Zoom in on neurodegeneration

Despite the existence of several scientific journals that publish research papers and reviews related to neurodegenerative diseases, a journal specifically devoted to the molecular and cellular aspects of disease mechanisms is lacking. Molecular Neurodegeneration is an open-access, peer-reviewed, online journal created to publish original research articles that address i) the mechanisms of neurodegeneration at the cellular, subcellular and molecular levels and ii) potential therapeutic interventions for neurodegenerative diseases. Through publication of reviews, editorial commentaries, and meeting reports, Molecular Neurodegeneration will also provide a forum to enhance the exchange of ideas and promote debate that is essential for scientific progress. Molecular Neurodegeneration will enable scientists to rapidly communicate their important research discoveries to their colleagues around the world.     

Passing the Red Pen: EvoS Journal Offers an Early Education in Peer Review

EvoS Journal: The Journal of the Evolutionary Studies Consortium is the open-access, peer-reviewed journal borne of the EvoS (Evolutionary Studies) Consortium movement. The journal has two separate, yet related goals: to publish scholarly articles regarding the intersection of higher education and evolutionary theory, and to publish articles written and reviewed by undergraduates that incorporate an evolutionary perspective. Undergraduates who publish and review for EvoS Journal get the chance to see their work published alongside that of experts within the field of evolutionary studies, and to see the interdisciplinary and widespread applications of evolutionary theory to human life and beyond. The current study examines whether the interdisciplinary nature of EvoS Journal and its initiation of students into the peer-review process set EvoS Journal apart from more traditional undergraduate journals. EvoS Journal was compared to other journals listed by the Council for Undergraduate Research. While EvoS Journal mirrors many traditional undergraduate journals in their employment of student reviewers and publishing work originating from any U.S. institution, it differs by both its interdisciplinary focus and by serving as an outlet for both student and professional publications. The implications are discussed in terms of the benefits of interdisciplinary and peer-review training to students in the classroom, including improvements in writing, interpersonal relations, and real-world skills.     

RECENT ORNITHOLOGIAL LITERATURE

Recent Ornithological Literature is a cooperative, volunteer project for the benefit of ornithologists the world over. The partnership began in 1983 (Auk 100, Ibis 125) when the AOU and BOU combined their Recent Literature sections to publish a single supplement of ornithological literature. The RAOU joined this partnership in 1987 (Emu 87). The AOU covers journals published in the Americas and the Philippines. The BOU covers journals published in Europe, Africa, and mainland Asia. The RAOU covers journals published in Australasia and other island nations of the Pacific. More than 150 volunteers scan about 650 titles and contribute abstracts regularly. Authors' addresses are included, if the journal lists them, to facilitate communication between readers and authors.
Recent Ornithological Literature strives for comprehensive coverage of the world's periodical literature of interest to persons studying wild birds. Readers are encouraged to consult the "List of Journals Scanned" published annually in the fourth supplement and to make recommendations for increasing journal coverage. Authors, editors, or publishers whose articles or journals are not covered by the ROL should send reprints, abstracts, or exchange issues to the editor responsible for covering the geographical area where the journal is published. Volunteer abstractors are welcomed.     

RECENT ORNITHOLOGIAL LITERATURE

Recent Ornithological Literature is a cooperative, volunteer project for the benefit of ornithologists the world over. The partnership began in 1983 (Auk 100, Ibis 125) when the AOU and BOU combined their Recent Literature sections to publish a single supplement of ornithological literature. The RAOU joined this partnership in 1987 (Emu 87). The AOU covers journals published in the Americas and the Philippines. The BOU covers journals published in Europe, Africa, and mainland Asia. The RAOU covers journals published in Australasia and other island nations of the Pacific. More than 150 volunteers scan about 650 titles and contribute abstracts regularly. Authors' addresses are included, if the journal lists them, to facilitate communication between readers and authors. Recent Ornithological Literature strives for comprehensive coverage of the world's periodical literature of interest to persons studying wild birds. Readers are encouraged to consult the “List of Journals Scanned” published annually in the fourth supplement and to make recommendations for increasing journal coverage. Authors, editors, or publishers whose articles or journals are not covered by the ROL should send reprints, abstracts, or exchange issues to the editor responsible for covering the geographical area where the journal is published. Volunteer abstractors are welcomed.     

