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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 70,838 bioRxiv papers from 309,132 authors.

Most downloaded bioRxiv papers, all time

in category scientific communication and education

491 results found. For more information, click each entry to expand.

1: Ten simple rules for structuring papers
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Posted to bioRxiv 28 Nov 2016

Ten simple rules for structuring papers
71,293 downloads scientific communication and education

Brett Mensh, Konrad P. Kording

Good scientific writing is essential to career development and to the progress of science. A well-structured manuscript allows readers and reviewers to get excited about the subject matter, to understand and verify the paper's contributions, and to integrate these contributions into a broader context. However, many scientists struggle with producing high-quality manuscripts and typically get little training in paper writing. Focusing on how readers consume information, we present a set of 10 simple rules to help you get across the main idea of your paper. These rules are designed to make your paper more influential and the process of writing more efficient and pleasurable.

2: A simple proposal for the publication of journal citation distributions
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Posted to bioRxiv 05 Jul 2016

A simple proposal for the publication of journal citation distributions
27,892 downloads scientific communication and education

Vincent Larivière, Véronique Kiermer, Catriona J. MacCallum, Marcia McNutt, Mark Patterson, Bernd Pulverer, Sowmya Swaminathan, Stuart Taylor, Stephen Curry

Although the Journal Impact Factor (JIF) is widely acknowledged to be a poor indicator of the quality of individual papers, it is used routinely to evaluate research and researchers. Here, we present a simple method for generating the citation distributions that underlie JIFs. Application of this straightforward protocol reveals the full extent of the skew of these distributions and the variation in citations received by published papers that is characteristic of all scientific journals. Although there are differences among journals across the spectrum of JIFs, the citation distributions overlap extensively, demonstrating that the citation performance of individual papers cannot be inferred from the JIF. We propose that this methodology be adopted by all journals as a move to greater transparency, one that should help to refocus attention on individual pieces of work and counter the inappropriate usage of JIFs during the process of research assessment.

3: The Reproducibility Of Research And The Misinterpretation Of P Values
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Posted to bioRxiv 31 May 2017

The Reproducibility Of Research And The Misinterpretation Of P Values
20,368 downloads scientific communication and education

David Colquhoun

We wish to answer this question If you observe a “significant” P value after doing a single unbiased experiment, what is the probability that your result is a false positive? The weak evidence provided by P values between 0.01 and 0.05 is explored by exact calculations of false positive risks. When you observe P = 0.05, the odds in favour of there being a real effect (given by the likelihood ratio) are about 3:1. This is far weaker evidence than the odds of 19 to 1 that might, wrongly, be inferred from the P value. And if you want to limit the false positive risk to 5%, you would have to assume that you were 87% sure that there was a real effect before the experiment was done. If you observe P = 0.001 in a well-powered experiment, it gives a likelihood ratio of almost 100:1 odds on there being a real effect. That would usually be regarded as conclusive, But the false positive risk would still be 8% if the prior probability of a real effect was only 0.1. And, in this case, if you wanted to achieve a false positive risk of 5% you would need to observe P = 0.00045. It is recommended that the terms “significant” and “non-significant” should never be used. Rather, P values should be supplemented by specifying the prior probability that would be needed to produce a specified (e.g. 5%) false positive risk. It may also be helpful to specify the minimum false positive risk associated with the observed P value. Despite decades of warnings, many areas of science still insist on labelling a result of P < 0.05 as “statistically significant”. This practice must account for a substantial part of the lack of reproducibility in some areas of science. And this is before you get to the many other well-known problems, like multiple comparisons, lack of randomisation and P-hacking. Science is endangered by statistical misunderstanding, and by university presidents and research funders who impose perverse incentives on scientists.

