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1.  Open access versus subscription journals: a comparison of scientific impact 
BMC Medicine  2012;10:73.
Background
In the past few years there has been an ongoing debate as to whether the proliferation of open access (OA) publishing would damage the peer review system and put the quality of scientific journal publishing at risk. Our aim was to inform this debate by comparing the scientific impact of OA journals with subscription journals, controlling for journal age, the country of the publisher, discipline and (for OA publishers) their business model.
Methods
The 2-year impact factors (the average number of citations to the articles in a journal) were used as a proxy for scientific impact. The Directory of Open Access Journals (DOAJ) was used to identify OA journals as well as their business model. Journal age and discipline were obtained from the Ulrich's periodicals directory. Comparisons were performed on the journal level as well as on the article level where the results were weighted by the number of articles published in a journal. A total of 610 OA journals were compared with 7,609 subscription journals using Web of Science citation data while an overlapping set of 1,327 OA journals were compared with 11,124 subscription journals using Scopus data.
Results
Overall, average citation rates, both unweighted and weighted for the number of articles per journal, were about 30% higher for subscription journals. However, after controlling for discipline (medicine and health versus other), age of the journal (three time periods) and the location of the publisher (four largest publishing countries versus other countries) the differences largely disappeared in most subcategories except for journals that had been launched prior to 1996. OA journals that fund publishing with article processing charges (APCs) are on average cited more than other OA journals. In medicine and health, OA journals founded in the last 10 years are receiving about as many citations as subscription journals launched during the same period.
Conclusions
Our results indicate that OA journals indexed in Web of Science and/or Scopus are approaching the same scientific impact and quality as subscription journals, particularly in biomedicine and for journals funded by article processing charges.
doi:10.1186/1741-7015-10-73
PMCID: PMC3398850  PMID: 22805105
impact; open access; peer review; scientific publishing
2.  The Development of Open Access Journal Publishing from 1993 to 2009 
PLoS ONE  2011;6(6):e20961.
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).
doi:10.1371/journal.pone.0020961
PMCID: PMC3113847  PMID: 21695139
3.  A Study of Innovative Features in Scholarly Open Access Journals 
Background
The emergence of the Internet has triggered tremendous changes in the publication of scientific peer-reviewed journals. Today, journals are usually available in parallel electronic versions, but the way the peer-review process works, the look of articles and journals, and the rigid and slow publication schedules have remained largely unchanged, at least for the vast majority of subscription-based journals. Those publishing firms and scholarly publishers who have chosen the more radical option of open access (OA), in which the content of journals is freely accessible to anybody with Internet connectivity, have had a much bigger degree of freedom to experiment with innovations.
Objective
The objective was to study how open access journals have experimented with innovations concerning ways of organizing the peer review, the format of journals and articles, new interactive and media formats, and novel publishing revenue models.
Methods
The features of 24 open access journals were studied. The journals were chosen in a nonrandom manner from the approximately 7000 existing OA journals based on available information about interesting journals and include both representative cases and highly innovative outlier cases.
Results
Most early OA journals in the 1990s were founded by individual scholars and used a business model based on voluntary work close in spirit to open-source development of software. In the next wave, many long-established journals, in particular society journals and journals from regions such as Latin America, made their articles OA when they started publishing parallel electronic versions. From about 2002 on, newly founded professional OA publishing firms using article-processing charges to fund their operations have emerged. Over the years, there have been several experiments with new forms of peer review, media enhancements, and the inclusion of structured data sets with articles. In recent years, the growth of OA publishing has also been facilitated by the availability of open-source software for journal publishing.
Conclusions
The case studies illustrate how a new technology and a business model enabled by new technology can be harnessed to find new innovative ways for the organization and content of scholarly publishing. Several recent launches of OA journals by major subscription publishers demonstrate that OA is rapidly gaining acceptance as a sustainable alternative to subscription-based scholarly publishing.
doi:10.2196/jmir.1802
PMCID: PMC3278101  PMID: 22173122
Scholarly publishing; open access; Internet; peer review
4.  Anatomy of the Epidemiological Literature on the 2003 SARS Outbreaks in Hong Kong and Toronto: A Time-Stratified Review 
PLoS Medicine  2010;7(5):e1000272.
Weijia Xing and colleagues reviewed the published epidemiological literature on SARS and show that less than a quarter of papers were published during the epidemic itself, suggesting that the research published lagged substantially behind the need for it.
Background
Outbreaks of emerging infectious diseases, especially those of a global nature, require rapid epidemiological analysis and information dissemination. The final products of those activities usually comprise internal memoranda and briefs within public health authorities and original research published in peer-reviewed journals. Using the 2003 severe acute respiratory syndrome (SARS) epidemic as an example, we conducted a comprehensive time-stratified review of the published literature to describe the different types of epidemiological outputs.
Methods and Findings
We identified and analyzed all published articles on the epidemiology of the SARS outbreak in Hong Kong or Toronto. The analysis was stratified by study design, research domain, data collection, and analytical technique. We compared the SARS-case and matched-control non-SARS articles published according to the timeline of submission, acceptance, and publication. The impact factors of the publishing journals were examined according to the time of publication of SARS articles, and the numbers of citations received by SARS-case and matched-control articles submitted during and after the epidemic were compared. Descriptive, analytical, theoretical, and experimental epidemiology concerned, respectively, 54%, 30%, 11%, and 6% of the studies. Only 22% of the studies were submitted, 8% accepted, and 7% published during the epidemic. The submission-to-acceptance and acceptance-to-publication intervals of the SARS articles submitted during the epidemic period were significantly shorter than the corresponding intervals of matched-control non-SARS articles published in the same journal issues (p<0.001 and p<0.01, respectively). The differences of median submission-to-acceptance intervals and median acceptance-to-publication intervals between SARS articles and their corresponding control articles were 106.5 d (95% confidence interval [CI] 55.0–140.1) and 63.5 d (95% CI 18.0–94.1), respectively. The median numbers of citations of the SARS articles submitted during the epidemic and over the 2 y thereafter were 17 (interquartile range [IQR] 8.0–52.0) and 8 (IQR 3.2–21.8), respectively, significantly higher than the median numbers of control article citations (15, IQR 8.5–16.5, p<0.05, and 7, IQR 3.0–12.0, p<0.01, respectively).
Conclusions
A majority of the epidemiological articles on SARS were submitted after the epidemic had ended, although the corresponding studies had relevance to public health authorities during the epidemic. To minimize the lag between research and the exigency of public health practice in the future, researchers should consider adopting common, predefined protocols and ready-to-use instruments to improve timeliness, and thus, relevance, in addition to standardizing comparability across studies. To facilitate information dissemination, journal managers should reengineer their fast-track channels, which should be adapted to the purpose of an emerging outbreak, taking into account the requirement of high standards of quality for scientific journals and competition with other online resources.
Please see later in the article for the Editors' Summary
Editors' Summary
Background
Every now and then, a new infectious disease appears in a human population or an old disease becomes much more common or more geographically widespread. Recently, several such “emerging infectious diseases” have become major public health problems. For example, HIV/AIDS, hepatitis C, and severe acute respiratory syndrome (SARS) have all emerged in the past three decades and spread rapidly round the world. When an outbreak (epidemic) of an emerging infectious disease occurs, epidemiologists (scientists who study the causes, distribution, and control of diseases in populations) swing into action, collecting and analyzing data on the new threat to human health. Epidemiological studies are rapidly launched to identify the causative agent of the new disease, to investigate how the disease spreads, to define diagnostic criteria for the disease, to evaluate potential treatments, and to devise ways to control the disease's spread. Public health officials then use the results of these studies to bring the epidemic under control.
Why Was This Study Done?
