Open Access Papers Research Articles

Low income countries have the highest percentages of open access publication: A systematic computational analysis of the biomedical literature.

Open access publication rates have been steadily increasing over time. In spite of this growth, academics in low income settings struggle to gain access to the full canon of research literature. While the vast majority of open access repositories and funding organizations with open access policies are based in high income countries, the geographic patterns of open access publication itself are not well characterized. In this study, we developed a computational approach to better understand the topical and geographical landscape of open access publications in the biomedical research literature. Surprisingly, we found a strong negative correlation between country per capita income and the percentage of open access publication. Open access publication rates were particularly high in sub-Saharan Africa, but vastly lower in the Middle East and North Africa, South Asia, and East Asia and the Pacific. These effects persisted when considering papers only bearing authors from within each region and income group. However, papers resulting from international collaborations did have a higher percentage of OA than single-country papers, and inter-regional collaboration increased OA publication for all world regions. There was no clear relationship between the number of open access policies in a region and the percentage of open access publications in that region. To understand the distribution of open access across topics of biomedical research, we examined keywords that were most enriched and depleted in open access papers. Keywords related to genomics, computational biology, animal models, and infectious disease were enriched in open access publications, while keywords related to the environment, nursing, and surgery were depleted in open access publications. This work identifies geographic regions and fields of research that could be priority areas for open access advocacy. The finding that open access publication rates are highest in sub-Saharan Africa and low income countries suggests that factors other than open access policy strongly influence authors’ decisions to make their work openly accessible. The high proportion of OA resulting from international collaborations indicates yet another benefit of collaborative research. Certain applied fields of medical research, notably nursing, surgery, and environmental fields, appear to have a greater proportion of fee-for-access publications, which presumably creates barriers that prevent researchers and practitioners in low income settings from accessing the literature in those fields.

Cattle Review

Introduction: This edition of Cattle Review considers three open access papers describing veterinary and farmer beliefs with respect to antimicrobial use, the concept of the ‘antibiotic footprint’, and the spread of bovine viral diarrhoea virus (BVDV).

Open access publishing and soil science – Trends and developments

About 42,000 soil papers are annually published, and the number of papers almost doubled in the past 10 years. Most growth has come from China, and about one-third of all soil papers are presently from China compared to 4% in 1999. The increase in papers has been accompanied by higher impact factors of the core soil science journals. There has been a proliferation of new publishers and journals, and some 1500 new internet publishers have been established. Scientific publishing is big and profiteable business. Open access publishing started in the early 2000s. In the top four soil science journals only 1% of the papers were published open access in 2008, but currently 5 to 20% of the papers are open access papers. Across all scientific disciplines the share of open access papers is about 28%. Some preliminary analysis suggests that open access papers in soil science tend to be more cited. The current cost of an open access paper in one of the 25 top soil science journals ranges from $750 to $4000. Funding agencies, some universities and scientific organizations are pushing towards a total open access approach of scientific publishing. Soil scientists should become involved in these discussions as it affects the way we disseminate our findings.

Hydrological Observatories Featured in VZJ Special Section

Hydrological Observatories Featured in VZJ Special Section

Commentary to ‘Predatory publishing or a lack of peer-review transparency? - a contemporary analysis of indexed open and non-open access papers in paediatric urology’

The existence of predatory practices in online open access journals has been a concern for over a decade and seems to be increasing. The authors looked at the impact of predatory publishing in pediatric urology and found that around 6.5% of pediatric urology publications are published in journals that met their criteria for a borderline/predatory journal. Predatory publishing or a lack of peer review transparency?—a contemporary analysis of indexed open and non-open access articles in paediatric urologyJournal of Pediatric UrologyVol. 15Issue 2PreviewThe advent of open access publishing has allowed for unrestricted and rapid knowledge dissemination and can generate higher citation levels. However, the establishment of predatory journals exploits this model and may lead to publication of non-peer reviewed work. Full-Text PDF Response to Editorial commentary: predatory publishing or a lack of peer-review transparency?—a contemporary analysis of indexed open and non-open access articles in pediatric urologyJournal of Pediatric UrologyVol. 15Issue 2PreviewThe overall prevalence and, indeed, perhaps incidence of predatory practices in online open access journals does appear to be increasing across all specialties, with a time-stable prevalence of 6.5% in our own findings within pediatric urology. Full-Text PDF

Organs-on-chips: latest developments

Welcome to the collection of the current must-read open-access papers in the field of organs-on-chips that have become available in the second half of 2018. This quarterly editorial column will be compiled by Dr. Andries D. van der Meer, University of Twente, The Netherlands. Feel free to contact him with tips about open-access papers on organs-on-chips and microphysiological systems that you feel should be included in upcoming collections.

