Progress toward Public Access to Science

Anneliese Taylor Libraries Take on Policy: Support for Open Access and Open Data The growth of open access (OA) journal publishing has exploded in the last decade. The number of full, immediate OA articles went from 2% to 11% of all articles published between 2000 and 2011. When hybrid and embargoed open access articles are included in the count, the 2011 total jumps to 17% across all disciplines. And looking at biomedical journals specifically, 36% of articles published were OA 1 . Alongside this impressive growth in what’s commonly referred to as gold open access publishing has been a multi-pronged effort to expand access to published articles through “green” open access. Green OA is the process of depositing a version of a published article in an open access repository, whether that be an institutional repository (IR) or a disciplinary repository, or even placing articles on an openly accessible web site. “Self-archiving” is frequently used interchangeably with green OA. It does not require authors to pay an article processing charge as many gold OA models do. Many publishers have a history of allowing authors to self-archive a version of their article. The version is typically the accepted author’s manuscript, incorporating changes from the peer-review process, but before the publisher has copyedited, formatted, and branded the manuscript for final publication. A very few publishers allow the final, published version to be uploaded via self-archiving. There may or may not be a delay period after publication before the manuscript can be made accessible. Open access policies passed at the institutional level or by research funders are an attempt to broaden public access on a larger scale. The potential to open up access via a formalized policy is significant, but not without some effort. The next sections will highlight health sciences libraries and their roles with green OA policies in the United States. NIH Public Access Policy The single largest influencer on the growth of green OA articles in the health sciences to date is the National Institutes of Health (NIH) Public Access Policy, passed in 2008. This policy requires peer- reviewed scholarly articles published by NIH-funded researchers to be submitted to PubMed Central (PMC). The articles are made publicly available no later than twelve months after the official publication date. 2 PMC is NIH’s freely accessible, full text article repository, with close to 3 million articles currently deposited. NIH Policy manuscripts are about 10% of this amount. The rest of the content comes from publishers that voluntarily deposit their articles, usually after a publication delay. Many health sciences (HS) libraries got involved in 2008 or earlier with support for researchers at their academy needing to comply with the policy. Efforts range from offering workshops and individual consultations to notifying authors which of their articles are non-compliant and what steps to take to make them compliant. There are a number of excellent NIH Policy LibGuides (e.g. Duke University and University of Washington) and video tutorials (e.g. New York University and Harvard University) created by librarians to assist researchers. An informal survey in 2013 of Association of Academic Health Sciences Libraries (AAHSL) member involvement in supporting the Policy indicated a high level of activity amongst health sciences libraries. Of the 25 responses, all but four were actively involved with a support role. It’s remarkable that HS

Constraints on Data Sharing

(2008). Excellence is a Moving Target. Journal of Manual & Manipulative Therapy: Vol. 16, No. 3, pp. 125-125.

Obama Signs Act to Make More Federally Funded Research Open Access: NIH Requirement Extended to Other Agencies

ABSTRACTThe University of Michigan's Taubman Health Sciences Library is a significant partner in collaborating with National Institutes of Health (NIH) grantees to maintain continued funding at our institution. The National Institutes of Health (NIH) Public Access Policy (NIHPAP) requires grantees to submit final peer-reviewed journal manuscripts that arise from NIH funds to PubMed Central (PMC), the NIH open-access digital repository. Because NIH is the University of Michigan's largest research sponsor, the continuation of that funding is dependent on compliance with NIHPAP. This paper describes the development of a process map (PM) to improve clarity and efficiency in complying with NIH funding requirements.

Advances in science depend on researchers being able to reproduce the findings of their peers, thus providing a solid platform from which to move forward with new lines of scientific inquiry. Yet for a variety of reasons, irreproducibility appears to be a growing problem in experimental research. Now funding agencies and research journals are crafting guidelines to ensure that published studies are well designed, well reported, and better able to generate reproducible results. © Jim Frazier Media reports have singled out a number of egregious cases of irreproducibility, including reports published in Nature earlier this year indicating that adult stem cells would become pluripotent if submerged in a mild acid bath.1,2 The findings were widely criticized after scientists were unable to reproduce the results in their own laboratories.3 Subsequently, the first author agreed to retract the reports.4 In another widely publicized example, the biopharmaceutical company Amgen claimed it could reproduce just 6 of 53 studies that were considered landmarks in basic cancer research, despite close cooperation with the original scientists to make sure the same experimental protocols were used.5 Experts blame the irreproducibility problem on a number of factors, including inadequate reporting of the methods used in published research studies. Mounting evidence links poor methods descriptions with overstated findings,6,7,8,9,10 but in other cases faulty conclusions can be attributed to poor study design. In particular, inadequate randomization and blinding can introduce biases that render a study incapable of accurately testing its thesis.11 Irreproducibility is especially problematic if it plagues findings that lead to human clinical trials or to regulations and policies that could affect public health. One such instance was documented by researchers at the National Institute of Neurological Disorders and Stroke (NINDS), who discovered that patients with amyotrophic lateral sclerosis had been enrolled in a clinical trial founded on inadequate preclinical data. According to NINDS director Story Landis, the patients weren’t doing nearly as well as hoped on the test treatment, a broad-spectrum antibiotic called minocycline. When NINDS researchers took a closer look at the preclinical studies upon which the trial was predicated, they found the authors had not reported whether the studies were randomized or blinded. Furthermore, the work was done using small numbers of animals. “That was a wake-up call,” Landis says. “Human clinical trials need to be based on solid preclinical findings.”