Clearly, epidemics of emerging infectious diseases can only be controlled rapidly and effectively if the results of epidemiological studies are made widely available in a timely manner. Public health bulletins (for example, the Morbidity and Mortality Weekly Report from the US Centers from Disease Control and Prevention) are an important way of disseminating information as is the publication of original research in peer-reviewed academic journals. But how timely is this second dissemination route? Submission, peer-review, revision, re-review, acceptance, and publication of a piece of academic research can be a long process, the speed of which is affected by the responses of both authors and journals. In this study, the researchers analyze how the results of academic epidemiological research are submitted and published in journals during and after an emerging infectious disease epidemic using the 2003 SARS epidemic as an example. The first case of SARS was identified in Asia in February 2003 and rapidly spread around the world. 8,098 people became ill with SARS and 774 died before the epidemic was halted in July 2003.
What Did the Researchers Do and Find?
The researchers identified more than 300 journal articles covering epidemiological research into the SARS outbreak in Hong Kong, China, and Toronto, Canada (two cities strongly affected by the epidemic) that were published online or in print between January 1, 2003 and July 31, 2007. The researchers' analysis of these articles shows that more than half them were descriptive epidemiological studies, investigations that focused on describing the distribution of SARS; a third were analytical epidemiological studies that tried to discover the cause of SARS. Overall, 22% of the journal articles were submitted for publication during the epidemic. Only 8% of the articles were accepted for publication and only 7% were actually published during the epidemic. The median (average) submission-to-acceptance and acceptance-to-publication intervals for SARS articles submitted during the epidemic were 55 and 77.5 days, respectively, much shorter intervals than those for non-SARS articles published in the same journal issues. After the epidemic was over, the submission-to-acceptance and acceptance-to-publication intervals for SARS articles was similar to that of non-SARS articles.
What Do These Findings Mean?
These findings show that, although the academic response to the SARS epidemic was rapid, most articles on the epidemiology of SARS were published after the epidemic was over even though SARS was a major threat to public health. Possible reasons for this publication delay include the time taken by authors to prepare and undertake their studies, to write and submit their papers, and, possibly, their tendency to first submit their results to high profile journals. The time then taken by journals to review the studies, make decisions about publication, and complete the publication process might also have delayed matters. To minimize future delays in the publication of epidemiological research on emerging infectious diseases, epidemiologists could adopt common, predefined protocols and ready-to-use instruments, which would improve timeliness and ensure comparability across studies, suggest the researchers. Journals, in turn, could improve their fast-track procedures and could consider setting up online sections that could be activated when an emerging infectious disease outbreak occurred. Finally, journals could consider altering their review system to speed up the publication process provided the quality of the final published articles was not compromised.
Additional Information
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1000272.
The US National Institute of Allergy and Infectious Diseases provides information on emerging infectious diseases
The US Centers for Control and Prevention of Diseases also provides information about emerging infectious diseases, including links to other resources, and information on SARS
Wikipedia has a page on epidemiology (note that Wikipedia is a free online encyclopedia that anyone can edit; available in several languages)
The World Health Organization has information on SARS (in several languages)
doi:10.1371/journal.pmed.1000272
PMCID: PMC2864302  PMID: 20454570
5.  Conflicts of Interest at Medical Journals: The Influence of Industry-Supported Randomised Trials on Journal Impact Factors and Revenue – Cohort Study 
PLoS Medicine  2010;7(10):e1000354.
Andreas Lundh and colleagues investigated the effect of publication of large industry-supported trials on citations and journal income, through reprint sales, in six general medical journals
Background
Transparency in reporting of conflict of interest is an increasingly important aspect of publication in medical journals. Publication of large industry-supported trials may generate many citations and journal income through reprint sales and thereby be a source of conflicts of interest for journals. We investigated industry-supported trials' influence on journal impact factors and revenue.
Methods and Findings
We sampled six major medical journals (Annals of Internal Medicine, Archives of Internal Medicine, BMJ, JAMA, The Lancet, and New England Journal of Medicine [NEJM]). For each journal, we identified randomised trials published in 1996–1997 and 2005–2006 using PubMed, and categorized the type of financial support. Using Web of Science, we investigated citations of industry-supported trials and the influence on journal impact factors over a ten-year period. We contacted journal editors and retrieved tax information on income from industry sources. The proportion of trials with sole industry support varied between journals, from 7% in BMJ to 32% in NEJM in 2005–2006. Industry-supported trials were more frequently cited than trials with other types of support, and omitting them from the impact factor calculation decreased journal impact factors. The decrease varied considerably between journals, with 1% for BMJ to 15% for NEJM in 2007. For the two journals disclosing data, income from the sales of reprints contributed to 3% and 41% of the total income for BMJ and The Lancet in 2005–2006.
Conclusions
Publication of industry-supported trials was associated with an increase in journal impact factors. Sales of reprints may provide a substantial income. We suggest that journals disclose financial information in the same way that they require them from their authors, so that readers can assess the potential effect of different types of papers on journals' revenue and impact.
Please see later in the article for the Editors' Summary
Editors' Summary
Background
Medical journals publish many different types of papers that inform doctors about the latest research advances and the latest treatments for their patients. They publish articles that describe laboratory-based research into the causes of diseases and the identification of potential new drugs. They publish the results of early clinical trials in which a few patients are given a potential new drug to check its safety. Finally and most importantly, they publish the results of randomized controlled trials (RCTs). RCTs are studies in which large numbers of patients are randomly allocated to different treatments without the patient or the clinician knowing the allocation and the efficacy of the various treatments compared. RCTs are best way of determining whether a new drug is effective and have to be completed before a drug can be marketed. Because RCTs are very expensive, they are often supported by drug companies. That is, drug companies provide grants or drugs for the trial or assist with data analysis and/or article preparation.
Why Was This Study Done?
Whenever a medical journal publishes an article, the article's authors have to declare any conflicts of interest such as financial gain from the paper's publication. Conflict of interest statements help readers assess papers—an author who owns the patent for a drug, for example, might put an unduly positive spin on his/her results. The experts who review papers for journals before publication provide similar conflict of interest statements. But what about the journal editors who ultimately decide which papers get published? The International Committee of Medical Journal Editors (ICMJE), which produces medical publishing guidelines, states that: “Editors who make final decisions about manuscripts must have no personal, professional, or financial involvement in any of the issues that they might judge.” However, the publication of industry-supported RCTs might create “indirect” conflicts of interest for journals by boosting the journal's impact factor (a measure of a journal's importance based on how often its articles are cited) and its income through the sale of reprints to drug companies. In this study, the researchers investigate whether the publication of industry-supported RCTs influences the impact factors and finances of six major medical journals.
What Did the Researchers Do and Find?
The researchers determined which RCTs published in the New England Journal of Medicine (NEJM), the British Medical Journal (BMJ), The Lancet, and three other major medical journals in 1996–1997 and 2005–2006 were supported wholly, partly, or not at all by industry. They then used the online academic citation index Web of Science to calculate an approximate impact factor for each journal for 1998 and 2007 and calculated the effect of the published RCTs on the impact factor. The proportion of RCTs with sole industry support varied between journals. Thus, 32% of the RCTs published in the NEJM during both two-year periods had industry support whereas only 7% of the RCTs published in the BMJ in 2005–2006 had industry support. Industry-supported trials were more frequently cited than RCTs with other types of support and omitting industry-supported RCTs from impact factor calculations decreased all the approximate journal impact factors. For example, omitting all RCTs with industry or mixed support decreased the 2007 BMJ and NEJM impact factors by 1% and 15%, respectively. Finally, the researchers asked each journal's editor about their journal's income from industry sources. For the BMJ and The Lancet, the only journals that provided this information, income from reprint sales was 3% and 41%, respectively, of total income in 2005–2006.
What Do These Findings Mean?
