Computational and Structural Biotechnology Journal (CSBJ), which will publish its first issue in April 2012. CSBJ aims to become a significant international participant in the interface of biology and computer science and publish high quality research across the entire biotechnology spectrum. A literature survey shows that the reliance upon computational methods has been growing steadily over the past three decades across all disciplines of biology. As the amount of available data grows in various biotechnology fields, the need for computational approaches to manage, analyze, predict and model grows as well. Furthermore, as technology advances, the focus of computational biology research expands to meet the new challenges and co-evolve with them. We have high expectations that CSBJ, by hosting high-quality research and review papers on modern biotechnology, will become a specialized forum and provide opportunities for communication among the scientists of the world.We are pleased to announce the launch of CSBJ is wide and ambitious; that's why we placed high-priority on ensuring the participation of well-known experts from around the globe in the Editorial team. The Editorial team consists of up- and –coming scientists, who are the new leaders in their respective fields, to ensure a smooth progression from the journal's launch to recognized status as a fully established publishing platform on all aspects of computational and structural biotechnology. There are currently more than 50-leading scientists in the Editorial board from top-quality universities as Harvard, Yale, ETH, DTU, Max Plank Institute, Columbia University, California Institute of Technology, University of Oxford and many other prestigious institutions. The Editor-in-Chief, the Associate Editors and the Editorial Board will work synergistically for fair, swift and transparent peer review process to publish timely and high-quality papers.The scope of CSBJ the Editor-in-Chief or corresponding specialists from the Editorial Board will immediately screen a submission. Appropriate manuscripts will be sent for peer review to at least two experts, who are expected to provide an independent assessment of suitability for publication in CSBJ. Based on their reports and scoring, a final decision will be made regarding acceptance of the manuscript. The Editor-in-Chief reserves the right to make final decisions concerning each manuscript submitted to the journal within the shortest possible period. We will aim to make editorial decisions in 6 weeks from the date the article was submitted through the journal submission system, generally with only one round of revisions. However, we encourage our Editorial Board members as well as our reviewers to be motivated critical advisers for improving a manuscript.To make a decision whether a manuscript fits the format and standards of CSBJ is not of course the first journal that by adapting the open-access model enables free and universal access resulting in dissemination to the widest possible audience. The advantages of the open access-publishing model, and especially the correlation between open-access with higher downloads and higher citations leading to higher Impact Factor, has already been suggested. It is also true that with a free and universal online access, the financial or grant status of the researcher will not influence his/her ability to access articles. At first sight the model of CSBJ does not significantly differ from that proposed by other open-access journals, however, in reality CSBJ is not just another open-access journal; the high publication fee that most of the journals request is excluding all the resource-poor countries. CSBJ wants scientists from developing countries not only as readers of the material that their counterparts in resource-rich countries publish, but as active participants in disseminating research findings. Therefore, for all articles accepted for publication a minimum article-processing charge will be levied to cover the costs incurred by open access publication.CSBJ.We invite you to work together with us to create this new and high-visibility open-access forum for modern biotechnology. We look forward to receiving your submissions for consideration in the second issue of


The Publications Committee of the International Organization of Medical Physics (IOMP) has prepared an editorial on plagiarism, which is reproduced here with some modifications, with permission from the IOMP. In addition, this editorial is also consistent with the Policy on Plagiarism of World Association of Medical Editors (WAME) [The Biomedical Imaging and Intervention Journal (s (WAME) .Plagiarism – from the Latin “plagiare,” meaning “to kidnap” – is defined as “the appropriation or imitation of the language, ideas and thoughts of another author and representation of them as one’s original work” . PlagiarPlagiarism undermines the authenticity of research manuscripts and the journals in which they are published. It also compromises the integrity of the scientific process and public regard for science. Plagiarism violates the literary rights of individuals whose work has been plagiarised and the property rights of copyright holders. Violation of literary or property rights may result in legal action against the individual(s) committing plagiarism. Although plagiarism has existed since the beginning of science, it seems to be increasing because the World Wide Web facilitates finding and copying the work of others.It is possible not only to plagiarise the work of others, but also one’s own work through reuse of identical or nearly identical portions of manuscripts without acknowledgment or citation. Simultaneous or subsequent submission of similar manuscripts with only minor differences and without citation between the manuscripts is, unfortunately, a rather common practice among authors hoping to acquire multiple publications from a research project. Scientific journals discourage this practice and usually will not permit it if exposed before publication. Occasionally, the same – or a very similar – article may be published in two journals because the journals reach different audiences and the article is of interest to both. This practice must be approved by the editors of both journals and the duplication must be