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Journal policy on research data and code availability is an important part of the ongoing shift toward publishing reproducible computational science. This article extends the literature by studying journal data sharing policies by year (for both 2011 and 2012) for a referent set of 170 journals. We make a further contribution by evaluating code sharing policies, supplemental materials policies, and open access status for these 170 journals for each of 2011 and 2012. We build a predictive model of open data and code policy adoption as a function of impact factor and publisher and find higher impact journals more likely to have open data and code policies and scientific societies more likely to have open data and code policies than commercial publishers. We also find open data policies tend to lead open code policies, and we find no relationship between open data and code policies and either supplemental material policies or open access journal status. Of the journals in this study, 38% had a data policy, 22% had a code policy, and 66% had a supplemental materials policy as of June 2012. This reflects a striking one year increase of 16% in the number of data policies, a 30% increase in code policies, and a 7% increase in the number of supplemental materials policies. We introduce a new dataset to the community that categorizes data and code sharing, supplemental materials, and open access policies in 2011 and 2012 for these 170 journals.  相似文献   

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Gold open access provides free distribution of trustworthy scientific knowledge for everyone. As publication modus, it has to withstand the bad reputation of predatory journals and overcome the preconceptions of those who believe that open access is synonymous with poor quality articles and high costs. Gold open access has a bright future and will serve the scientific community, clinicians without academic affiliations and the general public.  相似文献   

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Bernd Pulverer 《The EMBO journal》2016,35(24):2617-2619
Preprints reduce delays in sharing research results and increase the amount and diversity of data available to the scientific community. Support of this communication mechanism through appropriate policies by journals, funders and institutions will encourage community engagement. Widespread adoption would benefit both individual scientists and research, and it might improve publishing in scientific journals. Preprints are one step towards an Open Science future.  相似文献   

5.
The recent US law (H.R.2764) affecting NIH policy and the recent unanimous vote by the Arts and Science faculty of Harvard University in favour of a mandatory deposit of researchers' publications in a suitable repository have brought the Open Access movement into public light. After reviewing the historical background of Open Access, its evolution and extension in the United States, Great Britain, France and Canada are examined. Policies aiming at strengthening Open Access to scientific research are viewed as the direct consequence of treating scientific publishing as an integral part of the research cycle. It should, therefore, be wrapped into the financing of research. As the greater part of research is funded by public money, it appears legitimate to make its results as widely available as is possible. Open Access journals and repositories with strong deposit mandates form the backbone of the strategies to achieve the objective of Open Access. Despite the claims of some publishers, Open Access does not weaken or threaten the peer review process, and it does not conflict with copyright laws.  相似文献   

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As Open Science practices become more commonplace, there is a need for the next generation of scientists to be well versed in these aspects of scientific research. Yet, many training opportunities for early career researchers (ECRs) could better emphasize or integrate Open Science elements. Field courses provide opportunities for ECRs to apply theoretical knowledge, practice new methodological approaches, and gain an appreciation for the challenges of real‐life research, and could provide an excellent platform for integrating training in Open Science practices. Our recent experience, as primarily ECRs engaged in a field course interrupted by COVID‐19, led us to reflect on the potential to enhance learning outcomes in field courses by integrating Open Science practices and online learning components. Specifically, we highlight the opportunity for field courses to align teaching activities with the recent developments and trends in how we conduct research, including training in: publishing registered reports, collecting data using standardized methods, adopting high‐quality data documentation, managing data through reproducible workflows, and sharing and publishing data through appropriate channels. We also discuss how field courses can use online tools to optimize time in the field, develop open access resources, and cultivate collaborations. By integrating these elements, we suggest that the next generation of field courses will offer excellent arenas for participants to adopt Open Science practices.  相似文献   