RECENT ORNITHOLOGICAL LITERATURE

Recent Ornithological Literature is a cooperative, volunteer project for the benefit of ornithologists the world over. The partnership began in 1983 ( Auk 100, Ibis 125) when the AOU and BOU combined their Recent Literature sections to publish a single supplement of or- mythological literature. The RAOU joined this partnership in 1987 ( Emu 87). The AOU covers journals published in the Americas and the Philippines. The BOU covers journals published in Europe, Africa, and mainland Asia. The RAOU covers journals published in Australasia and other island nations of the Pacific. More than 150 volunteers scan about 650 titles and contribute abstracts regularly. Authors' addresses are included, if the journal lists them, to facilitate communication between readers and authors.
Recent Ornithological Literature strives for comprehensive coverage of the world's periodical literature of interest to persons studying wild birds. Readers are encouraged to consult the "List of Journals Scanned published annually in the fourth supplement and to make recommendations for increasing journal coverage. Authors, editors, or publishers whose articles or journals are not covered by the ROL should send reprints, abstracts, or exchange issues to the editor responsible for covering the geographical area where the journal is published. Volunteer abstractors are welcomed.     

Our use,misuse, and abandonment of a concept: Whither habitat?

The foundational concept of habitat lies at the very root of the entire science of ecology, but inaccurate use of the term compromises scientific rigor and communication among scientists and nonscientists. In 1997, Hall, Krausman & Morrison showed that ‘habitat’ was used correctly in only 55% of articles. We ask whether use of the term has been more accurate since their plea for standardization and whether use varies across the broader range of journals and taxa in the contemporary literature (1998–2012). We searched contemporary literature for ‘habitat’ and habitat‐related terms, ranking usage as either correct or incorrect, following a simplified version of Hall et al.'s definitions. We used generalized linear models to compare use of the term in contemporary literature with the papers reviewed by Hall et al. and to test the effects of taxa, journal impact in the contemporary articles and effects due to authors that cited Hall et al. Use of the term ‘habitat’ has not improved; it was still only used correctly about 55% of the time in the contemporary data. Proportionately more correct uses occurred in articles that focused on animals compared to ones that included plants, and papers that cited Hall et al. did use the term correctly more often. However, journal impact had no effect. Some habitat terms are more likely to be misused than others, notably ‘habitat type’, usually used to refer to vegetation type, and ‘suitable habitat’ or ‘unsuitable habitat’, which are either redundant or nonsensical by definition. Inaccurate and inconsistent use of the term can lead to (1) misinterpretation of scientific findings; (2) inefficient use of conservation resources; (3) ineffective identification and prioritization of protected areas; (4) limited comparability among studies; and (5) miscommunication of science‐based findings. Correct usage would improve communication with scientists and nonscientists, thereby benefiting conservation efforts, and ecology as a science.     

New journal: Algorithms for Molecular Biology

This editorial announces Algorithms for Molecular Biology, a new online open access journal published by BioMed Central. By launching the first open access journal on algorithmic bioinformatics, we provide a forum for fast publication of high-quality research articles in this rapidly evolving field. Our journal will publish thoroughly peer-reviewed papers without length limitations covering all aspects of algorithmic data analysis in computatioal biology. Publications in Algorithms for Molecular Biology are easy to find, highly visible and tracked by organisations such as PubMed. An established online submission system makes a fast reviewing procedure possible and enables us to publish accepted papers without delay. All articles published in our journal are permanently archived by PubMed Central and other scientific archives. We are looking forward to receiving your contributions.     