These findings show that the publication of industry-supported RCTs was associated with an increase in the approximate impact factors of these six major medical journals. Because these journals publish numerous RCTs, this result may not be generalizable to other journals. These findings also indicate that income from reprint sales can be a substantial proportion of a journal's total income. Importantly, these findings do not imply that the decisions of editors are affected by the possibility that the publication of an industry-supported trial might improve their journal's impact factor or income. Nevertheless, the researchers suggest, journals should live up to the same principles related to conflicts of interest as those that they require from their authors and should routinely disclose information on the source and amount of income that they receive.
Additional Information
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1000354.
This study is further discussed in a PLoS Medicine Perspective by Harvey Marcovitch
The International Committee of Medical Journal Editors provides information about the publication of medical research, including conflicts of interest
The World Association of Medical Editors also provides information on conflicts of interest in medical journals
Information about impact factors is provided by Thomson Reuters, a provider of intelligent information for businesses and professionals; Thomson Reuters also runs Web of Science
doi:10.1371/journal.pmed.1000354
PMCID: PMC2964336  PMID: 21048986
6.  Promotional Tone in Reviews of Menopausal Hormone Therapy After the Women's Health Initiative: An Analysis of Published Articles 
PLoS Medicine  2011;8(3):e1000425.
Adriane Fugh-Berman and colleagues analyzed a selection of published opinion pieces on hormone therapy and show that there may be a connection between receiving industry funding for speaking, consulting, or research and the tone of such opinion pieces.
Background
Even after the Women's Health Initiative (WHI) found that the risks of menopausal hormone therapy (hormone therapy) outweighed benefit for asymptomatic women, about half of gynecologists in the United States continued to believe that hormones benefited women's health. The pharmaceutical industry has supported publication of articles in medical journals for marketing purposes. It is unknown whether author relationships with industry affect promotional tone in articles on hormone therapy. The goal of this study was to determine whether promotional tone could be identified in narrative review articles regarding menopausal hormone therapy and whether articles identified as promotional were more likely to have been authored by those with conflicts of interest with manufacturers of menopausal hormone therapy.
Methods and Findings
We analyzed tone in opinion pieces on hormone therapy published in the four years after the estrogen-progestin arm of the WHI was stopped. First, we identified the ten authors with four or more MEDLINE-indexed reviews, editorials, comments, or letters on hormone replacement therapy or menopausal hormone therapy published between July 2002 and June 2006. Next, we conducted an additional search using the names of these authors to identify other relevant articles. Finally, after author names and affiliations were removed, 50 articles were evaluated by three readers for scientific accuracy and for tone. Scientific accuracy was assessed based on whether or not the findings of the WHI were accurately reported using two criteria: (1) Acknowledgment or lack of denial of the risk of breast cancer diagnosis associated with hormone therapy, and (2) acknowledgment that hormone therapy did not benefit cardiovascular disease endpoints. Determination of promotional tone was based on the assessment by each reader of whether the article appeared to promote hormone therapy. Analysis of inter-rater consistency found moderate agreement for scientific accuracy (κ = 0.57) and substantial agreement for promotional tone (κ = 0.65). After discussion, readers found 86% of the articles to be scientifically accurate and 64% to be promotional in tone. Themes that were common in articles considered promotional included attacks on the methodology of the WHI, arguments that clinical trial results should not guide treatment for individuals, and arguments that observational studies are as good as or better than randomized clinical trials for guiding clinical decisions. The promotional articles we identified also implied that the risks associated with hormone therapy have been exaggerated and that the benefits of hormone therapy have been or will be proven. Of the ten authors studied, eight were found to have declared payment for speaking or consulting on behalf of menopausal hormone manufacturers or for research support (seven of these eight were speakers or consultants). Thirty of 32 articles (90%) evaluated as promoting hormone therapy were authored by those with potential financial conflicts of interest, compared to 11 of 18 articles (61%) by those without such conflicts (p = 0.0025). Articles promoting the use of menopausal hormone therapy were 2.41 times (95% confidence interval 1.49–4.93) as likely to have been authored by authors with conflicts of interest as by authors without conflicts of interest. In articles from three authors with conflicts of interest some of the same text was repeated word-for-word in different articles.
Conclusion
There may be a connection between receiving industry funding for speaking, consulting, or research and the publication of promotional opinion pieces on menopausal hormone therapy.
Please see later in the article for the Editors' Summary
Editors' Summary
Background
Over the past three decades, menopausal hormones have been heavily promoted for preventing disease in women. However, the Women's Health Initiative (WHI) study—which enrolled more than 26,000 women in the US and which was published in 2004—found that estrogen-progestin and estrogen-only formulations (often prescribed to women around the age of menopause) increased the risk of stroke, deep vein thrombosis, dementia, and incontinence. Furthermore, this study found that the estrogen-progestin therapy increased rates of breast cancer. In fact, the estrogen-progestin arm of the WHI study was stopped in 2002 due to harmful findings, and the estrogen-only arm was stopped in 2004, also because of harmful findings. In addition, the study also found that neither therapy reduced cardiovascular risk or markedly benefited health-related quality of life measures.
Despite these results, two years after the results of WHI study were published, a survey of over 700 practicing gynecologists—the specialists who prescribe the majority of menopausal hormone therapies—in the US found that almost half did not find the findings of the WHI study convincing and that 48% disagreed with the decision to stop the trial early. Furthermore, follow-up surveys found similar results.
Why Was This Study Done?
It is unclear why gynecologists and other physicians continue to prescribe menopausal hormone therapies despite the results of the WHI. Some academics argue that published industry-funded reviews and commentaries may be designed to convey specific, but subtle, marketing messages and several academic analyses have used internal industry documents disclosed in litigation cases. So this study was conducted to investigate whether hormone therapy–promoting tone could be identified in narrative review articles and if so, whether these articles were more likely to have been authored by people who had accepted funding from hormone manufacturers.
What Did the Researchers Do and Find?
The researchers conducted a comprehensive literature search that identified 340 relevant articles published between July 2002 and June 2006—the four years following the cessation of the estrogen-progestin arm of the women's health initiative study. Ten authors had published four to six articles, 47 authored two or three articles, and 371 authored one article each. The researchers focused on authors who had published four or more articles in the four-year period under study and, after author names and affiliations were removed, 50 articles were evaluated by three readers for scientific accuracy and for tone. After individually analyzing a batch of articles, the readers met to provide their initial assessments, to discuss them, and to reach consensus on tone and scientific accuracy. Then after the papers were evaluated, each author was identified and the researchers searched for authors' potential financial conflicts of interest, defined as publicly disclosed information that the authors had received payment for research, speaking, or consulting on behalf of a manufacturer of menopausal hormone therapy.
Common themes in the 50 articles included arguments that clinical trial results should not guide treatment for individuals and suggestions that the risks associated with hormone therapy have been exaggerated and that the benefits of hormone therapy have been or will be proven. Furthermore, of the ten authors studied, eight were found to have received payment for research, speaking or consulting on behalf of menopause hormone manufacturers, and 30 of 32 articles evaluated as promoting hormone therapy were authored by those with potential financial conflicts of interest. Articles promoting the use of menopausal hormone therapy were more than twice as likely to have been written by authors with conflicts of interest as by authors without conflicts of interest. Furthermore, Three authors who were identified as having financial conflicts of interest were authors on articles where sections of their previously published articles were repeated word-for-word without citation.
What Do These Findings Mean?
The findings of this study suggest that there may be a link between receiving industry funding for speaking, consulting, or research and the publication of apparently promotional opinion pieces on menopausal hormone therapy. Furthermore, such publications may encourage physicians to continue prescribing these therapies to women of menopausal age. Therefore, physicians and other health care providers should interpret the content of review articles with caution. In addition, medical journals should follow the International Committee of Medical Journal Editors Uniform Requirements for Manuscripts, which require that all authors submit signed statements of their participation in authorship and full disclosure of any conflicts of interest.
Additional Information
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1000425.