4: Insights from a survey-based analysis of the academic job market
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Posted to bioRxiv 09 Oct 2019

Insights from a survey-based analysis of the academic job market
12,287 downloads scientific communication and education

Jason D. Fernandes, Sarvenaz Sarabipour, Christopher T. Smith, Natalie M. Niemi, Nafisa M. Jadavji, Ariangela J. Kozik, Alex S. Holehouse, Vikas Pejaver, Orsolya Symmons, Alexandre W. Bisson Filho, Amanda Haage

Applying for a faculty position is a critical phase of many postdoctoral careers, but most postdoctoral researchers in STEM fields enter the academic job market with little knowledge of the process and expectations. A lack of data has made it difficult for applicants to assess their qualifications relative to the general applicant pool and for institutions to develop effective hiring policies. We analyzed responses to a survey of faculty job applicants between May 2018 and May 2019. We establish various background scholarly metrics for a typical faculty applicant and present an analysis of the interplay between those metrics and hiring outcomes. Traditional benchmarks of a positive research track record above a certain threshold of qualifications were unable to completely differentiate applicants with and without offers. Our findings suggest that there is no single clear path to a faculty job offer and that metrics such as career transition awards and publications in high impact factor journals were neither necessary nor sufficient for landing a faculty position. The applicants perceived the process as unnecessarily stressful, time-consuming, and largely lacking in feedback, irrespective of a successful outcome. Our findings emphasize the need to improve the transparency of the faculty job application process. In addition, we hope these and future data will help empower trainees to enter the academic job market with clearer expectations and improved confidence.

5: Accelerating Scientific Publication in Biology
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Posted to bioRxiv 11 Jul 2015

Accelerating Scientific Publication in Biology
10,125 downloads scientific communication and education

Ronald D. Vale

Scientific publications enable results and ideas to be transmitted throughout the scientific community. The number and type of journal publications also have become the primary criteria used in evaluating career advancement. Our analysis suggests that publication practices have changed considerably in the life sciences over the past thirty years. More experimental data is now required for publication, and the average time required for graduate students to publish their first paper has increased and is approaching the desirable duration of Ph.D. training. Since publication is generally a requirement for career progression, schemes to reduce the time of graduate student and postdoctoral training may be difficult to implement without also considering new mechanisms for accelerating communication of their work. The increasing time to publication also delays potential catalytic effects that ensue when many scientists have access to new information. The time has come for life scientists, funding agencies, and publishers to discuss how to communicate new findings in a way that best serves the interests of the public and the scientific community.

6: The life of P.I. - Transitions to Independence in Academia
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Posted to bioRxiv 10 Mar 2019

The life of P.I. - Transitions to Independence in Academia
10,114 downloads scientific communication and education

Sophie E. Acton, Andrew Bell, Christopher P. Toseland, Alison Twelvetrees

The data in this report summarises the responses gathered from 365 principal investigators of academic laboratories, who started their independent positions in the UK within the last 6 years up to 2018. We find that too many new investigators express frustration and poor optimism for the future. These data also reveal, that many of these individuals lack the support required to make a successful transition to independence and that simple measures could be put in place by both funders and universities in order to better support these early career researchers. We use these data to make both recommendations of good practice and for changes to policies that would make significant improvements to those currently finding independence challenging. We find that some new investigators face significant obstacles when building momentum and hiring a research team. In particular, access to PhD students. We also find some important areas such as starting salaries where significant gender differences persist, which cannot be explained by seniority. Our data also underlines the importance of support networks, within and outside the department, and the positive influence of good mentorship through this difficult career stage.

7: Relative Citation Ratio (RCR): A new metric that uses citation rates to measure influence at the article level
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Posted to bioRxiv 22 Oct 2015

Relative Citation Ratio (RCR): A new metric that uses citation rates to measure influence at the article level
9,433 downloads scientific communication and education

B. Ian Hutchins, Xin Yuan, James M Anderson, George M Santangelo

Despite their recognized limitations, bibliometric assessments of scientific productivity have been widely adopted. We describe here an improved method that makes novel use of the co-citation network of each article to field-normalize the number of citations it has received. The resulting Relative Citation Ratio is article-level and field-independent, and provides an alternative to the invalid practice of using Journal Impact Factors to identify influential papers. To illustrate one application of our method, we analyzed 88,835 articles published between 2003 and 2010, and found that the National Institutes of Health awardees who authored those papers occupy relatively stable positions of influence across all disciplines. We demonstrate that the values generated by this method strongly correlate with the opinions of subject matter experts in biomedical research, and suggest that the same approach should be generally applicable to articles published in all areas of science. A beta version of iCite, our web tool for calculating Relative Citation Ratios of articles listed in PubMed, is available at https://icite.od.nih.gov .

