}T}/{h}\right) \right }\right] \right }{{\prod_{{\mathrm{i}}=2,4,{\mathrm{{\ldots}}}}^{p}} \left \left[{k_{{\mathrm{i}}}}/{ \left \left({k_{{\mathrm{B}}}T}/{h}\right) \right }\right] \right } \right {\mathrm{,}}\end{equation*}\end{document} where p (= 1, 2,…,n, where n is the total number of rate constants in the scheme) denotes the sequential position of the energy peaks and wells in the kinetic scheme (beginning with the first peak and ending outside the pore on the other side), and k i is the ith rate constant in the scheme (forward rate constants are odd numbered and reverse rate constants are even numbered). That is, ΔG(p) for p = 1, 3,…, n − 1 denotes the peak energies, whereas ΔG(p) for p = 2, 4,…, n denotes the well energies. The interrupted line in Fig. 1 (right-hand ordinate) shows such an energy profile. The generalization of is immediate, as the rate constant “profile” along the kinetic scheme can be represented by the function: 3 \documentclass[10pt]{article} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{pmc} \usepackage[Euler]{upgreek} \pagestyle{empty} \oddsidemargin -1.0in \begin{document} \begin{equation*}RCR_{{\mathit{ff}}} \left \left(p\right) \right =-{\mathrm{log}} \left \frac{{\prod_{{\mathrm{i}}=1,3,{\mathrm{{\ldots}}}}^{p}} \left \left({k_{{\mathrm{i}}}}/{ff}\right) \right }{{\prod_{{\mathrm{i}}=2,4,{\mathrm{{\ldots}}}}^{p}} \left \left({k_{{\mathrm{i}}}}/{ff}\right) \right } \right {\mathrm{,}}\end{equation*}\end{document} where ff is an arbitrary “frequency factor.” The three lines in Fig. 1 (left-hand ordinate) show rate constant representations (RCR) for ff = 1, 109, and 6 · 1012 s−1 (= k B T/h). (ff = 1 s−1 denotes the simplest version of , ff = 109 s−1 was chosen to approximate the frequency of diffusional transitions over a distance of 1 nm, and ff = k B T/h was chosen for comparison to .) It is instructive to consider briefly some features of and Fig. 1. First, the heights of the “peaks” vary with the choice of ff. The peaks shift in parallel up or down as ff is increased or decreased, which serves to emphasize how arbitrary a “barrier height” is—and to underscore the difficulties inherent in deducing an energy profile from a set of rate constants (compare Fig. 1 and the two different energy profiles deduced for ff = 6 · 1012 and 109 s−1). Second, the differences in height among the peaks are invariant, suggesting that they have mechanistic significance. It is unlikely that the frequency factors associated with each barrier crossing will be identical, however, and one cannot relate differences in peak height to differences in free energy without knowing the variation in ff. Third, the “well” depths relative to the electrolyte solution outside the pore are invariant, again suggesting that they have mechanistic significance. The different behaviors of the peaks and “wells” arise because of the qualitative difference between RCRff (p) for odd and even p: only for odd p does the value of RCRff (p) depend on ff. Visually, the peaks probably should be above the wells; compare the profile for ff = 1 s−1 vs. those for ff = 109 and 6 · 1012 s−1, which justifies the use of physically plausible, albeit arbitrary, frequency factors. applies generally, meaning that it is possible to provide graphic representations of the results of kinetic analyses without invoking the Eyring TST to describe situations where that theory is inapplicable—whether it be ion permeation, channel gating, protein conformational transitions, or other physiological processes. The Journal of General Physiology therefore will publish rate constant representations based on , or some equivalent, but will no longer publish energy profiles deduced from kinetic analyses unless the authors explicitly justify their choice of the underlying model using “generally accepted” physico-chemical reasoning. Olaf Sparre Andersen Editor The Journal of General Physiology
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            Is Open Access

            The Development of Open Access Journal Publishing from 1993 to 2009

            Open Access (OA) is a model for publishing scholarly peer reviewed journals, made possible by the Internet. The full text of OA journals and articles can be freely read, as the publishing is funded through means other than subscriptions. Empirical research concerning the quantitative development of OA publishing has so far consisted of scattered individual studies providing brief snapshots, using varying methods and data sources. This study adopts a systematic method for studying the development of OA journals from their beginnings in the early 1990s until 2009. Because no comprehensive index of OA articles exists, systematic manual data collection from journal web sites was conducted based on journal-level data extracted from the Directory of Open Access Journals (DOAJ). Due to the high number of journals registered in the DOAJ, almost 5000 at the time of the study, stratified random sampling was used. A separate sample of verified early pioneer OA journals was also studied. The results show a very rapid growth of OA publishing during the period 1993–2009. During the last year an estimated 191 000 articles were published in 4769 journals. Since the year 2000, the average annual growth rate has been 18% for the number of journals and 30% for the number of articles. This can be contrasted to the reported 3,5% yearly volume increase in journal publishing in general. In 2009 the share of articles in OA journals, of all peer reviewed journal articles, reached 7,7%. Overall, the results document a rapid growth in OA journal publishing over the last fifteen years. Based on the sampling results and qualitative data a division into three distinct periods is suggested: The Pioneering years (1993–1999), the Innovation years (2000–2004), and the Consolidation years (2005–2009).
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              Open Access to the Scientific Journal Literature: Situation 2009

              Background The Internet has recently made possible the free global availability of scientific journal articles. Open Access (OA) can occur either via OA scientific journals, or via authors posting manuscripts of articles published in subscription journals in open web repositories. So far there have been few systematic studies showing how big the extent of OA is, in particular studies covering all fields of science. Methodology/Principal Findings The proportion of peer reviewed scholarly journal articles, which are available openly in full text on the web, was studied using a random sample of 1837 titles and a web search engine. Of articles published in 2008, 8,5% were freely available at the publishers' sites. For an additional 11,9% free manuscript versions could be found using search engines, making the overall OA percentage 20,4%. Chemistry (13%) had the lowest overall share of OA, Earth Sciences (33%) the highest. In medicine, biochemistry and chemistry publishing in OA journals was more common. In all other fields author-posted manuscript copies dominated the picture. Conclusions/Significance The results show that OA already has a significant positive impact on the availability of the scientific journal literature and that there are big differences between scientific disciplines in the uptake. Due to the lack of awareness of OA-publishing among scientists in most fields outside physics, the results should be of general interest to all scholars. The results should also interest academic publishers, who need to take into account OA in their business strategies and copyright policies, as well as research funders, who like the NIH are starting to require OA availability of results from research projects they fund. The method and search tools developed also offer a good basis for more in-depth studies as well as longitudinal studies.

                Author and article information

                PeerJ Inc. (San Francisco, USA )
                13 February 2018
                : 6
                [1 ]Impactstory , Sanford, NC, USA
                [2 ]École de bibliothéconomie et des sciences de l’information, Université de Montréal , Montréal, QC, Canada
                [3 ]Observatoire des Sciences et des Technologies (OST), Centre Interuniversitaire de Recherche sur la Science et la Technologie (CIRST), Université du Québec à Montréal , Montréal, QC, Canada
                [4 ]Canadian Institute for Studies in Publishing, Simon Fraser University , Vancouver, BC, Canada
                [5 ]Public Knowledge Project , Canada
                [6 ]Scholarly Communications Lab, Simon Fraser University , Vancouver, Canada
                [7 ]Information School, University of Washington , Seattle, USA
                [8 ]FlourishOA , USA
                [9 ]School of Information Studies, University of Ottawa , Ottawa, ON, Canada
                ©2018 Piwowar et al.

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                The authors received no funding for this work.
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