The US National Heart, Lung, and Blood Institute has more information on the Womens Health Initiative
The US National Institutes of Health provide more information about the effects of menopausal hormone replacement therapy
The Office of Women's Health, U.S. Department of Health and Human Services provides information on menopausal hormone therapy
The International Committee of Medical Journal Editors Uniform Requirements for Manuscripts presents Uniform Requirements for Manuscripts published in biomedical journals
The National Womens Health Network, a consumer advocacy group that takes no industry money, has factsheets and articles about menopausal hormone therapy
PharmedOut, a Georgetown University Medical Center project, has many resources on pharmaceutical marketing practices
doi:10.1371/journal.pmed.1000425
PMCID: PMC3058057  PMID: 21423581
7.  Misrepresentation of Randomized Controlled Trials in Press Releases and News Coverage: A Cohort Study 
PLoS Medicine  2012;9(9):e1001308.
A study conducted by Amélie Yavchitz and colleagues examines the factors associated with “spin” (specific reporting strategies, intentional or unintentional, that emphasize the beneficial effect of treatments) in press releases of clinical trials.
Background
Previous studies indicate that in published reports, trial results can be distorted by the use of “spin” (specific reporting strategies, intentional or unintentional, emphasizing the beneficial effect of the experimental treatment). We aimed to (1) evaluate the presence of “spin” in press releases and associated media coverage; and (2) evaluate whether findings of randomized controlled trials (RCTs) based on press releases and media coverage are misinterpreted.
Methods and Findings
We systematically searched for all press releases indexed in the EurekAlert! database between December 2009 and March 2010. Of the 498 press releases retrieved and screened, we included press releases for all two-arm, parallel-group RCTs (n = 70). We obtained a copy of the scientific article to which the press release related and we systematically searched for related news items using Lexis Nexis.
“Spin,” defined as specific reporting strategies (intentional or unintentional) emphasizing the beneficial effect of the experimental treatment, was identified in 28 (40%) scientific article abstract conclusions and in 33 (47%) press releases. From bivariate and multivariable analysis assessing the journal type, funding source, sample size, type of treatment (drug or other), results of the primary outcomes (all nonstatistically significant versus other), author of the press release, and the presence of “spin” in the abstract conclusion, the only factor associated, with “spin” in the press release was “spin” in the article abstract conclusions (relative risk [RR] 5.6, [95% CI 2.8–11.1], p<0.001). Findings of RCTs based on press releases were overestimated for 19 (27%) reports. News items were identified for 41 RCTs; 21 (51%) were reported with “spin,” mainly the same type of “spin” as those identified in the press release and article abstract conclusion. Findings of RCTs based on the news item was overestimated for ten (24%) reports.
Conclusion
“Spin” was identified in about half of press releases and media coverage. In multivariable analysis, the main factor associated with “spin” in press releases was the presence of “spin” in the article abstract conclusion.
Editors' Summary
Background
The mass media play an important role in disseminating the results of medical research. Every day, news items in newspapers and magazines and on the television, radio, and internet provide the general public with information about the latest clinical studies. Such news items are written by journalists and are often based on information in “press releases.” These short communications, which are posted on online databases such as EurekAlert! and sent directly to journalists, are prepared by researchers or more often by the drug companies, funding bodies, or institutions supporting the clinical research and are designed to attract favorable media attention to newly published research results. Press releases provide journalists with the information they need to develop and publish a news story, including a link to the peer-reviewed journal (a scholarly periodical containing articles that have been judged by independent experts) in which the research results appear.
Why Was This Study Done?
In an ideal world, journal articles, press releases, and news stories would all accurately reflect the results of health research. Unfortunately, the findings of randomized controlled trials (RCTs—studies that compare the outcomes of patients randomly assigned to receive alternative interventions), which are the best way to evaluate new treatments, are sometimes distorted in peer-reviewed journals by the use of “spin”—reporting that emphasizes the beneficial effects of the experimental (new) treatment. For example, a journal article may interpret nonstatistically significant differences as showing the equivalence of two treatments although such results actually indicate a lack of evidence for the superiority of either treatment. “Spin” can distort the transposition of research into clinical practice and, when reproduced in the mass media, it can give patients unrealistic expectations about new treatments. It is important, therefore, to know where “spin” occurs and to understand the effects of that “spin”. In this study, the researchers evaluate the presence of “spin” in press releases and associated media coverage and analyze whether the interpretation of RCT results based on press releases and associated news items could lead to the misinterpretation of RCT results.
What Did the Researchers Do and Find?
The researchers identified 70 press releases indexed in EurekAlert! over a 4-month period that described two-arm, parallel-group RCTs. They used Lexis Nexis, a database of news reports from around the world, to identify associated news items for 41 of these press releases and then analyzed the press releases, news items, and abstracts of the scientific articles related to each press release for “spin”. Finally, they interpreted the results of the RCTs using each source of information independently. Nearly half the press releases and article abstract conclusions contained “spin” and, importantly, “spin” in the press releases was associated with “spin” in the article abstracts. The researchers overestimated the benefits of the experimental treatment from the press release as compared to the full-text peer-reviewed article for 27% of reports. Factors that were associated with this overestimation of treatment benefits included publication in a specialized journal and having “spin” in the press release. Of the news items related to press releases, half contained “spin”, usually of the same type as identified in the press release and article abstract. Finally, the researchers overestimated the benefit of the experimental treatment from the news item as compared to the full-text peer-reviewed article in 24% of cases.
What Do These Findings Mean?
These findings show that “spin” in press releases and news reports is related to the presence of “spin” in the abstract of peer-reviewed reports of RCTs and suggest that the interpretation of RCT results based solely on press releases or media coverage could distort the interpretation of research findings in a way that favors experimental treatments. This interpretation shift is probably related to the presence of “spin” in peer-reviewed article abstracts, press releases, and news items and may be partly responsible for a mismatch between the perceived and real beneficial effects of new treatments among the general public. Overall, these findings highlight the important role that journal reviewers and editors play in disseminating research findings. These individuals, the researchers conclude, have a responsibility to ensure that the conclusions reported in the abstracts of peer-reviewed articles are appropriate and do not over-interpret the results of clinical research.
Additional Information
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1001308.
The PLOS Hub for Clinical Trials, which collects PLOS journals relating to clinical trials, includes some other articles on “spin” in clinical trial reports
EurekAlert is an online free database for science press releases
The UK National Health Service Choices website includes Beyond the Headlines, a resource that provides an unbiased and evidence-based analysis of health stories that make the news for both the public and health professionals
The US-based organization HealthNewsReview, a project supported by the Foundation for Informed Medical Decision Making, also provides expert reviews of news stories
doi:10.1371/journal.pmed.1001308
PMCID: PMC3439420  PMID: 22984354
8.  The process and costs of publishing medical journals in Sri Lanka: an economic evaluation 
BMJ Open  2011;1(1):e000057.
Objectives
Medical journals have contributed to the advancement of medicine by helping to disseminate scientific knowledge and providing a forum for medical communities to debate issues in depth. To the authors' knowledge, there are no studies examining the process of medical journal publication in developing Asian countries. The authors analysed the process and costs of publishing medical journals in Sri Lanka, a developing country in South Asia.
Methods
Data were collected by interviewing the editors and perusing the records at the editorial offices of the respective medical journals. Articles published in 2009 (or 2008 for journals not published in 2009) were analysed by perusing the respective journals.
Results
A total of 44 medical journals were published in Sri Lanka's history, of which only 28 journals remained in publication after 2007. A majority (54%) of the journals published after 2007 were published once per year. Seventeen journals in publication after 2007 were published in paper version only, and 11 journals were also available online. The mean cost of printing one issue was Sri Lankan Rupees (LKR) 97 720 (US$888) (range LKR 28 000–270 000). The cost of distribution ranged from LKR 2000 to 140 000 (US$18–1273). The mean cost of publishing one article was LKR 6646 (US$60). A total of 456 articles were published in 2009 (/2008). The total number of pages published was 1723.