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ABSTRACT: Copyright and licensing of scientific data, internationally, are complex and present legal barriers to data sharing, integration and reuse, and therefore restrict the most efficient transfer and discovery of scientific knowledge. Much data are included within scientific journal articles, their published tables, additional files (supplementary material) and reference lists. However, these data are usually published under licenses which are not appropriate for data. Creative Commons CC0 is an appropriate and increasingly accepted method for dedicating data to the public domain, to enable data reuse with the minimum of restrictions. BioMed Central is committed to working towards implementation of open data-compliant licensing in its publications. Here we detail a protocol for implementing a combined Creative Commons Attribution license (for copyrightable material) and Creative Commons CC0 waiver (for data) agreement for content published in peer-reviewed open access journals. We explain the differences between legal requirements for attribution in copyright, and cultural requirements in scholarship for giving individuals credit for their work through citation. We argue that publishing data in scientific journals under CC0 will have numerous benefits for individuals and society, and yet will have minimal implications for authors and minimal impact on current publishing and research workflows. We provide practical examples and definitions of data types, such as XML and tabular data, and specific secondary use cases for published data, including text mining, reproducible research, and open bibliography. We believe this proposed change to the current copyright and licensing structure in science publishing will help clarify what users -- people and machines -- of the published literature can do, legally, with journal articles and make research using the published literature more efficient. We further believe this model could be adopted across multiple publishers, and invite comment on this article from all stakeholders in scientific research.  相似文献   

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The usage of preprint servers in ecology and evolution is increasing, allowing research to be rapidly disseminated and available through open access at no cost. Early Career Researchers (ECRs) often have limited experience with the peer review process, which can be challenging when trying to build publication records and demonstrate research ability for funding opportunities, scholarships, grants, or faculty positions. ECRs face different challenges relative to researchers with permanent positions and established research programs. These challenges might also vary according to institution size and country, which are factors associated with the availability of funding for open access journals. We predicted that the career stage and institution size impact the relative usage of preprint servers among researchers in ecology and evolution. Using data collected from 500 articles (100 from each of two open access journals, two closed access journals, and a preprint server), we showed that ECRs generated more preprints relative to non‐ECRs, for both first and last authors. We speculate that this pattern is reflective of the advantages of quick and open access research that is disproportionately beneficial to ECRs. There is also a marginal association between first author, institution size, and preprint usage, whereby the number of preprints tends to increase with institution size for ECRs. The United States and United Kingdom contributed the greatest number of preprints by ECRs, whereas non‐Western countries contributed relatively fewer preprints. This empirical evidence that preprint usage varies with the career stage, institution size, and country helps to identify barriers surrounding large‐scale adoption of preprinting in ecology and evolution.  相似文献   

9.
The risk of accidental or deliberate misuse of biological research is increasing as biotechnology advances. As open science becomes widespread, we must consider its impact on those risks and develop solutions that ensure security while facilitating scientific progress. Here, we examine the interaction between open science practices and biosecurity and biosafety to identify risks and opportunities for risk mitigation. Increasing the availability of computational tools, datasets, and protocols could increase risks from research with misuse potential. For instance, in the context of viral engineering, open code, data, and materials may increase the risk of release of enhanced pathogens. For this dangerous subset of research, both open science and biosecurity goals may be achieved by using access-controlled repositories or application programming interfaces. While preprints accelerate dissemination of findings, their increased use could challenge strategies for risk mitigation at the publication stage. This highlights the importance of oversight earlier in the research lifecycle. Preregistration of research, a practice promoted by the open science community, provides an opportunity for achieving biosecurity risk assessment at the conception of research. Open science and biosecurity experts have an important role to play in enabling responsible research with maximal societal benefit.

The risk of biotechnology being misused is growing and may even be increased by moves towards open science. How can we ensure that the goals of both open science and biosecurity are met?  相似文献   