8: The Readability Of Scientific Texts Is Decreasing Over Time
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Posted to bioRxiv 22 Mar 2017

The Readability Of Scientific Texts Is Decreasing Over Time
7,896 downloads scientific communication and education

Pontus Plavén-Sigray, Granville James Matheson, Björn Christian Schiffler, William Hedley Thompson

Clarity and accuracy of reporting are fundamental to the scientific process. The understandability of written language can be estimated using readability formulae. Here, in a corpus consisting of 707 452 scientific abstracts published between 1881 and 2015 from 122 influential biomedical journals, we show that the readability of science is steadily decreasing. Further, we demonstrate that this trend is indicative of a growing usage of general scientific jargon. These results are concerning for scientists and for the wider public, as they impact both the reproducibility and accessibility of research findings.

9: Why clinical trials are terminated
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Posted to bioRxiv 02 Jul 2015

Why clinical trials are terminated
7,288 downloads scientific communication and education

Theodore R. Pak, Maria D. Rodriguez, Frederick P. Roth

Background: Evidence-based clinical practice relies on unbiased reporting of negative results. Meta-analysis of drug safety and efficacy across many clinical trials is difficult given the unconstrained nature of reasons that are provided to ClinicalTrials.gov to explain clinical trial terminations. Methods and Findings: We scanned all trials in ClinicalTrials.gov marked with the “terminated” status (N=3122), meaning the trial had been stopped before the scheduled end date. Under the current reporting framework, any number of reasons may be given for termination, and these need not conform to a controlled vocabulary. Here we develop a controlled vocabulary for trial termination, and map each terminated trial to as many as three vocabulary terms. Mapping to this “ontology of termination” allows further analysis and conclusions. First, we identify the subset of terminated trials that ended citing safety concerns (6.2%) or failure to establish efficacy (10.8%), and were further able to stratify these rates across trials of different phases. Second, we examine termination reasons where a stricter data model could have preserved more evidentiary value, either because the data model was misused (7.6%) or because the given reason left unclear whether the decision to terminate was based on analysis of the data (74.9%, with 20.4% mentioning a decision-maker that may have had access to the data). Third, we show that imposing a controlled vocabulary of reasons for termination would avoid ambiguity and improve the evidentiary value of clinical trials. Conclusions: We encourage wider use of an “ontology of termination” and propose four questions that should be posed on trial termination. These simple steps would promote transparency and enable ready access to negative trial results for meta-analysis.

10: The Prevalence of Inappropriate Image Duplication in Biomedical Research Publications
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Posted to bioRxiv 20 Apr 2016

The Prevalence of Inappropriate Image Duplication in Biomedical Research Publications
7,272 downloads scientific communication and education

Elisabeth M. Bik, Arturo Casadevall, Ferric C. Fang

Inaccurate data in scientific papers can result from honest error or intentional falsification. This study attempted to determine the percentage of published papers containing inappropriate image duplication, a specific type of inaccurate data. The images from a total of 20,621 papers in 40 scientific journals from 1995-2014 were visually screened. Overall, 3.8% of published papers contained problematic figures, with at least half exhibiting features suggestive of deliberate manipulation. The prevalence of papers with problematic images rose markedly during the past decade. Additional papers written by authors of papers with problematic images had an increased likelihood of containing problematic images as well. As this analysis focused only on one type of data, it is likely that the actual prevalence of inaccurate data in the published literature is higher. The marked variation in the frequency of problematic images among journals suggest that journal practices, such as pre-publication image screening, influence the quality of the scientific literature.

11: Tracking the popularity and outcomes of all bioRxiv preprints
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Posted to bioRxiv 13 Jan 2019

Tracking the popularity and outcomes of all bioRxiv preprints
6,589 downloads scientific communication and education

Richard J. Abdill, Ran Blekhman

Researchers in the life sciences are posting work to preprint servers at an unprecedented and increasing rate, sharing papers online before (or instead of) publication in peer-reviewed journals. Though the increasing acceptance of preprints is driving policy changes for journals and funders, there is little information about their usage. Here, we collected and analyzed data on all 37,648 preprints uploaded to bioRxiv.org, the largest biology-focused preprint server, in its first five years. We find preprints are being downloaded more than ever before (1.1 million tallied in October 2018 alone) and that the rate of preprints being posted has increased to a recent high of 2,100 per month. We also find that two-thirds of preprints posted before 2017 were later published in peer-reviewed journals, and find a relationship between journal impact factor and preprint downloads. Lastly, we developed Rxivist.org, a web application providing multiple ways of interacting with preprint metadata.