acknowledged in each article.When there is a possibility of plagiarism – often through an allegation of plagiarism by the original author, a reviewer or an interested third party – the journal’s editor should act quickly. The editor should examine the original material and the publication alleged to have performed plagiarism. If the editor concludes that no plagiarism has occurred, the accuser should be notified, and no further action is necessary.If the evidence suggests that plagiarism may have occurred, the editor should contact the accused author(s), the author(s) whose work may have been plagiarised, and the copyright holder of the original material if different from the author(s). The correspondence should include the alleged plagiarising language and a copy of the original and suspected work. If all parties agree that plagiarism – whether intentional or unintentional – has occurred, a written letter of apology should be sent promptly by the offending author(s) to the editor and to the author(s) and copyright holder of the plagiarised work. If the offending work has been published, a notice of plagiarism, citing both the plagiarised and the offending articles and containing the exact text that has been plagiarised, should be published in the next available issue of the journal in which the offending article was published. The plagiarising author(s) must agree that all dissemination of the offending article will be accompanied by the notice of plagiarism.If the accused author(s) denies that plagiarism has occurred, the editor must explore the accusation further, preferably through a mechanism already established by the journal to investigate allegations of scientific misconduct. All parties to the allegation should be encouraged to submit corroborating evidence, and the accused author(s) should be granted an opportunity – at no expense to the journal – to testify in person in defence against the allegation. The investigation should be concluded within a reasonable period of time .If the mechanism to investigate the allegation of plagiarism concludes in support of the allegation, then the process for the case in which plagiarism is admitted should be instituted. Further, the editor must decide whether the plagiarism should be reported to the guilty parties’ supervisor, employer, and/or professional organisation.If the mechanism rules against the accusation of plagiarism, a letter stating this ruling should be provided to the accuser, the author(s) accused of plagiarism, the author(s) of the original work, and the copyright holder if different from the author(s). In either case, these actions should constitute closure of the allegation of plagiarism.Self-policing is a major strength of the scientific community and suspected plagiarism should always be reported, even if the suspected plagiariser is a colleague or superior. An allegation of plagiarism is a serious accusation and should never be taken lightly. Further, laboratory directors, senior authors, and other individuals in leadership positions should educate junior members of a research team about responsible conduct in preparing scientific manuscripts for publication.biij fully supports the initiative in combating plagiarism and will try to closely adhere to the above detailed mechanism in handling reported cases of plagiarism. Although there are no such reports or accusations hitherto, the Editorial Board has taken the liberty of randomly checking the integrity of submitted papers for evidence of plagiarism. The Board has been using Google Scholar (http://google.com/scholar/) as a tool in the evaluation process, and is currently trying the services of the CrossCheck plagiarism detection service by CrossRef (http://crossref.org/).biij retains the right to alter the above mechanism in handling plagiarism cases should the currently worrying advent of plagiarism in scientific literature decrease in the future.


During the Year 2013 Pakistan Journal of Medical Sciences achieved yet another landmark when it managed to be covered by PubMed Central with the result that now all the manuscripts published in the journal effective January 2013 are now accessible through this important global database i.e. PubMed Central. (http://www.ncbi.nlm.nih.gov/pmc/) It will ensure that the contributions by the authors have increased visibility and readership thereby improving the chances of citation as well. We had been planning for this for the last three years but financial constraints had been the major hindrance. However, now we have made arrangements with one of the commercial concerns overseas who prepares the XML files for submission to PubMed Central which is a pre requisite. We believe this investment is worth and will further improve the standard of the journal and its ranking in biomedical journals. In order to facilitate the authors in early publication of their accepted manuscripts reducing the waiting time, we also increased the frequency of publication from quarterly to bimonthly during 2013 while efforts are also being made to accelerate the Peer Review process and reduce the time but sometimes it is beyond our control since the Reviewers are all busy people and they perform these academic duties in honorary capacity, hence one cannot force them to convey their comments immediately, though many Reviewers are quite efficient and try to complete the review process meeting the deadlines.Screening for plagiarism1 During the last six months, after triage, only one hundred fifty manuscripts which are about 20% of all the submissions were accepted for further processing. Twelve were rejected because during screening similarity index score was more than 20% and in some cases it was as high as 40-60%. While screening for plagiarism, we remove the title as well as references from the manuscript. Three manuscripts which had similarity index score between 20-25% were returned to the authors requesting them to revise them and then resubmit by making necessary changes so that the similarity index score is less than 20%. While looking at the similarity index score one has to be careful as most often the plagiarized parts are in Methods section of the manuscript followed by Discussion. In some cases since the methodology is mostly the same in experimental studies, one has to be a bit lenient