10.
Biomedical journals must adhere to strict standards of editorial quality. In a globalized academic scenario, biomedical journals must compete firstly to publish the most relevant original research and secondly to obtain the broadest possible visibility and the widest dissemination of their scientific contents. The cornerstone of the scientific process is still the peer-review system but additional quality criteria should be met. Recently access to medical information has been revolutionized by electronic editions.Bibliometric databases such as MEDLINE, the ISI Web of Science and Scopus offer comprehensive online information on medical literature. Classically, the prestige of biomedical journals has been measured by their impact factor but, recently, other indicators such as SCImago SJR or the Eigenfactor are emerging as alternative indices of a journal's quality. Assessing the scholarly impact of research and the merits of individual scientists remains a major challenge. Allocation of authorship credit also remains controversial.Furthermore, in our Kafkaesque world, we prefer to count rather than read the articles we judge. Quantitative publication metrics (research output) and citations analyses (scientific influence) are key determinants of the scientific success of individual investigators. However, academia is embracing new objective indicators (such as the “h” index) to evaluate scholarly merit. The present review discusses some editorial issues affecting biomedical journals, currently available bibliometric databases, bibliometric indices of journal quality and, finally, indicators of research performance and scientific success.  相似文献   

11.
The Genome Sequence Archive (GSA) is a data repository for archiving raw sequence data, which provides data storage and sharing services for worldwide scientific communities. Considering explosive data growth with diverse data types, here we present the GSA family by expanding into a set of resources for raw data archive with different purposes, namely, GSA (https://ngdc.cncb.ac.cn/gsa/), GSA for Human (GSA-Human, https://ngdc.cncb.ac.cn/gsa-human/), and Open Archive for Miscellaneous Data (OMIX, https://ngdc.cncb.ac.cn/omix/). Compared with the 2017 version, GSA has been significantly updated in data model, online functionalities, and web interfaces. GSA-Human, as a new partner of GSA, is a data repository specialized in human genetics-related data with controlled access and security. OMIX, as a critical complement to the two resources mentioned above, is an open archive for miscellaneous data. Together, all these resources form a family of resources dedicated to archiving explosive data with diverse types, accepting data submissions from all over the world, and providing free open access to all publicly available data in support of worldwide research activities.  相似文献   

12.
Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development and deployment of methods for measuring and documenting data quality metrics. On September 18, 2010, the United States National Cancer Institute convened the "International Workshop on Proteomic Data Quality Metrics" in Sydney, Australia, to identify and address issues facing the development and use of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed and agreed up on two primary needs for the wide use of quality metrics: 1) an evolving list of comprehensive quality metrics and 2) standards accompanied by software analytics. Attendees stressed the importance of increased education and training programs to promote reliable protocols in proteomics. This workshop report explores the historic precedents, key discussions, and necessary next steps to enhance the quality of open access data. By agreement, this article is published simultaneously in the Journal of Proteome Research, Molecular and Cellular Proteomics, Proteomics, and Proteomics Clinical Applications as a public service to the research community. The peer review process was a coordinated effort conducted by a panel of referees selected by the journals.  相似文献   

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Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development and deployment of methods for measuring and documenting data quality metrics. On September 18, 2010, the U.S. National Cancer Institute (NCI) convened the "International Workshop on Proteomic Data Quality Metrics" in Sydney, Australia, to identify and address issues facing the development and use of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed and agreed upon two primary needs for the wide use of quality metrics: (i) an evolving list of comprehensive quality metrics and (ii) standards accompanied by software analytics. Attendees stressed the importance of increased education and training programs to promote reliable protocols in proteomics. This workshop report explores the historic precedents, key discussions, and necessary next steps to enhance the quality of open access data. By agreement, this article is published simultaneously in Proteomics, Proteomics Clinical Applications, Journal of Proteome Research, and Molecular and Cellular Proteomics, as a public service to the research community. The peer review process was a coordinated effort conducted by a panel of referees selected by the journals.  相似文献   

15.
Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development and deployment of methods for measuring and documenting data quality metrics. On September 18, 2010, the U.S. National Cancer Institute (NCI) convened the "International Workshop on Proteomic Data Quality Metrics" in Sydney, Australia, to identify and address issues facing the development and use of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed and agreed up on two primary needs for the wide use of quality metrics: (1) an evolving list of comprehensive quality metrics and (2) standards accompanied by software analytics. Attendees stressed the importance of increased education and training programs to promote reliable protocols in proteomics. This workshop report explores the historic precedents, key discussions, and necessary next steps to enhance the quality of open access data. By agreement, this article is published simultaneously in the Journal of Proteome Research, Molecular and Cellular Proteomics, Proteomics, and Proteomics Clinical Applications as a public service to the research community. The peer review process was a coordinated effort conducted by a panel of referees selected by the journals.  相似文献   