Conclusion
The infrastructure for medical journal publishing in Sri Lanka has many good qualities such as free access, minimum charges for authors and potential for online availability. The journals are solely academic (non-profit), but the costs remain high.
Article summary
Article focus
To analyse the process and costs of publishing medical journals in a developing country.
To identify a list of medical journals published in the country.
To analyse the number and types of articles published in recent Sri Lankan medical journals.
Key messages
Sri Lankan medical journals are freely accessible with minimum charges for authors.
Sri Lankan medical journals are solely academic (non-commercial) and non-profit in nature.
The publication costs remain high.
Strengths and limitations of this study
There is a lack of a comprehensive list of medical journals in the country.
The limited number of publications from the fields of allied health sciences (nursing, pharmacy and physiotherapy) were not included.
doi:10.1136/bmjopen-2011-000057
PMCID: PMC3191407  PMID: 22021741
9.  Open Access to the Scientific Journal Literature: Situation 2009 
PLoS ONE  2010;5(6):e11273.
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.
doi:10.1371/journal.pone.0011273
PMCID: PMC2890572  PMID: 20585653
10.  Characteristics and Trends of Orthopedic Publications between 2000 and 2009 
Clinics in Orthopedic Surgery  2011;3(3):225-229.
Background
This study was undertaken to investigate the trends of orthopedic publications during the last decade, and to document the country of origin, journal, funding source, and language of contribution using PubMed.
Methods
Orthopedic articles published between 2000 and 2009 were retrieved from PubMed using the following search terms: "orthopaedic[Affiliation] AND ("2000/1/1"[PDAT]: "2009/12/31"[PDAT])" and "orthopedic[Affiliation] AND ("2000/1/1"[PDAT]: "2009/12/31"[PDAT])." The articles were downloaded in XML file format, which contained the following information: article title, author names, journal names, publication dates, article types, languages, authors' affiliations and funding sources. These information was extracted, sorted, and rearranged using the database's management software. We investigated the annual number of published orthopedic articles worldwide and the annual rate of increase. Furthermore, the country of publication origin, journal, funding source, and language of contribution were also investigated.
Results
A total of 46,322 orthopedic articles were published and registered in PubMed in the last 10 years. The worldwide number of published orthopedic articles increased from 2,889 in 2000 to 6,909 in 2009, showing an annual increase of 384.6 articles, or an annualized compound rate of 10.2%. The United States ranked highest in the number of published orthopedic articles, followed by Japan, the United Kingdom, Germany, and the Republic of Korea. Among the orthopedic articles published worldwide during the last 10 years, 37.9% pertained studies performed in the United States. Fifty-seven point three percent (57.3%) of articles were published in journals established in the United States. Among the published orthopaedic articles, 4,747 articles (10.2%) disclosed financial support by research funds, of which 4,688 (98.8%) articles utilized research funds from the United States. Most articles were published in English (97.2%, 45,030 articles).
Conclusions
The number of published orthopedic articles has been increasing over the last decade. The number of orthopedic articles, journals publication, and funding sources were dominated by research conducted in the United States, while share and growth of Asian countries including Japan, the Republic of Korea, and China were notable.
doi:10.4055/cios.2011.3.3.225
PMCID: PMC3162203  PMID: 21909470
Bibliometrics; Orthopedics; Research trend; Periodicals as topics
11.  Comparative Study of Scientific Publications in Urology and Nephrology Journals Originating from USA, China and Japan (2001–2010) 
PLoS ONE  2012;7(8):e42200.
Background
In the past decade, scientific research has developed rapidly in China, but the growth seems to vary widely between different disciplines. In this study, we aimed to compare the quantity and quality of publications in urology and nephrology journals from USA, China and Japan.
Methods
Journals listed in the “Urology and Nephrology” category of Science Citation Index Expanded subject categories were included. Scientific papers in these journals written by researchers from USA, Japan and China were retrieved from the “PubMed” and “Web of Knowledge” online databases.
Results
The annual number of total scientific articles increased significantly from 2001 to 2010 in China, and has ranked second in the world since 2006. In the field of urology and nephrology, the annual number increased significantly from 2001 to 2010 in USA and China; but not in Japan. The share of articles increased significantly over time in China, decreased significantly in Japan, and remained unchanged in USA. In 2010, USA contributed 32.17% of the total world output in urology and nephrology field and ranked 1st; Japan contributed 5.19% and ranked 5th; China contributed 3.83% and ranked 9th. Publications from USA had the highest accumulated IFs and the highest total citations of articles (USA>Japan>China, p<0.001). No significant difference was found in average IF among the three countries. USA published the most articles in the top 10 urology and nephrology journals (USA(35165)>Japan(6704)>China(2233), p<0.001). Researchers from USA published more clinical trials and randomized controlled trials than Japan and China (USA>Japan>China, p<0.001).
Conclusion
Although China has undergone significant increase in annual number and percentage of scientific publication in urology and nephrology journals in the past decade, it still lags far behind USA and Japan in the field of urology and nephrology in terms of quantity and quality.
doi:10.1371/journal.pone.0042200
PMCID: PMC3411650  PMID: 22870301
12.  Bibliometric analysis of the volume and visibility of Saudi publications in leading anesthesia journals 
Saudi Journal of Anaesthesia  2012;6(4):393-397.
Context:
The quantity and quality of publications by a country indicates its contribution towards scientific development.
Aims:
To examine the volume and impact of the Saudi anesthesia publications in leading anesthesia journals.
Settings and Design:
Fifteen leading anesthesia journals were identified. Saudi publications in these journals from 1991 to 2011 were searched in the databases of Pubmed and Web of Knowledge.
Methods:
For each article, the journal and time of publication, the type of the article and the affiliation of the first author were analysed. The visibility of the publications was related to the number of citations and was analysed for the years 2000 to 2008. Data were compared with selected Arab countries.
Statistical Analysis:
Two visibility indices were used. The first relates the average citations per Saudi articles in the years following publication to the average global citations. The second relates the average citations per Saudi article in the two years following publication to the impact factor of the journal of publication. The h-index was used as a measure of both volume and visibility.
Results:
Anesthesiologists from Saudi affiliations published 173 documents in leading 15 anesthesia journals betweent the years 1991-2011, with a marked increase in the last 6 years. Anesthesia and Analgesia journal published 24% of Saudi articles. Saudi universities contributed to 55% of Saudi publications. The visibility of the Saudi articles was 0.7 of the international figures.
Conclusions:
Saudi anesthesia publications are increasing in recent years. Although the visibility of Saudi publications is below international figures, it compares favourably to Arab countries.
doi:10.4103/1658-354X.105879
PMCID: PMC3591561  PMID: 23494080
Bibliometric; h-index; impact factor; scientometrics; visibility indices
13.  Publishing perishing? Towards tomorrow's information architecture 
BMC Bioinformatics  2007;8:17.
Scientific articles are tailored to present information in human-readable aliquots. Although the Internet has revolutionized the way our society thinks about information, the traditional text-based framework of the scientific article remains largely unchanged. This format imposes sharp constraints upon the type and quantity of biological information published today. Academic journals alone cannot capture the findings of modern genome-scale inquiry.
Like many other disciplines, molecular biology is a science of facts: information inherently suited to database storage. In the past decade, a proliferation of public and private databases has emerged to house genome sequence, protein structure information, functional genomics data and more; these digital repositories are now a vital component of scientific communication. The next challenge is to integrate this vast and ever-growing body of information with academic journals and other media. To truly integrate scientific information we must modernize academic publishing to exploit the power of the Internet. This means more than online access to articles, hyperlinked references and web-based supplemental data; it means making articles fully computer-readable with intelligent markup and Structured Digital Abstracts.