and accommodative but extensive plagiarism in discussion is not at all tolerated. Earlier after an agreement with CrossRef we had started giving Digital Object Identifier (DOI) numbers to all the manuscripts. In order to protect the authors and ourselves from publication of plagiarized material, we also entered into an agreement with CrossCheck to use their software iThenticate for screening of manuscripts for plagiarism. This software though a bit expensive but has the advantage over other tools used for screening for plagiarism because this not only covers what is freely available on the internet but it also has access to journal publications that are not accessible free online.Impact Factor: We have always believed that Impact Factor is Not and should Not be considered as the only criteria to evaluate the quality and standard of a Journal but it has its own importance and gets weightage from various academic institutions and organizations.2 Impact Factor has its own merits, advantages and disadvantages. At times the Editors are in a dilemma while accepting manuscripts for publication because in order to increase their Impact Factor, they are more interested to accept, process and ensure early publication of those manuscripts which have higher chances of citation. Case Reports get the least priority. On the other hand, impatience by the authors who wish to see their manuscripts in print early, the few quality journals are under too much pressure to publish more manuscripts once they are approved after going through the peer review. Increased submissions leads to increased number of manuscripts which eventually get accepted after peer review and thus publication but it then adversely affects the Journal’s Impact Factor. Despite the fact that citations from Pakistan Journal of Medical Sciences have progressively increase every year since 2009 but its Impact Factor got reduced since we published more manuscripts. Since we follow author friendly policy, we do not wish to deprive the authors from publishing their research work just for the sake of Impact Factor but we are hopeful that in the days to come as more and more quality manuscripts will get published, it will also ensure greater citations which will improve this Impact Factor as well in the days to come. However, great care is taken to ensure that only good quality manuscripts are accepted for publication which results in increased rejection rate which is not at all liked for the authors whose manuscripts are not accepted for further processing and publication. But one has to work within the constraints of financial as well as human resources and ensure timely publication through effective and efficient coordination with the authors and reviewers which is not an easy task.1 More recently some scientists have hypothesized that “using journal rank as an assessment tool is bad scientific practice”. They have suggested a library-based scholarly communication system. They believe that “this new system which will use modern information technology will vastly improve the filter, sort and discovery functions of the current journal system”. 4 They have further pointed out that it is not at all surprising to find out that even higher ranking journals are also more likely to publish fraudulent work than lower ranking journals.5 However, we believe that instead of becoming a victim of this vicious circle, editors in the developing resource constraint countries should try to improve the quality and standard of their journals making best use of the available financial and human resources. Consistency and hard work by the journal’s editorial team will pay rich dividends and ensure gradual improvement in journal ranking.Some scientists have suggested numerous other alternate metrics to judge and evaluate the quality and standard of a journal like H-Index and M-Index but they have their own drawbacks.


The ability to establish lifelong latency after primary infection is a common denominator of large DNA viruses of the Herpesviridae family. Herpes viruses are endemic to humans worldwide and contribute to the meta-genome of 70-100% of the world's population. The significance of herpes viruses as pathogens has been increasingly recognized during the past few decades, with the escalation in the number of patients undergoing immunosuppressive therapy after organ or bone marrow transplantation, and the rising incidence of AIDS. The ability of these viruses to ensure their survival by controlling cellular and immunological functions  and autoJournal of Virology and Virology. However, many others are published in specialist journals focusing on immunology, pathology, transplantation, and other areas. We aim for Herpesviridae to be our community's premier journal, bringing together the interdisciplinary niches of research on this important virus family Our goal is to focus the efforts of many specialities into one journal by providing an Open Access platform to gather and advance our scientific efforts. Herpesviridae is in its infancy and is therefore very flexible. In close co-operation with you -- our colleagues in the field -- we hope to develop it into a journal that we would all like to publish in and read. For that reason, your input is vital for our ability to continue improving the journal. All input will be considered carefully, and we will reply in a timely manner.A search in PubMed  reveals Herpesviridae is the focus on you as the author and how you can best publish your scientific work. Together with our internationally well-renowned Editorial Board [Herpesviridae uses a closed peer review system in which articles are reviewed by at least two experts selected by the assigned Editors-in-Chief, after an initial screening for suitability. With rapid publication in mind, we will weight the reviews that we receive and prioritize the concerns raised, so that revision time and effort can be focused on the most pressing improvements.One of the major differences with al Board , consistHerpesviridae is an online publication only. Thus, articles will not be restricted in size, will be available immediately after acceptance, and will be listed shortly thereafter in PubMed. Furthermore, Herpesviridae is an Open Access journal, enabling universal accessibility and ensuring that your work reaches