RECENT ORNITHOLOGICAL LITERATURE

Recent Ornithological Literature is a cooperative, volunteer project for the benefit of ornithologists the world over. The partnership began in 1983 (Auk 100, Ibis 125) when the AOU and BOU combined their Recent Literature sections to publish a single supplement of or- mythological literature. The RAOU joined this partnership in 1987 (Emu 87). The AOU covers journals published in the Americas and the Philippines. The BOU covers journals published in Europe, Africa, and mainland Asia. The RAOU covers journals published in Australasia and other island nations of the Pacific. More than 150 volunteers scan about 650 titles and contribute abstracts regularly. Authors' addresses are included, if the journal lists them, to facilitate communication between readers and authors. Recent Ornithological Literature strives for comprehensive coverage of the world's periodical literature of interest to persons studying wild birds. Readers are encouraged to consult the “List of Journals Scanned published annually in the fourth supplement and to make recommendations for increasing journal coverage. Authors, editors, or publishers whose articles or journals are not covered by the ROL should send reprints, abstracts, or exchange issues to the editor responsible for covering the geographical area where the journal is published. Volunteer abstractors are welcomed.     

Formalizing the definition of meta‐analysis in Molecular Ecology

Meta‐analysis, the statistical synthesis of pertinent literature to develop evidence‐based conclusions, is relatively new to the field of molecular ecology, with the first meta‐analysis published in the journal Molecular Ecology in 2003 (Slate & Phua 2003). The goal of this article is to formalize the definition of meta‐analysis for the authors, editors, reviewers and readers of Molecular Ecology by completing a review of the meta‐analyses previously published in this journal. We also provide a brief overview of the many components required for meta‐analysis with a more specific discussion of the issues related to the field of molecular ecology, including the use and statistical considerations of Wright's F_ST and its related analogues as effect sizes in meta‐analysis. We performed a literature review to identify articles published as ‘meta‐analyses’ in Molecular Ecology, which were then evaluated by at least two reviewers. We specifically targeted Molecular Ecology publications because as a flagship journal in this field, meta‐analyses published in Molecular Ecology have the potential to set the standard for meta‐analyses in other journals. We found that while many of these reviewed articles were strong meta‐analyses, others failed to follow standard meta‐analytical techniques. One of these unsatisfactory meta‐analyses was in fact a secondary analysis. Other studies attempted meta‐analyses but lacked the fundamental statistics that are considered necessary for an effective and powerful meta‐analysis. By drawing attention to the inconsistency of studies labelled as meta‐analyses, we emphasize the importance of understanding the components of traditional meta‐analyses to fully embrace the strengths of quantitative data synthesis in the field of molecular ecology.     

Emerging journals. The benefits of and challenges for publishing scientific journals in and by emerging countries

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.     

How to Write a Medical Research Paper for an International Journal

Western-raised scientists are taught with the traditional concepts of:purpose,method,observation and conclusion.This is not true for Chinese educated students.Since all international journals publish papers following these,or similar parameters,the Chinese scientist who wishes to publish in such a journal,must adjust his thinking to fit within this scheme.In this presentation we wish to assist our Chinese colleagues on how this thought process can be followed.     

Species Distribution Models and Impact Factor Growth in Environmental Journals: Methodological Fashion or the Attraction of Global Change Science

In this work, I evaluate the impact of species distribution models (SDMs) on the current status of environmental and ecological journals by asking the question to which degree development of SDMs in the literature is related to recent changes in the impact factors of ecological journals. The hypothesis evaluated states that research fronts are likely to attract research attention and potentially drive citation patterns, with journals concentrating papers related to the research front receiving more attention and benefiting from faster increases in their impact on the ecological literature. My results indicate a positive relationship between the number of SDM related articles published in a journal and its impact factor (IF) growth during the period 2000–09. However, the percentage of SDM related papers in a journal was strongly and positively associated with the percentage of papers on climate change and statistical issues. The results support the hypothesis that global change science has been critical in the development of SDMs and that interest in climate change research in particular, rather than the usage of SDM per se, appears as an important factor behind journal IF increases in ecology and environmental sciences. Finally, our results on SDM application in global change science support the view that scientific interest rather than methodological fashion appears to be the major driver of research attraction in the scientific literature.     