16.
The Organisation for Economic Co-operation and Development (OECD) has published a new set of principles and guidelines to promote open access to datasets and results from publicly funded research. However, there is reason to think twice about the implications of making demands for transparency and open access for publicly funded research only. How will such demands affect incentives and research agendas? Might this new regulation of publicly funded research have undesirable effects on the quality and value of research? Placing the OECD guidelines in a broader context of research regulation, we argue that they might provide a further push toward collaboration with commercially sponsored research and reinforce incentive structures that favour the creation of commercial value.  相似文献   

17.
Many research-funding agencies now require open access to the results of research they have funded, and some also require that researchers make available the raw data generated from that research. Similarly, the journal Trials aims to address inadequate reporting in randomised controlled trials, and in order to fulfil this objective, the journal is working with the scientific and publishing communities to try to establish best practice for publishing raw data from clinical trials in peer-reviewed biomedical journals. Common issues encountered when considering raw data for publication include patient privacy – unless explicit consent for publication is obtained – and ownership, but agreed-upon policies for tackling these concerns do not appear to be addressed in the guidance or mandates currently established. Potential next steps for journal editors and publishers, ethics committees, research-funding agencies, and researchers are proposed, and alternatives to journal publication, such as restricted access repositories, are outlined.  相似文献   

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Recent concerns about the reproducibility of science have led to several calls for more open and transparent research practices and for the monitoring of potential improvements over time. However, with tens of thousands of new biomedical articles published per week, manually mapping and monitoring changes in transparency is unrealistic. We present an open-source, automated approach to identify 5 indicators of transparency (data sharing, code sharing, conflicts of interest disclosures, funding disclosures, and protocol registration) and apply it across the entire open access biomedical literature of 2.75 million articles on PubMed Central (PMC). Our results indicate remarkable improvements in some (e.g., conflict of interest [COI] disclosures and funding disclosures), but not other (e.g., protocol registration and code sharing) areas of transparency over time, and map transparency across fields of science, countries, journals, and publishers. This work has enabled the creation of a large, integrated, and openly available database to expedite further efforts to monitor, understand, and promote transparency and reproducibility in science.

This study uses novel open source automated tools to monitor transparency across all 2.75 million open access articles on PubMed Central, discovering that different disciplines, journals and publishers abide by principles of transparency to varying degrees over time.  相似文献   