12: Author-Reviewer Homophily in Peer Review
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Posted to bioRxiv 29 Aug 2018

Author-Reviewer Homophily in Peer Review
6,016 downloads scientific communication and education

Dakota Murray, Kyle Siler, Vincent Larivière, Wei Mun Chan, Andrew M. Collings, Jennifer Raymond, Cassidy R Sugimoto

The fairness of scholarly peer review has been challenged by evidence of disparities in publication outcomes based on author demographic characteristics. To assess this, we conducted an exploratory analysis of peer review outcomes of 23,876 initial submissions and 7,192 full submissions that were submitted to the biosciences journal eLife between 2012 and 2017. Women and authors from nations outside of North America and Europe were underrepresented both as gatekeepers (editors and peer reviewers) and authors. We found evidence of a homophilic relationship between the demographics of the gatekeepers and authors and the outcome of peer review; that is, there were higher rates of acceptance in the case of gender and country homophily. The acceptance rate for manuscripts with male last authors was seven percent, or 3.5 percentage points, greater than for female last authors (95% CI = [0.5, 6.4]); this gender inequity was greatest, at nine percent or about 4.8 percentage points (95% CI = [0.3, 9.1]), when the team of reviewers was all male; this difference was smaller and not significantly different for mixed-gender reviewer teams. Homogeny between countries of the gatekeeper and the corresponding author was also associated with higher acceptance rates for many countries. To test for the persistence of these effects after controlling for potentially confounding variables, we conducted a logistic regression including document and author metadata. Disparities in acceptance rates associated with gender and country of affiliation and the homophilic associations remained. We conclude with a discussion of mechanisms that could contribute to this effect, directions for future research, and policy implications. Code and anonymized data have been made available at https://github.com/murrayds/elife-analysis

13: Scanning the Horizon: Towards transparent and reproducible neuroimaging research
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Posted to bioRxiv 16 Jun 2016

Scanning the Horizon: Towards transparent and reproducible neuroimaging research
6,006 downloads scientific communication and education

Russell A. Poldrack, Chris I. Baker, Joke Durnez, Krzysztof J. Gorgolewski, Paul M. Matthews, Marcus Munafò, Thomas E. Nichols, Jean-Baptiste Poline, Edward Vul, Tal Yarkoni

Functional neuroimaging techniques have transformed our ability to probe the neurobiological basis of behaviour and are increasingly being applied by the wider neuroscience community. However, concerns have recently been raised that the conclusions drawn from some human neuroimaging studies are either spurious or not generalizable. Problems such as low statistical power, flexibility in data analysis, software errors, and lack of direct replication apply to many fields, but perhaps particularly to fMRI. Here we discuss these problems, outline current and suggested best practices, and describe how we think the field should evolve to produce the most meaningful answers to neuroscientific questions.

14: A Data Citation Roadmap for Scholarly Data Repositories
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Posted to bioRxiv 28 Dec 2016

A Data Citation Roadmap for Scholarly Data Repositories
5,915 downloads scientific communication and education

Martin Fenner, Mercè Crosas, Jeffrey Grethe, David Kennedy, Henning Hermjakob, Philippe Rocca-Serra, Gustavo Durand, Robin Berjon, Sebastian Karcher, Maryann Martone, Timothy Clark

This article presents a practical roadmap for scholarly data repositories to implement data citation in accordance with the Joint Declaration of Data Citation Principles, a synopsis and harmonization of the recommendations of major science policy bodies. The roadmap was developed by the Repositories Expert Group, as part of the Data Citation Implementation Pilot (DCIP) project, an initiative of FORCE11.org and the NIH BioCADDIE (https://biocaddie.org) program. The roadmap makes 11 specific recommendations, grouped into three phases of implementation: a) required steps needed to support the Joint Declaration of Data Citation Principles, b) recommended steps that facilitate article/data publication workflows, and c) optional steps that further improve data citation support provided by data repositories.