Here, we examine the changing roles of scholarly journals and databases. We present our vision of the optimal information architecture for the biosciences, and close with tangible steps to improve our handling of scientific information today while paving the way for an expansive central index in the future.
doi:10.1186/1471-2105-8-17
PMCID: PMC1781953  PMID: 17239245
14.  Twelve Years of Scientific Production on Medline by Latin American Spine Surgeons 
PLoS ONE  2014;9(2):e87945.
Background
Despite the small contribution of LA in the Science Citation Index (SCI), a growing contribution by LA research to international literature has been observed in recent years.
Study Design
Systematic review.
Purpose
To evaluate the scientific contribution of Latin American (LA) Spine Surgeons in the last decade.
Methods
A literature search of publications by LA spinal surgeons on topics concerning the spine or spinal cord was performed using an online database; Pubmed.gov. The results were limited to articles published from January 2000 to December 2011. The quality of the publication was evaluated with the journal impact factor (IF), Oxford classification and number of citations.
Results
This study comprised 320 articles published in the Medline database by LA spine surgeons from 2000 to 2011. In recent years, there has been an increase in the number of publications by LA spine surgeons. It was observed that 38.4% of LA papers were published in LA journals. 46.6% of the articles were published in journals with an IF lower than 1, and there was no statistically significant difference in the number of articles published in journals with a higher IF during the period. Linear-by-linear association analysis demonstrated an improvement in the level of evidence provided by LA articles published in recent years.
Conclusions
This study showed a growth in the number of publications in last 12 years by LA spinal surgeons. It is necessary to discuss a way to increase quantity and quality of scientific publications, mainly through a better education in research.
doi:10.1371/journal.pone.0087945
PMCID: PMC3914870  PMID: 24505336
15.  Medline-based bibliometric analysis of gastroenterology journals between 2001 and 2007 
AIM: To analyze the MEDLINE-indexed publications in gastroenterology specialty journals from 2001 to 2007. Special attention was paid to specific types of articles, the number of publications for individual authors and the author count in each journal.
METHODS: The bibliographic entries of papers belonging to journals listed under the subject heading of “gastroenterology” were downloaded from MEDLINE on the PubMed web site. The analysis was limited to journal articles published between January 1, 2001 and December 31, 2007. The analytical dimensions of an article included journal, publication year, publication type, and author name (the last name and initials).
RESULTS: According to MEDLINE, 81 561 articles were published in 91 gastroenterology journals from 2001 to 2007. The number of articles increased from 9447 in 2001 to 13 340 in 2007. Only 12 journals had more than 2000 articles indexed in MEDLINE. The “World Journal of Gastroenterology” had the largest number of publications (5684 articles), followed by “Hepato-Gastroenterology” (3036) and “Gastrointestinal Endoscopy” (3005). Of all the articles published, reviews accounted for 17.2% and case reports for 15.4%. Only 3739 randomized controlled trials (4.6% of all articles) were published and their annual number increased from 442 in 2001 to 572 in 2007. Among 141 741 author names appearing in the articles of gastroenterology journals, 92 429 had published only in one journal, 22 585 in two journals, 9996 in three journals, and 16 731 in more than three journals. The “World Journal of Gastroenterology” had the greatest number of authors (17 838), followed by “Gastroenterology” (12 770), “Digestive Diseases and Sciences” (11 395), “American Journal of Gastroenterology” (10 889), and “Hepatology” (10 588).
CONCLUSION: Global gastroenterology publications displayed a continuous growth in the new millennium. The change was most striking in certain journals. Regular bibliometric analyses on the trends and specific topics would help researchers publish more efficiently and allow editors to adjust the policy more accurately.
doi:10.3748/wjg.15.2933
PMCID: PMC2699018  PMID: 19533822
Bibliographic databases; Bibliometrics; Biomedical research; Gastroenterology; MEDLINE
16.  What do evidence-based secondary journals tell us about the publication of clinically important articles in primary healthcare journals? 
BMC Medicine  2004;2:33.
Background
We conducted this analysis to determine i) which journals publish high-quality, clinically relevant studies in internal medicine, general/family practice, general practice nursing, and mental health; and ii) the proportion of clinically relevant articles in each journal.
Methods
We performed an analytic survey of a hand search of 170 general medicine, general healthcare, and specialty journals for 2000. Research staff assessed individual articles by using explicit criteria for scientific merit for healthcare application. Practitioners assessed the clinical importance of these articles. Outcome measures were the number of high-quality, clinically relevant studies published in the 170 journal titles and how many of these were published in each of four discipline-specific, secondary "evidence-based" journals (ACP Journal Club for internal medicine and its subspecialties; Evidence-Based Medicine for general/family practice; Evidence-Based Nursing for general practice nursing; and Evidence-Based Mental Health for all aspects of mental health). Original studies and review articles were classified for purpose: therapy and prevention, screening and diagnosis, prognosis, etiology and harm, economics and cost, clinical prediction guides, and qualitative studies.
Results
We evaluated 60,352 articles from 170 journal titles. The pass criteria of high-quality methods and clinically relevant material were met by 3059 original articles and 1073 review articles. For ACP Journal Club (internal medicine), four titles supplied 56.5% of the articles and 27 titles supplied the other 43.5%. For Evidence-Based Medicine (general/family practice), five titles supplied 50.7% of the articles and 40 titles supplied the remaining 49.3%. For Evidence-Based Nursing (general practice nursing), seven titles supplied 51.0% of the articles and 34 additional titles supplied 49.0%. For Evidence-Based Mental Health (mental health), nine titles supplied 53.2% of the articles and 34 additional titles supplied 46.8%. For the disciplines of internal medicine, general/family practice, and mental health (but not general practice nursing), the number of clinically important articles was correlated withScience Citation Index (SCI) Impact Factors.
Conclusions
Although many clinical journals publish high-quality, clinically relevant and important original studies and systematic reviews, the articles for each discipline studied were concentrated in a small subset of journals. This subset varied according to healthcare discipline; however, many of the important articles for all disciplines in this study were published in broad-based healthcare journals rather than subspecialty or discipline-specific journals.
doi:10.1186/1741-7015-2-33
PMCID: PMC518974  PMID: 15350200
17.  A Comprehensive Survey of Retracted Articles from the Scholarly Literature 
PLoS ONE  2012;7(10):e44118.
Background
The number of retracted scholarly articles has risen precipitously in recent years. Past surveys of the retracted literature each limited their scope to articles in PubMed, though many retracted articles are not indexed in PubMed. To understand the scope and characteristics of retracted articles across the full spectrum of scholarly disciplines, we surveyed 42 of the largest bibliographic databases for major scholarly fields and publisher websites to identify retracted articles. This study examines various trends among them.
Results
We found, 4,449 scholarly publications retracted from 1928–2011. Unlike Math, Physics, Engineering and Social Sciences, the percentages of retractions in Medicine, Life Science and Chemistry exceeded their percentages among Web of Science (WoS) records. Retractions due to alleged publishing misconduct (47%) outnumbered those due to alleged research misconduct (20%) or questionable data/interpretations (42%). This total exceeds 100% since multiple justifications were listed in some retraction notices. Retraction/WoS record ratios vary among author affiliation countries. Though widespread, only miniscule percentages of publications for individual years, countries, journals, or disciplines have been retracted. Fifteen prolific individuals accounted for more than half of all retractions due to alleged research misconduct, and strongly influenced all retraction characteristics. The number of articles retracted per year increased by a factor of 19.06 from 2001 to 2010, though excluding repeat offenders and adjusting for growth of the published literature decreases it to a factor of 11.36.
Conclusions
Retracted articles occur across the full spectrum of scholarly disciplines. Most retracted articles do not contain flawed data; and the authors of most retracted articles have not been accused of research misconduct. Despite recent increases, the proportion of published scholarly literature affected by retraction remains very small. Articles and editorials discussing retractions, or their relation to research integrity, should always consider individual cases in these broad contexts. However, better mechanisms are still needed for raising researchers’ awareness of the retracted literature in their field.
doi:10.1371/journal.pone.0044118
PMCID: PMC3480361  PMID: 23115617
18.  Citation Advantage of Open Access Articles 
PLoS Biology  2006;4(5):e157.