Bibliometric and Altmetric Analysis of Three Social Science Disciplines

This article analyses scientific publications of international prestige in three social science disciplines (communication, economics and sociology) to identify possible production patterns. Emphasis is placed on the study of impact and visibility, both through bibliometric and altmetric indicators to determine similarities and differences and to establish possible inter-variable relationships. The use of measures such as the presence in social media for the study of the visibility of documents is discussed. A total of 112 300 papers published from 2013 to 2015 in the three disciplines analysed was retrieved from the Social Science Citation Index (SSCI). Economics accounted for the largest number and was observed to have a ‘stable’ and consolidated output profile. Collaboration, impact and visibility were found to be inter-related in the three fields. The proportion of papers with mentions in the social media was high (around 50 %) in communication and sociology, suggesting a relationship between the object of study and the medium for disseminating the findings. Tweets were the most common type of mentions. While the correlation between academic impact (citation/doc) and mentions in blog posts and tweets was observed to be low, the percentage of papers cited (78 % to 96 %) and the mean number of citations per paper were greater among those with than those without mentions in the social media (especially those mentioned in Google+, MSM, videos and Wikipedia). The proportion of open access (OA) papers with mentions in the social media was higher than the percentage of open access papers as a whole in two of the three disciplines.

Assessment of Self Archiving in Digital Repositories: Is there any Difference between Science and Agriculture Scholars?

This study examines the differences in scholarly publishing and self-archiving practices of academic scholars in the faculties of agriculture and science in University of Peradeniya, Sri Lanka. Survey method was adapted and a questionnaire specifically designed was used to achieve the objectives of the study. The study population consisted of all permanent academic staff in the two faculties. The study established that majority of the respondents of both faculties were aware of self-archiving concept as a means for providing open access but not many of them had experience in self-archiving. Majority of respondents from both faculties began this activity two to three years ago and they learnt about self-archiving by working in a field with established subject based archives. The original motivators for self-archiving were self motivation and declared citation advantage of open access papers. Agriculture scholars deposited more full text articles in digital repositories than science scholars. When analyzing the results of this study, it was proved that most of the scholars in agriculture faculty preferred to deposit conference papers while science scholars mostly preferred preprint materials. PDF is the most preferred file format to deposit in the digital repositories.

Computational reproducibility in geoscientific papers: Insights from a series of studies with geoscientists and a reproduction study

ABSTRACTReproducibility is a cornerstone of science and thus for geographic research as well. However, studies in other disciplines such as biology have shown that published work is rarely reproducible. To assess the state of reproducibility, specifically computational reproducibility (i.e. rerunning the analysis of a paper using the original code), in geographic research, we asked geoscientists about this topic using three methods: a survey (n = 146), interviews (n = 9), and a focus group (n = 5). We asked participants about their understanding of open reproducible research (ORR), how much it is practiced, and what obstacles hinder ORR. We found that participants had different understandings of ORR and that there are several obstacles for authors and readers (e.g. effort, lack of openness). Then, in order to complement the subjective feedback from the participants, we tried to reproduce the results of papers that use spatial statistics to address problems in the geosciences. We selected 41 open access papers from Copernicus and Journal of Statistical Software and executed the R code. In doing so, we identified several technical issues and specific issues with the reproduced figures depicting the results. Based on these findings, we propose guidelines for authors to overcome the issues around reproducibility in the computational geosciences.

Antifibrinolytic therapy for preventing oral bleeding in people on anticoagulants undergoing minor oral surgery or dental extractions.