15: Female grant applicants are equally successful when peer reviewers assess the science, but not when they assess the scientist
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Posted to bioRxiv 12 Dec 2017

Female grant applicants are equally successful when peer reviewers assess the science, but not when they assess the scientist
5,886 downloads scientific communication and education

Holly O. Witteman, Michael Hendricks, Sharon Straus, Cara Tannenbaum

Background: Previous research shows that men often receive more research funding than women, but does not provide empirical evidence as to why this occurs. In 2014, the Canadian Institutes of Health Research (CIHR) created a natural experiment by dividing all investigator-initiated funding into two new grant programs: one with and one without an explicit review focus on the caliber of the principal investigator. Methods: We analyzed application success among 23,918 grant applications from 7,093 unique principal investigators in a 5-year natural experiment across all investigator-initiated CIHR grant programs in 2011-2016. We used Generalized Estimating Equations to account for multiple applications by the same applicant and an interaction term between each principal investigator's self-reported sex and grant programs to compare success rates between male and female applicants under different review criteria. Results: The overall grant success rate across all competitions was 15.8%. After adjusting for age and research domain, the predicted probability of funding success in traditional programs was 0.9 percentage points higher for male than for female principal investigators (OR 0.934, 95% CI 0.854-1.022). In the new program focused on the proposed science, the gap was 0.9 percentage points in favour of male principal investigators (OR 0.998, 95% CI 0.794-1.229). In the new program with an explicit review focus on the caliber of the principal investigator, the gap was 4.0 percentage points in favour of male principal investigators (OR 0.705, 95% CI 0.519-0.960). Interpretation: This study suggests gender gaps in grant funding are attributable to less favourable assessments of women as principal investigators, not differences in assessments of the quality of science led by women. We propose ways for funders to avoid allowing gender bias to influence research funding. Funding: This study was unfunded.

16: Analysis and Correction of Inappropriate Image Duplication: The Molecular and Cellular Biology Experience
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Posted to bioRxiv 24 Jun 2018

Analysis and Correction of Inappropriate Image Duplication: The Molecular and Cellular Biology Experience
4,367 downloads scientific communication and education

Elisabeth M. Bik, Ferric C. Fang, Amy L. Kullas, Roger J. Davis, Arturo Casadevall

The present study analyzed 960 papers published in Molecular and Cellular Biology (MCB) from 2009-2016 and found 59 (6.1%) to contain inappropriately duplicated images. The 59 instances of inappropriate image duplication led to 42 corrections, 5 retractions and 12 instances in which no action was taken. Our experience suggests that the majority of inappropriate image duplications result from errors during figure preparation that can be remedied by correction. Nevertheless, ~10% of papers with inappropriate image duplications in MCB were retracted. If this proportion is representative, then as many as 35,000 papers in the literature are candidates for retraction due to image duplication. The resolution of inappropriate image duplication concerns after publication required an average of 6 h of journal staff time per published paper. MCB instituted a pilot program to screen images of accepted papers prior to publication that identified 12 manuscripts (14.5% out of 83) with image concerns in two months. The screening and correction of papers before publication required an average of 30 min of staff time per problematic paper. Image screening can identify papers with problematic images prior to publication, reduces post-publication problems and requires significantly less staff time than the correction of problems after publication.

17: Research challenges in Africa – an exploratory study on the experiences and opinions of African researchers
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Posted to bioRxiv 17 Oct 2018

Research challenges in Africa – an exploratory study on the experiences and opinions of African researchers
4,283 downloads scientific communication and education

Lem Ngongalah, Wepngong Emerson, Ngwa Niba Rawlings, James Muleme Musisi

Background: Insufficient research is a major impediment to growth, development and advancement of health in Africa. Africa produces less than 1% of global research output. Meanwhile, African countries face some of the toughest challenges worldwide, most of which can only be tackled through robust and efficient research. Addressing the barriers to conducting research in Africa is a step towards improving research capacity and output. This study aimed to identify the key challenges affecting research practice and output in Africa; and to highlight priority areas for improvement. Methods: A cross-sectional survey was administered through an online questionnaire, including participants from six countries in Sub-Saharan Africa. Participants included research professionals, research students, research groups and academics. Results: A total of 424 participants responded to this survey. The ability to conduct and produce high-quality research was seen to be influenced by multiple factors, most of which were related to the research environment in African countries. Priority areas for improvement included providing more training, raising awareness on the importance of research in Africa, encouraging governments to commit to research and increasing collaboration between researchers in Africa. Conclusion: The conditions under which research is done in Africa are severely flawed and do not encourage engagement in research, or continuity of research activity. African governments need to develop initiatives that accelerate and support research and research-based education in Africa, in order to build a solid foundation for research, increase research capacity, and enable institutions to provide valuable training and develop sustainable research opportunities in Africa.