BackgroundComputational methods have been used to find duplicate biomedical publications in MEDLINE. Full text articles are becoming increasingly available, yet the similarities among them have not been systematically studied. Here, we quantitatively investigated the full text similarity of biomedical publications in PubMed Central.Methodology/Principal Findings72,011 full text articles from PubMed Central (PMC) were parsed to generate three different datasets: full texts, sections, and paragraphs. Text similarity comparisons were performed on these datasets using the text similarity algorithm eTBLAST. We measured the frequency of similar text pairs and compared it among different datasets. We found that high abstract similarity can be used to predict high full text similarity with a specificity of 20.1% (95% CI [17.3%, 23.1%]) and sensitivity of 99.999%. similarity and full text similarity have a moderate correlation (Pearson correlation coefficient: −0.423) when the similarity ratio is above 0.4. Among pairs of articles in PMC, method sections are found to be the most repetitive (frequency of similar pairs, methods: 0.029, introduction: 0.0076, results: 0.0043). In contrast, among a set of manually verified duplicate articles, results are the most repetitive sections (frequency of similar pairs, results: 0.94, methods: 0.89, introduction: 0.82). Repetition of introduction and methods sections is more likely to be committed by the same authors (odds of a highly similar pair having at least one shared author, introduction: 2.31, methods: 1.83, results: 1.03). There is also significantly more similarity in pairs of review articles than in pairs containing one review and one nonreview paper (frequency of similar pairs: 0.0167 and 0.0023, respectively).Conclusion/SignificanceWhile quantifying abstract similarity is an effective approach for finding duplicate citations, a comprehensive full text analysis is necessary to uncover all potential duplicate citations in the scientific literature and is helpful when establishing ethical guidelines for scientific publications.

Journal of Optometry in PubMed and PubMed Central

We are delighted to announce that the AME Case Reports ( ACR ) ( Figure 1 ) has passed all the evaluation required by PubMed Central (PMC). PMC is a free, full-text archive of biomedical and life science journal articles maintained by the US National Institutes of Health’s National Library of Medicine (NIH/NLM). Articles deposited in PMC are also searchable from the NIH/NLM PubMed database, which is perhaps the most familiar citation database to researchers around the world.

From the *Department of Anesthesiology and Perioperative Care and Medicine, University of California, Irvine, California †Child Study Center, Yale University School of Medicine, New Haven, Connecticut ‡American College of Perioperative Medicine, Corona Del Mar, California §Department of Anesthesiology, The Robert Larner, M.D. College of Medicine, The University of Vermont, Burlington, Vermont ∥Department of Orthopaedic Surgery, University of Virginia, Charlottesville, Virginia. Accepted for publication January 3, 2023. Funding: None. Conflicts of Interest: See Disclosures at the end of the article. This article is being copublished by the Journal of Arthroplasty and Anesthesia & Analgesia. Minor differences in style may appear in each publication, but the article is substantially the same in each journal. Address correspondence to Zeev N. Kain, MD, MBA, Departments of Anesthesiology and Perioperative Care and Medicine, University of California, Irvine, CA. Address e-mail to [email protected].