RECENT ORNITHOLOGICAL LITERATURE

Beginning in 1983 (Auk 100, Ibis 125) the AOU and BOU combined their Recent Literature sections, to publish a single supplement of ornithological literature to which members of both unions contribute. The RAOU joined this partnership in 1987 (Emu 87). The AOU covers journals published in the Americas and The Philippines. The BOU covers journals published in Europe, Africa, and mainland Asia. The RAOU covers journals published in Australasia and other island nations of the Pacific. More than 150 volunteers scan about 650 titles and contribute abstracts regularly. Authors' addresses are included, if the journal lists them, to facilitate communication between readers and authors.
Recent Ornithological Literature strives for comprehensive coverage of the world's periodical literature of interest to persons studying wild birds. Readers are encouraged to consult the "List of Journals Scanned" published annually in the October supplement and to make recommendations for increasing journal coverage.     

RECENT ORNITHOLOGICAL LITERATURE

Beginning in 1983 (Auk 100, Ibis 125) the AOU and BOU combined their Recent Literature sections, to publish a single supplement of ornithological literature to which members of both unions contribute. The RAOU joined this partnership in 1987 (Emu 87). The AOU covers journals published in the Americas and The Philippines. The BOU covers journals published in Europe, Africa, and mainland Asia. The RAOU covers journals published in Australasia and other island nations of the Pacific. More than 150 volunteers scan about 650 titles and contribute abstracts regularly. Authors' addresses are included, if the journal lists them, to facilitate communication between readers and authors.
Recent Ornithological Literature strives for comprehensive coverage of the world's periodical literature of interest to persons studying wild birds. Readers are encouraged to consult the "List of Journals Scanned" published annually in the October supplement and to make recommendations for increasing journal coverage.     

Three Journal Similarity Metrics and Their Application to Biomedical Journals

In the present paper, we have created several novel journal similarity metrics. The MeSH odds ratio measures the topical similarity of any pair of journals, based on the major MeSH headings assigned to articles in MEDLINE. The second metric employed the 2009 Author-ity author name disambiguation dataset as a gold standard for estimating the author odds ratio. This gives a straightforward, intuitive answer to the question: Given two articles in PubMed that share the same author name (lastname, first initial), how does knowing only the identity of the journals (in which the articles were published) predict the relative likelihood that they are written by the same person vs. different persons? The article pair odds ratio detects the tendency of authors to publish repeatedly in the same journal, as well as in specific pairs of journals. The metrics can be applied not only to estimate the similarity of a pair of journals, but to provide novel profiles of individual journals as well. For example, for each journal, one can define the MeSH cloud as the number of other journals that are topically more similar to it than expected by chance, and the author cloud as the number of other journals that share more authors than expected by chance. These metrics for journal pairs and individual journals have been provided in the form of public datasets that can be readily studied and utilized by others.     

Elementary and middle level biology topics: a content analysis of Science and Children and Science Scope from 1990 to 2014

Science and Children and Science Scope are peer-reviewed science practitioner journals that publish articles for science educators who teach children of ages 5–10 years and 10–13 years, respectively. As such, these articles are a reflection of the science concepts that are being communicated to science educators. This comprehensive literature review was completed to determine the extent to which the articles included in these journals from 1990 to 2014 focused on biology topics, incorporated other non-science subjects and science disciplines, and encouraged inquiry-based learning. The results indicate that out of the 2701 total articles, 557 (21%) focused on biology. The biology topic covered most often by both journals was animals. The biology topics covered least often were fungi, photosynthesis, respiration and viruses. The findings are taken into consideration and the educational implications for the journals and educators are discussed.