Individuals on continuous treatment with vitamin K antagonists (VKAs) or direct oral anticoagulants (DOACs) are at increased risk of bleeding complications during and after oral or dental procedures. Anticoagulant treatment is preferably continued at the same dose, since dose reduction or discontinuation of treatment is associated with an increased risk of thromboembolism. The use of haemostatic measures during or after the procedure (or both) could enable continuation of the oral anticoagulant treatment. We aimed to assess the efficacy of antifibrinolytic agents for preventing bleeding complications in people on oral anticoagulants undergoing minor oral surgery or dental extractions. We searched the Cochrane Cystic Fibrosis and Genetic Disorders Coagulopathies Trials Register, compiled from electronic database searches and handsearching of journals and conference abstract books. We also searched the reference lists of relevant articles and reviews. We searched PubMed, Embase and the Cochrane Library. Additional searches were performed using ClinicalTrials.gov, the International Clinical Trials Registry Platform (ICTRP), the CINAHL database of nursing and allied health services, the open access ProQuest dissertation database, papers and reports from the American College of Clinical Pharmacy (ACCP) and abstract books from annual scientific conferences.Date of last search: 04 January 2018. Randomised and quasi-randomised controlled trials in people on continuous treatment with VKAs or DOACs undergoing oral or dental procedures using antifibrinolytic agents (tranexamic acid (TXA) or epsilon aminocaproic acid) to prevent perioperative bleeding compared to no intervention or usual care with or without placebo. Two authors independently screened the titles and abstracts of all identified articles. Full texts were obtained from potentially relevant abstracts and two authors independently assessed these for inclusion based of the selection criteria. A third author verified trial eligibility. Two authors independently performed data extraction and risk of bias assessments using standardized forms. The quality of the evidence was assessed using GRADE. No eligible trials in people on continuous treatment with DOACs undergoing oral or dental procedures were identified.Three randomised trials and one quasi-randomised trial (follow-up in all was seven days) in people on continuous treatment with VKAs were included with a total of 253 participants (mean age 60 years). Two trials published in 1989 and 1993 compared the antifibrinolytic agent TXA with placebo in people using VKAs. Two other trials were published in 1999 and 2015 and compared TXA with gelatin sponge and sutures, and dry gauze compression, respectively. In all included trials, those who were treated with VKAs had international normalised ratio (INR) values within the therapeutic range and TXA was applied locally, not systemically.The two trials from 1989 and 1993 comparing TXA with placebo showed a statistically significant beneficial effect regarding the number of major postoperative bleeding episodes requiring intervention, with a pooled risk difference (RD) of -0.25 (95% confidence interval (CI) -0.36 to -0.14) (128 participants) (moderate-quality evidence). For the two trials that compared TXA with either gelatin sponge and sutures or with dry gauze compression, there was no difference between the TXA and the standard care group, RD 0.02 (95% CI -0.07 to 0.11) (125 participants) (moderate-quality evidence). The combined RD of all included trials was -0.13 (95% CI -0.30 to 0.05) (moderate-quality evidence). There were no side effects of antifibrinolytic therapy that required treatment withdrawal (128 participants) (moderate-quality evidence). Despite heterogeneity between trials with respect to the different haemostatic measures used in the control groups, the trials were comparable regarding design and baseline participant characteristics.Overall, we considered the risk of bias to be low in the trials comparing TXA with placebo and moderate in the trials comparing TXA with alternative haemostatic measures. Based on the results of this Cochrane Review, there seems to be a beneficial effect of locally applied TXA in preventing oral bleeding in people on continuous treatment with VKAs undergoing minor oral surgery or dental extractions. However, the small number of identified randomised controlled trials, the relatively small number of participants included in the trials and the differences in standard therapy and treatment regimens between trials, do not allow us to conclude definite efficacy of antifibrinolytic therapy in this population.We were unable to identify any eligible trials in people on continuous treatment with DOACs undergoing oral or dental procedures. Therefore, a beneficial effect of antifibrinolytic therapy can currently only be assumed based on data from the people using VKAs.

Review of Open Access Papers for Eruption Crisis in Puna (Big Island of Hawai’i)

Review of Open Access Papers for Eruption Crisis in Puna (Big Island of Hawai’i)

Difference in the impact of open-access papers published by China and the USA

We analyze the impact of open-access (OA) articles published by China and the USA by using Web of Science (WoS) data covering a period of 5 years (2011–2015), five indexes (citation and four altmetric indexes), five disciplines, and three types of articles. With regard to article type, Type I papers are those wherein the authors are all from China or the USA. Type II are those in which the first author is from China or the USA. Type III includes those in which the first author is not from China or the USA. We found that the proportion of OA papers in WoS has been growing in recent years. In terms of citations and altmetric indexes, the mean value of the USA is larger than that of China in general; Type II articles possess the highest value among all papers in the USA, whereas Type III has the highest value in China. Compared with the scenario in citations, social sciences and humanities possess larger altmetric values in China and the USA. The correlation among indicators is similar for the OA papers from China and the USA. Generally, citations cannot effectively represent the altmetric indexes. The gap between China and the USA is the largest in the altmetric attention score and Type I, and the smallest in citations and Type III. Measuring the international impact of OA papers using only citations underestimates the gap between China and the USA.