The Policy Forum by Leon E. Rosenberg ( Science 's Compass, 15 Jan. p. [331][1]) and letters from William R. Brinkley and Ajit Varki ( Science 's Compass, 5 Feb. p. 791) concerning the decline of physician-scientists and their research are commendable. However, a subtle but critical point, which has a major impact on the situation, has not been mentioned. The problem stems from the all-inclusive classification by Rosenberg of physician-scientists as those performing “basic, disease-oriented, patient-oriented, population-oriented, and prevention-oriented” investigation. Upon careful analysis of the data and consideration of the kinds of research being performed by the extremely diverse group of M.D.'s and M.D./Ph.D.'s, it is clear that the problem for prototypical physician-scientists (that is, those performing laboratory-based, disease-oriented research) is much more precarious than appreciated. ![Figure][2] Can the classical physician-scientist survive?CREDIT: VISUALS UNLIMITED M.D.'s performing typical clinical research and those doing pure basic science who do not see patients are in fact comparatively well off and therefore should not be included in the discussion. Rather, the critical decline in M.D.'s performing research has been limited largely to traditional physician-scientists, those performing laboratory-based investigation who extend into the clinical arena. The immediate future for this group is clouded by the almost complete exhaustion of M.D.'s who desire this classical career pathway. Evidence for this comes from the trend in M.D.-focused National Institutes of Health (NIH) training grants. Although many of these slots are still being filled by M.D.'s (and this looks fine to NIH), most training programs have refocused their objectives to train clinical researchers. Therefore, these training grants are being filled by M.D.'s who will perform pure clinical research; indeed, in 1999, the emphasis on M.D. research has shifted squarely to evidence-based medicine/outcomes research. Furthermore, given the influence of managed care, the palpable emphasis now being placed on this type of clinical research in medical schools, and the new K23 and K24 awards (which have been designated for clinical researchers to the exclusion of laboratory-based M.D.'s), M.D.-driven clinical research is almost certainly assured of future success. This is not the case for laboratory-based M.D.'s. The depletion of these physician-scientists is only beginning, and the problem is going to be amplified dramatically in the next few years. The critical question is whether it is too late. It very well may be. If there is any hope, however, then the steps highlighted by Rosenberg, Brinkley, Varki, and others must be endorsed by the entire medical community and acted upon immediately. # {#article-title-2} Like many clinicians, I have identified common problems that are easily definable, but not easily treatable. I would like to have the opportunity to research some of these issues, but do not have the time as a full-time clinician. When I have discussed this with my boss, he has told me if I could produce some promising data, he would give me protected time to develop them. However, I can't get protected time to get the initial data with my busy clinical schedule. Thus, I am in a “Catch- 22.” If I get the data, I can get protected time. Yet, without the protected time, it will be very difficult to get the data. Despite these obstacles, I am trying to pull some of the early pieces together in my “off hours.” This is difficult and may ultimately not be fruitful. I would love the opportunity to be able to apply for a starter program for mid-career clinicians who would like to research a clinical issue. I believe that I have insights into disease processes that are worth exploring. Yet, they will remain at the level of a hypothesis or an anecdote unless I am able to have the time to systematically develop an approach to study them. # {#article-title-3} Unmentioned in Rosenberg's Policy Forum are the significant disadvantages for a physician-scientist being funded by NIH. For example, a physician-scientist earning $150,000 per year who receives NIH funding for 50% of time and effort would have a shortfall of $15,375, assuming a fringe benefit rate of 23%. He or she must cover malpractice insurance; support the training of medical students, residents, and fellows; and support the clinic operations. These expenses easily reach $60,000 per year; none is covered by NIH grants, and the physician-scientist is held responsible. If one assumes that the physician-scientist can meet his or her financial obligations by a 47-hour work week seeing patients, he or she would have to work an additional 7.8 hours a week to make up the shortfall. Even being paid the NIH salary cap, he or she would still have to work an additional 5.3 hours a week to meet the uncovered costs. Most physician-scientists put in these hours, but is it any wonder that medical students would be leery of pursuing a career in research? One could argue that these additional expenses should be covered by the clinical department or by indirect costs. However, there are numerous reasons why this is unlikely to occur. Further, the physician-scientist would have to go “hat in hand” in order to get special consideration. One realistic solution is for NIH and other funding agencies to recognize the special and extra costs associated with a physician-scientist's work. These funding agencies should grant to the individual physician-scientist the necessary funds to cover these expenses in order to ensure that those funds directly support the physician-scientist doing the research. Otherwise, not only will we see fewer physicians entering research; we will see more physicians leaving. # {#article-title-4} Not that many years ago, a department in a medical school which provided clinical care could obtain enough money through its revenues generated by patient care reimbursement to underwrite a meaningful portion of the faculty effort required to do clinical research. While one might argue that such reimbursement was not intended for this purpose, it was a practice understood and accepted by all involved, and the money spent for these research efforts by and large was a good investment for the country in general. The cost-cutting efforts that have affected all of medicine, including but not restricted to managed care and HMOs (health maintenance organizations), are in the process of rapidly eliminating this subsidy to clinical science. I do not know the amount of money this represented, but it certainly ran to many millions—perhaps hundreds of millons—of dollars. Its loss will be strongly felt, not just by the physician-scientists whose efforts would have been supported in this way, but also by the many hundreds of thousands of patients who would have benefited. Not only are changes in health care delivery practices making it extremely difficult to recruit patients into clinical studies, but paying for the time that is needed to complete these studies is becoming increasingly problematic. Any endeavor to prevent the extinction of this species of scientist will need to address these issues. [1]: /lookup/doi/10.1126/science.283.5400.331 [2]: pending:yes