Open access (OA) to the research literature has the potential to accelerate recognition and dissemination of research findings, but its actual effects are controversial. This was a longitudinal bibliometric analysis of a cohort of OA and non-OA articles published between June 8, 2004, and December 20, 2004, in the same journal (PNAS: Proceedings of the National Academy of Sciences). Article characteristics were extracted, and citation data were compared between the two groups at three different points in time: at “quasi-baseline” (December 2004, 0–6 mo after publication), in April 2005 (4–10 mo after publication), and in October 2005 (10–16 mo after publication). Potentially confounding variables, including number of authors, authors' lifetime publication count and impact, submission track, country of corresponding author, funding organization, and discipline, were adjusted for in logistic and linear multiple regression models. A total of 1,492 original research articles were analyzed: 212 (14.2% of all articles) were OA articles paid by the author, and 1,280 (85.8%) were non-OA articles. In April 2005 (mean 206 d after publication), 627 (49.0%) of the non-OA articles versus 78 (36.8%) of the OA articles were not cited (relative risk = 1.3 [95% Confidence Interval: 1.1–1.6]; p = 0.001). 6 mo later (mean 288 d after publication), non-OA articles were still more likely to be uncited (non-OA: 172 [13.6%], OA: 11 [5.2%]; relative risk = 2.6 [1.4–4.7]; p < 0.001). The average number of citations of OA articles was higher compared to non-OA articles (April 2005: 1.5 [SD = 2.5] versus 1.2 [SD = 2.0]; Z = 3.123; p = 0.002; October 2005: 6.4 [SD = 10.4] versus 4.5 [SD = 4.9]; Z = 4.058; p < 0.001). In a logistic regression model, controlling for potential confounders, OA articles compared to non-OA articles remained twice as likely to be cited (odds ratio = 2.1 [1.5–2.9]) in the first 4–10 mo after publication (April 2005), with the odds ratio increasing to 2.9 (1.5–5.5) 10–16 mo after publication (October 2005). Articles published as an immediate OA article on the journal site have higher impact than self-archived or otherwise openly accessible OA articles. We found strong evidence that, even in a journal that is widely available in research libraries, OA articles are more immediately recognized and cited by peers than non-OA articles published in the same journal. OA is likely to benefit science by accelerating dissemination and uptake of research findings.
A longitudinal bibliometric analysis of citations to papers published in the PNAS between June 8, 2004 and December 20, 2004 reveals that the open-access articles were more immediately recognized and cited by peers.
doi:10.1371/journal.pbio.0040157
PMCID: PMC1459247  PMID: 16683865
19.  Korea's Contribution to Radiological Research Included in Science Citation Index Expanded, 1986-2010 
Korean Journal of Radiology  2012;13(5):523-529.
Objective
To evaluate scientific papers published by Korean radiologists in the Science Citation Index Expanded (SCIE) radiology journals, between 1986 and 2010.
Materials and Methods
The Institute for Scientific Information Web of Knowledge-Web of Science (SCIE) database was searched for all articles published by Korean radiologists, in SCIE radiology journals, between 1986 and 2010. We performed the analysis by typing "Korea" and "radiol" in the address section and selecting the subject area of "Radiology, Nuclear Medicine, and Medical Imaging" with the use of the general search function of the software. Analyzed parameters included the total number of publications, document types, journals, and institutions. In addition, we analyzed where Korea ranks, compared to other countries, in terms of the number of published articles. All these data were analyzed according to five time periods: 1986-1990, 1991-1995, 1996-2000, 2001-2005, and 2006-2010.
Results
Overall, 4974 papers were published by Korean radiologists, in 99 different SCIE journals, between 1986 and 2010, of which 4237 (85.2%) were article-type papers. Of the total 115395 articles, worldwide, published in radiology journals, Korea's share was 3.7%, with an upward trend over time (p < 0.005). The journal with the highest number of articles was the American Journal of Roentgenology (n = 565, 13.3%). The institution which produced the highest number of publications was Seoul National University (n = 932, 22.0%).
Conclusion
The number of scientific articles published by Korean radiologists in the SCIE radiology journals has increased significantly between 1986 and 2010. Korea was ranked 4th among countries contributing to radiology research during the last 5 years.
doi:10.3348/kjr.2012.13.5.523
PMCID: PMC3435847  PMID: 22977317
Citation analysis; Publication; Radiologic research; Korea
20.  Virtual slides in peer reviewed, open access medical publication 
Diagnostic Pathology  2011;6:124.
Background
Application of virtual slides (VS), the digitalization of complete glass slides, is in its infancy to be implemented in routine diagnostic surgical pathology and to issues that are related to tissue-based diagnosis, such as education and scientific publication.
Approach
Electronic publication in Pathology offers new features of scientific communication in pathology that cannot be obtained by conventional paper based journals. Most of these features are based upon completely open or partly directed interaction between the reader and the system that distributes the article. One of these interactions can be applied to microscopic images allowing the reader to navigate and magnify the presented images. VS and interactive Virtual Microscopy (VM) are a tool to increase the scientific value of microscopic images.
Technology and Performance
The open access journal Diagnostic Pathology http://www.diagnosticpathology.org has existed for about five years. It is a peer reviewed journal that publishes all types of scientific contributions, including original scientific work, case reports and review articles. In addition to digitized still images the authors of appropriate articles are requested to submit the underlying glass slides to an institution (DiagnomX.eu, and Leica.com) for digitalization and documentation. The images are stored in a separate image data bank which is adequately linked to the article. The normal review process is not involved. Both processes (peer review and VS acquisition) are performed contemporaneously in order to minimize a potential publication delay. VS are not provided with a DOI index (digital object identifier). The first articles that include VS were published in March 2011.
Results and Perspectives
Several logistic constraints had to be overcome until the first articles including VS could be published. Step by step an automated acquisition and distribution system had to be implemented to the corresponding article. The acceptance of VS by the reader is high as well as by the authors. Of specific value are the increased confidence to and reputation of authors as well as the presented information to the reader. Additional associated functions such as access to author-owned related image collections, reader-controlled automated image measurements and image transformations are in preparation.
Virtual Slides
The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1232133347629819.
doi:10.1186/1746-1596-6-124
PMCID: PMC3275477  PMID: 22182763
Virtual slide; virtual microcopy; open access publication; image interpretation; image content information
21.  Open access and openly accessible: a study of scientific publications shared via the internet 
BMJ : British Medical Journal  2005;330(7500):1128.
Objectives To determine how often reprints of scientific publications are shared online, whether journal readership level is a predictor, how the amount of file sharing changes with the age of the article, and to what degree open access publications are shared on non-journal websites.
Design The internet was searched using an application programming interface to Google, a popular and freely available search engine.
Main outcome measures The proportion of reprints of journal articles published between 1994 and 2004 from within 13 subscription based and four open access journals that could be located online at non-journal websites.
Results The probability that an article could be found online at a non-journal website correlated with the journal impact factor and the time since initial publication. Papers from higher impact journals and more recent articles were more likely to be located. On average, for the high impact journal articles published in 2003, over a third could be located at non-journal websites. Similar trends were observed for the delayed or full open access publications.