Correction to “Impact of Open Access Papers in Hybrid Journals”

Correction to “Impact of Open Access Papers in Hybrid Journals”

Impact of Open Access Papers in Hybrid Journals

Impact of Open Access Papers in Hybrid Journals

Editorial: maintaining open access to high quality publications at no cost to authors

The inability to access scientific literature freely can be a major obstacle in the advancement of science. Many reputable journals offering optional open access incur a substantial upfront payment to cover their publication costs, and hence many authors cannot afford to publish open access papers in a journal with an established reputation. Publishers charging for article processing claim that the charge is necessary to maintain their reputation and costs for peer review, editing and indexing articles. Thus, some open-access publications have a less rigorous peer-review and editorial process.

Gold Open Access Publishing in Mega-Journals: Developing Countries Pay the Price of Western Premium Academic Output

Open access publishing (OAP) makes research output freely available, and several national governments have now made OAP mandatory for all publicly funded research. Gold OAP is a common form of OAP where the author pays an article processing charge (APC) to make the article freely available to readers. However, gold OAP is a cause for concern because it drives a redistribution of valuable research money to support open access papers in ‘mega-journals’ with more permissive acceptance criteria. We present a data-driven evaluation of the financial ramifications of gold OAP and provide evidence that gold OAP in mega-journals is biased toward Western industrialized countries. From 2011 to 2015, the period of our data collection, countries with developing economies had a disproportionately greater share of articles published in the lower-tier mega-journals and thus paid article APCs that cross-subsidize publications in the top-tier journals of the same publisher. Conversely, scientists from Western developed countries had a disproportionately greater share of articles published in those same top-tier journals. The global inequity of the cross-subsidizing APC model was demonstrated across five different mega-journals, showing that the issue is a common problem. We need to develop stringent and fair criteria that address the global financial implications of OAP, as publication fees should reflect the real cost of publishing and be transparent for authors.

The state of open access

On page 24 you’ll find David Kramer’s in-depth report on the current state of open-access publishing. Open access and its place in the landscape of academic journals have changed since November 2012, when Physics Today last covered the topic. Besides authors, publishers, and policy makers, other actors are now on the open-access stage, among them charitable foundations, scholarly collaboration networks, and, yes, pirates who post unauthorized copies of papers on Russian servers.CYNTHIA CUMMINGSPPT|High resolutionMy attitude toward open access is conflicted. On the one hand, I agree that the fruits of publicly funded research should be freely available, especially to scientists in poor countries and to scientists employed by companies and colleges that can’t afford journal subscriptions. On the other hand, I’m well aware that Physics Today is funded in part by the profits that AIP’s publishing subsidiary makes from selling subscriptions to its 19 journals. If Physics Today had to rely solely on advertising and subscription revenue, it would have to shrink and change format.Regardless of where you, I, or anyone else stands on open access, there are forces in play that are hard for publishers to resist. One of those forces arises from the nature of the principal end product of scholarly research, a paper that’s usually in the form of a PDF. The P in PDF stands for portable, which is what PDFs all too easily are. For Physics Today’s August 2009 issue, I wrote a feature article about iron-based superconductors, which had been discovered just two years earlier. Google Scholar lists 16 unauthorized PDFs of the article, 13 of which are on Chinese websites. (I couldn’t find the article on Sci-Hub, the pirate website founded by a Kazakhstani grad student.)Portability isn’t the only disrupting force at play. University library budgets have not kept up with inflation or with the growth in the number of the world’s scientists and their output. The cash crunch is forcing librarians to scrutinize journals based on price and usage. Subscriptions to those that don’t meet increasingly stringent criteria are not renewed.Despite those trends, some aspects of scholarly publishing remain the same. It’s just as hard now as it was in the 19th century to conceive of an experiment or theory that is both original and significant enough to be worth publishing in a scientific journal. Reviewing your peers’ papers before publication continues to be an unpaid yet valuable duty. And a paper’s final version of record still needs to be archived, online if not in bound volumes on library shelves.When I ask physicists and other scientists how they choose where to publish their work, I tend to get the same answers. Scientists want their papers to be read, so they publish in journals that their peers read. A physicist told me once that he regretted publishing in the prestigious Proceedings of the Royal Society because his fellow fluid dynamicists didn’t read that journal. Physics of Fluids, he mused, would have been a better choice.Some physicists tell me that if they have a hot result, they’ll go for a journal with a high impact factor, such as Physical Review Letters, Nature, or Science. But in the digital age, as George Lozano, Vincent Larivière, and Yves Gingras discovered in an extensive bibliometric study, the correlation between a journal’s impact factor and a paper’s citations is weakening.11. G. A. Lozano, V. Larivière, Y. Gingras, J. Am. Soc. Inf. Sci. Tec. 63, 2140 (2012). https://doi.org/10.1002/asi.22731One of the findings in David’s report in this issue is that open-access papers in the physical sciences currently make up just 10–12% of the total. That modest proportion likely reflects the continuing appeal and reputation of traditional journals. But as any marketing guru will tell you, appeal and reputation are intangible components of a brand. The contest for the best papers in physics will likely be won by the publishers who nurture those intangibles, regardless of access model.ReferencesSection:ChooseTop of pageReferences <<CITING ARTICLES1. G. A. Lozano, V. Larivière, Y. Gingras, J. Am. Soc. Inf. Sci. Tec. 63, 2140 (2012). https://doi.org/10.1002/asi.22731, Google ScholarCrossref© 2017 American Institute of Physics.