Public library computer training for older adults to access high-quality Internet health information

The need to involve children in clinical research is clear. Without the inclusion of children in research, pediatric practitioners must rely on data from adult subjects, which often have little relevance in pediatric practice. Indeed, the lack of empirical studies on pediatric-specific therapies and disease states often forces pediatricians to base their therapies on their own personal experiences rather than on published data. The National Institutes of Health (NIH) recognizes that including children in research is essential, and in 1998 released the NIH Policy and Guidelines on the Inclusion of Children as Participants in Research Involving Human Subjects, which requires NIH-funded research to include children unless there are “scientific and ethical reasons not to include them” (1998). The policy further specifies seven accepted justifications for the exclusion of children. Due to this NIH policy, the United States Food and Drug Administration (US FDA) Modernization Act of 1997 (Center for Drug Evaluation and Research 1997), and the 1998 FDA Final Rule (US FDA 1998), there has been increasing pressure and improved opportunities for investigators to enroll children in clinical research.

Race, ethnicity, and epilepsy research

BioTechniquesVol. 48, No. 2 From the EditorOpen AccessSocial ScienceThe EditorsThe Editors*E-mail Address: bioeditor@biotechniques.comBioTechniquesSearch for more papers by this authorPublished Online:3 Apr 2018https://doi.org/10.2144/000113355AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinkedInRedditEmail The recent announcement that the National Institutes of Health (NIH) is creating a “Facebook for scientists” means yet another group is moving out into the turbulent waters of social media. The $12.2-million NIH effort aims to create an interface where scientists can seek out collaborators and researchers with similar interests. The effort will cull data on these researchers from university web sites and journals to generate research summaries and lists of relevant publications and projects. This will mean that researchers will not have to actively update their pages in order to stay current within the new system.Facebook itself has thrived due in large measure to the interest of its users in updating their pages and status with regular frequency, leading those connected to these users to check in with equal frequency. The same holds true for Twitter (those who continue to update their Tweets regularly are read most often) and blogs (post more often, get more readers who respond). In the case of the NIH effort, where most of the updating is proposed to be automatic, the question arises: what will this site offer that LinkedIn or other social sites—including ResearchGATE, LabRoots, OpenWetWare, LabSpaces, or any of the only mildly popular online scientist resources—do not? And what will prompt researchers to visit this site regularly, find collaborators, or discuss research ideas?NIH's effort could encounter the same issues and concerns that all the others have encountered in applying social networking to scientists, generating repeat, and fostering interactive users. Although the NIH's automatic update model does deal with this to some extent, will researchers visit regularly and take advantage of what the site has to offer? Working in a lab is generally a solitary pursuit: most scientists work on a project and only discuss it with direct collaborators until the later stages just before publication. But although this is the working model, it does not mean that these researchers will not use social media during their projects; it simply means that getting them to the point of use could prove harder than with other groups.The tipping point for increased social media usage by scientists might actually come during the next five to ten years (which is perfectly timed with the NIH site's debut). Most likely this will not come from any advance in the interface or a unique web site model; instead the change will come when younger investigators get their first positions in the academic world. Since these researchers will be more familiar with social media and interactive web sites, they will in turn be more trusting of using these sites and updating their own information. And as these investigators train the next generation of scientists, the idea of using social media to advance basic and applied research will gain traction and become more mainstream among all scientists.So the NIH effort could find its greatest success by initially motivating young scientists—graduate students and assistant professors, the ones most likely to initially take the plunge into this form of social media—to use the site, and then using those scientists to evangelize the virtues of the site and expound on its interactions with other colleagues. We may recall that this is much akin to what happened with Facebook itself: teenagers and young adults first identified the use and benefit of the site while their parents entered this virtual world much later (and much to the chagrin of their children!).We applaud the initiative and efforts of NIH in creating a new sharing site for researchers around the globe. Science is becoming an increasingly collaborative enterprise, and there exists a need to assist researchers in finding necessary information from peers quickly. Through continuing efforts such as this, and the emergence of the next generation of scientist raised on social media, it is only a matter of time before science finally does have its global “Facebook.” As always, post your thoughts and comments at our Molecular Biology Forums under “To the Editor” (http://molecular-biology.forums.biotechniques.com) or send an email directly to the editors (bioeditor@biotechniques.com).FiguresReferencesRelatedDetails Vol. 48, No. 2 Follow us on social media for the latest updates Metrics History Published online 3 April 2018 Published in print February 2010 Information© 2010 Author(s)PDF download