20.
Meneghini R 《EMBO reports》2012,13(2):106-108
Emerging countries have established national scientific journals as an alternative publication route for their researchers. However, these journals eventually need to catch up to international standards.Since the first scientific journal was founded—The Philosophical Transactions of the Royal Society in 1665—the number of journals dedicated to publishing academic research has literally exploded. The Thomson Reuters Web of Knowledge database alone—which represents far less than the total number of academic journals—includes more than 11,000 journals from non-profit, society and commercial publishers, published in numerous languages and with content ranging from the natural sciences to the social sciences and humanities. Notwithstanding the sheer scale and diversity of academic publishing, however, there is a difference between the publishing enterprise in developed countries and emerging countries in terms of the commercial rationale behind the journals.…‘national'' or even ‘local'' journals are published and supported because they report important, practical information that would be declined by international journals…Although all academic journals seek to serve their readership by publishing the highest quality and most interesting advances, a growing trend in the twentieth century has also seen publishers in developed countries viewing academic publishing as a way of generating profit, and the desire of journal editors to publish the best and most interesting science thereby serves the commercial interest of publishers who want people to buy the publication.In emerging countries, however, there are few commercial reasons to publish a journal. Instead, ‘national'' or even ‘local'' journals are published and supported because they report important, practical information that would be declined by international journals, either because the topic is of only local or marginal interest, or because the research does not meet the high standards for publication at an international level. Consequently, most ‘national'' journals are not able to finance themselves and depend on public funding. In Brazil, for instance, the national journals account for one-third of the publications of all scientific articles from Brazil and are mostly funded by the government. Other emerging countries that invest in research—notably China, India and Russia—also have a sizable number of national journals, most of which are published in their native language.There is little competition between developed countries to publish the most or the best scientific journals. There is clear competition between the top-flight journals—Nature and Science, for example—but this competition is academically and/or commercially, rather than nationally, based. In fact, countries with similar scientific calibres in terms of the research they generate, differ greatly in terms of the number of journals published within their borders. According to the Thomson Reuters database, for example, the Netherlands, Switzerland and Sweden published 847, 202 and 30 scientific journal, respectively, in 2010—the Netherlands has been a traditional haven for publishers. However, the number of articles published by researchers in these countries in journals indexed by Thomson Reuters—a rough measurement of scientific productivity—does not differ significantly.To overcome the perceived dominance of international journals […] some emerging countries have increased the number of national journalsScientists who edit directly or serve on the editorial boards of high-quality, international journals have a major responsibility because they guide the direction and set the standards of scientific research. In deciding what to publish, they define the quality of research, promote emerging research areas and set the criteria by which research is judged to be new and exciting; they are the gatekeepers of science. The distribution of these scientists also reflects the division between developed and emerging countries in scientific publishing. Using the Netherlands, Switzerland and Sweden as examples, they respectively contributed 235, 256 and 160 scientists to the editorial teams or boards of 220 high-impact, selected journals in 2005 (Braun & Diospatonyi, 2005). These numbers are comparable with the scientific production of these countries in terms of publications. On the other hand, Brazil, South Korea and Russia, countries as scientifically productive in terms of total number of articles as the Netherlands, Switzerland and Sweden, contributed only 28, 29 and 55 ‘gatekeepers'', respectively. A principal reason for this difference is, of course, the more variable quality of the science produced in emerging countries, but it is nevertheless clear that their scientists are under-represented on the teams that define the course and standards of scientific research.To overcome the perceived dominance of international journals, and to address the significant barriers to getting published that their scientists face, some emerging countries have increased the number of national journals (Sumathipala et al, 2004). Such barriers have been well documented and include poor written English and the generally lower or more variable quality of the science produced in emerging countries. However, although English, which is the lingua franca of modern science (Meneghini & Packer, 2007), is not as great a barrier as some would claim, there is some evidence of a conscious or subconscious bias among reviewers and editors in judging articles from emerging countries. (Meneghini et al, 2008; Sumathipala et al, 2004).A third pressure has also forced some emerging countries to introduce more national journals in which to publish academic research from within their borders: greater scientific output. During the past two or three decades, several of these countries have made huge investments into research—notably China, India and Brazil, among others—which has enormously increased their scientific productivity. Initially, the new national journals aspired to adopt the rigid rules of peer review and the quality standards of international journals, but this approach did not produce satisfactory results in terms of the quality of papers published. On the one hand, it is hard for national journals to secure the expertise of scientists competent to review their submissions; on the other, the reviewers who do agree tend to be more lenient, ostensibly believing that peer review as rigorous as that of international journals would run counter to the purpose of making scientific results publicly available, at least on the national level.The establishment of national journals has, in effect, created two parallel communication streams for scientists in emerging countries: publication in international journals—the selective route—and publication in national journals—the regional route. On the basis of their perceived chances to be accepted by an international journal, authors can choose the route that gives them the best opportunity to make their results public. Economic conditions are also important as the resources to produce national journals come from government, so national journals can face budget cuts in times of austerity. In the worst case, this can lead to the demise of national journals to the disadvantage of authors who have built their careers by publishing in them.