18: Manuscript 101: A Data-Driven Writing Exercise For Beginning Scientists
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Posted to bioRxiv 18 May 2017

Manuscript 101: A Data-Driven Writing Exercise For Beginning Scientists
4,002 downloads scientific communication and education

Michael A. Halbisen, Amy Ralston

Learning to write a scientific manuscript is one of the most important and rewarding scientific training experiences, yet most young scientists only embark on this experience relatively late in graduate school, after gathering sufficient data in the lab. Yet, familiarity with the process of writing a scientific manuscript and receiving peer reviews, often leads to a more focused and driven experimental approach. To jump-start this training, we developed a protocol for teaching manuscript writing and reviewing in the classroom, appropriate for new graduate or upper-level undergraduate students of developmental biology. First, students are provided one of four cartoon data sets, which are focused on genetic models of animal development. Students are instructed to use their creativity to convert evidence into argument, and then to integrate their interpretations into a manuscript, including an illustrated, mechanistic model figure. After student manuscripts are submitted, manuscripts are redacted and distributed to classmates for peer review. Here, we present our cartoon datasets, homework instructions, and grading rubrics as a new resource for the scientific community. We also describe methods for developing new datasets so that instructors can adapt this activity to other disciplines. Our data-driven manuscript writing exercise, as well as the formative and summative assessments resulting from the peer review, enables students to learn fundamental concepts in developmental genetics. In addition, students practice essential skills of scientific communication, including arguing from evidence, developing and testing models, the unique conventions of scientific writing, and the joys of scientific story telling.

19: Is most published research really false?
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Posted to bioRxiv 27 Apr 2016

Is most published research really false?
3,936 downloads scientific communication and education

Jeffrey T. Leek, Leah R. Jager

There has been an increasing concern that most published medical findings are false. But what does it mean to be false? Here we describe the range of definitions of false discoveries in the scientific literature. We summarize the philosophical, statistical, and experimental evidence for each type of false discovery. We discuss common underpinning problems with the scientific and data analytic practices and point to tools and behaviors that can be implemented to reduce the problems with published scientific results.

20: Looking Into Pandora's Box: The Content Of Sci-Hub And Its Usage
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Posted to bioRxiv 08 Apr 2017

Looking Into Pandora's Box: The Content Of Sci-Hub And Its Usage
3,789 downloads scientific communication and education

Bastian Greshake

Despite the growth of Open Access, illegally circumventing paywalls to access scholarly publications is becoming a more mainstream phenomenon. The web service Sci-Hub is amongst the biggest facilitators of this, offering free access to around 62 million publications. So far it is not well studied how and why its users are accessing publications through Sci-Hub. By utilizing the recently released corpus of Sci-Hub and comparing it to the data of ~28 million downloads done through the service, this study tries to address some of these questions. The comparative analysis shows that both the usage and complete corpus is largely made up of recently published articles, with users disproportionately favoring newer articles and 35% of downloaded articles being published after 2013. These results hint that embargo periods before publications become Open Access are frequently circumnavigated using Guerilla Open Access approaches like Sci-Hub. On a journal level, the downloads show a bias towards some scholarly disciplines, especially Chemistry, suggesting increased barriers to access for these. Comparing the use and corpus on a publisher level, it becomes clear that only 11% of publishers are highly requested in comparison to the baseline frequency, while 45% of all publishers are significantly less accessed than expected. Despite this, the oligopoly of publishers is even more remarkable on the level of content consumption, with 80% of all downloads being published through only 9 publishers. All of this suggests that Sci-Hub is used by different populations and for a number of different reasons and that there is still a lack of access to the published scientific record. A further analysis of these openly available data resources will undoubtedly be valuable for the investigation of academic publishing.

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