Who needs Access to Research? The Case of Pharmaceutical Industry

Watch the VIDEO of the presentation.Despite what many people claim about how Open Access to scientific research will be good for society (beyond academia), the body of literature on the issue of Open Access hardly offers any evidence on that. Anecdotal evidence exists for how some practicing doctors, small companies, policymakers or patient groups can benefit from such access. Yet, there are very few formal studies to quantify or measure such benefits. This study attempts to tackle part of the issue by analyzing citations to research papers in patent documents of US pharmaceutical companies to identify variables that correlate with how much Open Access papers a company cites in its patents. The ratio of citations to OA Journals (as identified in the Directory of Open Access Journals) to all journal citations in a given patent document is treated as the dependent variable in a multiple regression analysis. The main hypothesis to be tested in this study is that the high cost of journal subscription discriminates against small companies leading them to rely more on Open Access references in researching new drugs. Several control parameters are to be included like whether the company co-owns the patent with a university or with a different company, the availability and popularity of open access journals at the year prior to patent grant and whether the patented technology is pharmaceutical or not. The main limitation to the study is that it only considers gold open access papers. While one can argue that clarifying who needs access does not matter because (if the Open Access Movement succeeds) all research will be available for anyone on the internet anyway, this study assumes that such clarification still maters. Knowing who needs access will help to determine the venues where Open Access is to be advocated, the kind of political support the Open Access Movement should get and, perhaps more importantly, who should bear the cost of making the scientific literature Open Access.

Usage Trends of Open Access and Local Journals: A Korean Case Study.

Articles from open access and local journals are important resources for research in Korea and the usage trends of these articles are important indicators for the assessment of the current research practice. We analyzed an institutional collection of published papers from 1998 to 2014 authored by researchers from Seoul National University, and their references from papers published between 1998 and 2011. The published papers were collected from Web of Science or Scopus and were analyzed according to the proportion of articles from open access journals. Their cited references from published papers in Web of Science were analyzed according to the proportion of local (South Korean) or open access journals. The proportion of open access papers was relatively stable until 2006 (2.5 ~ 5.2% in Web of Science and 2.7 ~ 4.2% in Scopus), but then increased to 15.9% (Web of Science) or 18.5% (Scopus) in 2014. We analyzed 2,750,485 cited references from 52,295 published papers. We found that the overall proportion of cited articles from local journals was 1.8% and that for open access journals was 3.0%. Citations of open access articles have increased since 2006 to 4.1% in 2011, although the increase in open access article citations was less than for open access publications. The proportion of citations from local journals was even lower. We think that the publishing / citing mismatch is a term to describe this difference, which is an issue at Seoul National University, where the number of published papers at open access or local journals is increasing but the number of citations is not. The cause of this discrepancy is multi-factorial but the governmental / institutional policies, social / cultural issues and authors' citing behaviors will explain the mismatch. However, additional measures are also necessary, such as the development of an institutional citation database and improved search capabilities with respect to local and open access documents.

Open Access Papers Have a Greater Citation Advantage in the Author-Pays Model Compared to Toll Access Papers in Springer and Elsevier Open Access Journals

Open Access Papers Have a Greater Citation Advantage in the Author-Pays Model Compared to Toll Access Papers in Springer and Elsevier Open Access Journals