Conclusions Decentralised sharing of scientific reprints through the internet creates a degree of de facto open access that, though highly incomplete in its coverage, is none the less biased towards publications of higher popular demand.
doi:10.1136/bmj.38422.611736.E0
PMCID: PMC557897  PMID: 15827063
22.  Funding free and universal access to Journal of Neuroinflammation 
Journal of Neuroinflammation is an Open Access, online journal published by BioMed Central. Open Access publishing provides instant and universal availability of published work to any potential reader, worldwide, completely free of subscriptions, passwords, and charges. Further, authors retain copyright for their work, facilitating its dissemination. Open Access publishing is made possible by article-processing charges assessed "on the front end" to authors, their institutions, or their funding agencies. Beginning November 1, 2004, the Journal of Neuroinflammation will introduce article-processing charges of around US$525 for accepted articles. This charge will be waived for authors from institutions that are BioMed Central members, and in additional cases for reasons of genuine financial hardship. These article-processing charges pay for an electronic submission process that facilitates efficient and thorough peer review, for publication costs involved in providing the article freely and universally accessible in various formats online, and for the processes required for the article's inclusion in PubMed and its archiving in PubMed Central, e-Depot, Potsdam and INIST. There is no remuneration of any kind provided to the Editors-in-Chief, to any members of the Editorial Board, or to peer reviewers; all of whose work is entirely voluntary. Our article-processing charge is less than charges frequently levied by traditional journals: the Journal of Neuroinflammation does not levy any additional page or color charges on top of this fee, and there are no reprint costs as publication-quality pdf files are provided, free, for distribution in lieu of reprints. Our article-processing charge will enable full, immediate, and continued Open Access for all work published in Journal of Neuroinflammation. The benefits from such Open Access will accrue to readers, through unrestricted access; to authors, through the widest possible dissemination of their work; and to science and society in general, through facilitation of information availability and scientific advancement.
doi:10.1186/1742-2094-1-19
PMCID: PMC528856  PMID: 15485579
23.  Where on earth to publish? A sample survey comparing traditional and open access publishing in the oncological field 
Background
The paper intends to help scientific authors to make the best choice of journals in which to publish, by describing and comparing journal features in the area of oncology. For this purpose, the authors identified impact factor (IF) ranking, cost options and copyright conditions offered to authors wishing to publish in full open access (OA), subscription-based or hybrid journals.
Methods
Data referring to articles published in 2010 by three Italian research institutions (National Institute of Health – Rome (ISS), Regina Elena National Cancer Institute – Rome (IRE), National Cancer Institute – Milan (INT) in journals (78) managed according to different business models, all listed in the Journal Citation Reports, subject category Oncology, were collected and analysed. The journals surveyed were ranked according to IF, position in quartiles, publication charges, usage rights in published articles, self-archiving conditions in OAI-compliant repositories digital archives.
Results
Almost half (34) the journals surveyed were included in the first quartile, thus revealing authors’ preference for journals with a high IF. The prevalent journal business model was the hybrid formula (based on subscriptions but also offering a paid OA option) with 51 journals, followed by subscription-based only journals accounting for 22, while just 5 full OA journals were identified. In general, no relationship was found between IF and article publication charges, in terms of correspondence between more expensive fees and higher IF.
Conclusions
The issue of OA journals as compared with traditional subscription-based journals is highly debated among stakeholders: library administrators facing financial restrictions, authors seeking to locate the best outlet for their research, publishers wishing to increase their revenues by offering journals with wider appeal. Against this background, factors such as the quest for alternatives to high-cost business models, investments in setting up institutional repositories hosting the published versions of articles and efforts to overcome copyright barriers and gain free access to scientific literature are all crucial.
doi:10.1186/1756-9966-32-4
PMCID: PMC3618298  PMID: 23339627
Open access publishing; Scientific publications; Oncology; Surveys; Italy
24.  Do urology journals enforce trial registration? A cross-sectional study of published trials 
BMJ Open  2011;1(2):e000430.
Objectives
(1) To assess endorsement of trial registration in author instructions of urology-related journals and (2) to assess whether randomised controlled trials (RCTs) in the field of urology were effectively registered.
Design
Cross-sectional study of author instructions and published trials.
Setting
Journals publishing in the field of urology.
Participants
First, the authors analysed author instructions of 55 urology-related journals indexed in ‘Journal Citation Reports 2009’ (12/2010). The authors divided these journals in two groups: those requiring and those not mentioning trial registration as a precondition for publication. Second, the authors chose the five journals with the highest impact factor (IF) from each group.
Intervention
MEDLINE search to identify RCTs published in these 10 journals in 2009 (01/2011); search of the clinical trials meta-search interface of WHO (International Clinical Trials Registry Platform) for RCTs that lacked information about registration (01–03/2011). Two authors independently assessed the information.
Outcome measures
Proportion of journals providing advice about trial registration and proportion of trials registered.
Results
Of 55 journals analysed, 26 (47.3%) provided some editorial advice about trial registration. Journals with higher IFs were more likely to mention trial registration explicitly (p=0.015). Of 106 RCTs published in 2009, 63 were registered (59.4%) with a tendency to an increase after 2005 (83.3%, p=0.035). 71.4% (30/42) of the RCTs that were published in journals mentioning and requiring registration, and 51.6% (33/64) of the RCTs that were published in journals that did not mention trial registration explicitly were registered. This difference was statistically significant (p=0.04).
Conclusions
The existence of a statement about trial registration in author instructions resulted in a higher proportion of registered RCTs in those journals. Journals with higher IFs were more likely to mention trial registration.
Article summary
Article focus
Trial registration can increase scientific transparency, but its implementation in specialty fields such as urology is unclear.
To assess the endorsement of trial registration in the author instructions of urology-related journals.
To assess whether randomised controlled trials in the field were effectively registered.
Key messages
A statement of trial registration in author instructions resulted in a higher proportion of registered randomised controlled trials.
Journals with high impact factors were more likely to mention trial registration.
We suggest, though, that ensuring trial registration is not the responsibility only of the editors. Medical scientists should realise that trial registration is necessary to contribute to transparency in research.
Strength and limitations of this study
Two authors independently assessed information regarding editorial advice about trial registration and identified the randomised controlled trials.
Potential bias occurred if registered randomised controlled trials were reported without giving a registration number and we could not identify them in the meta-search interface of WHO (International Clinical Trials Registry Platform).
Results might not be representative of the uro-nephrological field as a whole and reported figures may overestimate compliance with trial registration.
doi:10.1136/bmjopen-2011-000430
PMCID: PMC3236819  PMID: 22146890
25.  Twenty Years of Research on Mineral Trioxide Aggregate: A Scientometric Report 
Iranian Endodontic Journal  2013;8(1):1-5.
Introduction
Mineral trioxide aggregate (MTA) has been suggested for root-end filling, vital pulp therapy, apical plug, perforations repair, and root canal filling. Since the introduction of MTA in 1993, many studies about this material have been published. The aim of this survey was to illustrate statistical information about published articles in PubMed-index journals vis-à-vis the various aspects of this biomaterial.
Material and Methods
A PubMed search was performed to retrieve the relative articles from 1993 to August 2012. The data of each article including publication year, journal name, number of authors, first author name, affiliations and study design were recorded. Citation of each article till 2009 was obtained from Scopus and Google scholar databases. Data were analyzed to determine the related scientometric indicators.
Results
In total, 1027 articles were found in PubMed-indexed journals which show considerable increase from 2 papers in 1993 to 139 in 2011. While ~62% of articles had no level of evidence, only ~5% could be classified as having the highest level of evidence (LOE1); however, the majority of LOE1 articles originated from Iran (~1%: n=10). Journal of Endodontics, as the top rank journal, published 31.7% of MTA related articles. The majority of articles were four-authored (19.6%). Most of the articles originated from USA (21.9%), Brazil (18.5%) and Iran (8.76%). The average number of citation for the top ten articles from Scopus was 231.
Conclusion
This data demonstrates that during the past two decades, research on this novel endodontic biomaterial had a rapid positive trend especially during the last 5 years. Further high-level evidence articles for the various clinical applications of MTA would result in superior clinical decision making and stronger scientific-based endodontic practice.
PMCID: PMC3570971  PMID: 23411944
Biomaterial; Endodontic; Mineral trioxide aggregate; MTA; PubMed; Scientometric

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