…to not publish, for any reason, is to break the process of science and potentially inhibit progressThere is some anecdotal evidence that authors who often or almost exclusively publish in international journals hold national journals in some contempt—they regard them as a way of avoiding the effort and hassle of publishing internationally. Moreover, although the way in which governments regard and support the divergent routes varies between countries, in general, scientists who endure and succeed through the selective route often receive more prestige and have more influence in shaping national science policies. Conversely, authors who choose the regional publication route regard their efforts as an important contribution to the dissemination of information generated by the national scientific community, which might otherwise remain locked away—by either language or access policies. Either way, it is worth mentioning that publication is obviously not the end point of a scientific discovery: the results should feed into the pool of knowledge and might inspire other researchers to pursue new avenues or devise new experiments. Hence, to not publish, for any reason, is to break the process of science and potentially inhibit progress.The choice of pursuing publication in regional or international journals also has direct consequences for the research being published. The selective, international route ensures greater visibility, especially if the paper is published in a high-impact journal. The regional route also makes the results and experiments public, but it fails to attract international visibility, in particular if the research is not published in English.It seems that, for the foreseeable future, this scenario will not change. If it is to change, however, then the revolution must be driven by the national journals. In fact, a change that raises the quality and value of national journals would be prudent because it would give scientists from emerging countries the opportunity to sit on the editorial boards of, or referee for, the resulting high-quality national journals. In this way, the importance of national journals would be enhanced and scientists from emerging countries would invest effort and gain experience in serving as editors or referees.The regional route has various weaknesses, however, the most important of which is the peer-review process. Peer-review at national journals is simply of a lower standard owing to several factors that include a lack of training in objective research assessment, greater leniency and tolerance of poor-quality science, and an unwillingness by top researchers to participate because they prefer to give their time to the selective journals. This creates an awkward situation: on the one hand, the inability to properly assess submissions, and on the other hand, a lack of motivation to do so.Notwithstanding these difficulties, most editors and authors of national journals hope that their publications will ultimately be recognized as visible, reliable sources of information, and not only as instruments to communicate national research to the public. In other words, their aspiration is not only to publish good science—albeit of lesser interest to international journals—but also to attain the second or third quartiles of impact factors in their areas. These journals should eventually be good enough to compete with the international ones, mitigating their national character and attracting authors from other countries.The key is to raise the assessment procedures at national journals to international standards, and to professionalize their operations. Both goals are interdependent. The vast majority of national journals are published by societies and research organizations and their editorial structures are often limited to local researchers. As a result, they are shoestring operations that lack proper administrative support and international input, and can come across as amateurish. The SciELO (Scientific Electronic Library Online), which indexes national journals and measures their quality, can require certain changes when it indexes a journal, including the requirement to internationalize the editorial body or board.…experienced international editors should be brought in to strengthen national journals, raise their quality and educate local editors…In terms of improving this status quo, a range of other changes could be introduced. First, more decision-making authority should be given to publishers to decide how to structure the editorial body. The choice of ad hoc assistants—that is, professional scientists who can lend expertise at the editorial level should be selected by the editors—who should also assess journal performance. Moreover, publishers should try to attract international scientists with editorial experience to join a core group of two or three chief or senior editors. Their English skills, their experience in their research field and their influence in the community would catalyse a rapid improvement of the journals and their quality. In other words, experienced international editors should be brought in to strengthen national journals, raise their quality and educate local editors with the long-term objective to join the international scientific editing community. It would eventually merge the national and the selective routes of publishing into a single international route of scientific communication.Of course, there is a long way to go. The problem is that many societies and organizations do not have sufficient resources—money or experience—to attract international scientists as editors. However, new publishing and financial models could provide incentives to attract this kind of expertise. Ultimately, relying on government money alone is neither a reliable nor sufficient source of income to make national journals successful. One way of enhancing revenue streams might be to switch to an open-access model that would charge author fees that could be reinvested to improve the journals. In Brazil, for instance, almost all journals have adopted the open access model (Hedlund et al, 2004). The author fees—around US$1,250—if adopted, would provide financial support for increasing the quality and performance of the journals. Moreover, increased competition between journals at a national level should create a more dynamic and competitive situation among journals, raising the general quality of the science they publish. This would also feed back to the scientific community and help to raise the general standards of science in emerging countries.  相似文献   

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