the widest possible audience [Herpesviridae will publish high quality articles that have undergone stringent peer review, will hopefully result in high citations for published articles and consequently a high Impact Factor in the future.audience . AuthorsHerpesviridae publishes articles contributing to overall knowledge on the role of herpes viruses in health and disease. Articles from diverse fields, from experimental biological studies to clinical studies, are welcome. We aim to publish high-quality Reviews, Research articles, Short Reports, Editorials, Letters to the Editor, Case Reports, Clinical studies, and Meeting Reports of special interest. The articles will be deposited in freely accessible, full-text repositories such as PubMed Central in accordance with the policies of many major funding agencies [agencies -13.Herpesviridae, the key to the success of this journal ultimately rests with you, our authors, reviewers, and readers. We are very excited about Herpesviridae and the opportunities that it provides to our field. We hope you will seize the opportunity to contribute and develop this new journal. We welcome your comments, advice and submissions.Alongside, all the advantages of


Biologists should submit their preprints to open servers, a practice common in mathematics and physics, to open and accelerate the scientific process. Public preprint servers allow authors to make manuscripts publicly available before, or in parallel to, submitting them to journals for traditional peer review. The rationale for preprint servers is fundamentally simple: to make the results of research available to the scientific community as soon as possible, instead of waiting until the peer-review process is fully completed. Sharing manuscripts using preprint servers has numerous advantages, including: 1) rapid dissemination of work-in-progress to a wider audience; 2) immediate visibility of the research output for early-career scientists; 3) improved peer review by encouraging feedback from the entire research community; and 4) a fair and straightforward way to establish precedence.http://haldanessieve.org/), a new blog discussing arXiv papers in population genetics, can help make arXiv attractive for scientists looking to promote their work Open preprint servers offer a great opportunity for open science, especially if the community embraces the idea of discussing preprints. Initiatives like Haldane's Sieve  is the most widely used preprint server today, and its use is almost universal in some branches of mathematics and physics. arXiv has a system of moderators and endorsers. At least one author of a paper must be an endorser that has either previously submitted a paper or has received permission to submit. Moderators have the power to change the classification of a manuscript.arXiv (http://figshare.com) is an open server allowing scientists to submit any research output: manuscript, figures, datasets, videos, theses, presentations, and so on. There are no rules to limit what constitutes a research output and, unlike arXiv, there is no endorser system. A flexible tag system is used to classify each item.figshare (https://peerj.com/) is a new commercial open access publisher focused on the biological sciences that provides a preprint server and a peer-reviewed journal. Preprints can optionally be made private. One preprint per year can be posted for free, with a onetime  fee for unlimited public preprints. Preprints can be posted to PeerJ regardless of where they will be submitted for publication.PeerJ (http://f1000research.com/) will eventually be reviewed. Thus, F1000Research offers a hybrid model with publicly available manuscripts at time of submission and standard peer reviews that occur as part of the submission process. Manuscripts are considered “accepted” and will only be indexed after two positive referee responses.Whereas arXiv, figshare, and PeerJ offer an option to submit a manuscript without having it reviewed, papers submitted to F1000Research (https://github.com/). GitHub is one of several hosting services for collaborative development using the Git version control system (VCS). It allows numerous contributers to work asynchronously on the same project, often in parallel branches, all of which can be effortlessly merged and version controlled. Git is primarily used for software development This manuscript was developed entirely as an open project on GitHub (http://www.researchgate.net/) can be used to submit preprints Scientific publishing is more diversified than ever. There are now many alternative options for submitting articles before formal publication. For example, social networks such as ResearchGate . While submitting to preprint servers has become more common in the past few years, the number of biology papers submitted to preprint servers still represents only a small fraction of the total research produced in biology .Nature even felt compelled to respond to the rumor that they refused manuscripts submitted to arXiv by saying that “Nature never wishes to stand in the way of communication between researchers. We seek rather to add value for authors and the community at large in our peer review, selection and editing” There are a number of reasons why biologists have not developed a culture of sharing preprints, many of which are based on common misconceptions. For example, in contrast to other fields, there is a perception in biology that public preprints make it easier to steal ideas The ongoing discussions on the publication process, peer review, and alternative publication models are all symptoms of the current uneasiness with the ever-growing obsession with bibliographic metrics such as the impact factor Developing a preprint culture in biology will not solve all problems with the current publication process. However, it might significantly reduce its negative consequences. The role of peer review is to judge the scientific quality of a study. It is the first barrier against the fraudulent and poor quality science that could impede scientific progress. In practice, the peer-review system is not only used to evaluate scientific quality but also to judge pertinence. On the other hand, preprints are not filtered, neither for their quality nor their pertinence. Widespread adoption of preprint servers has the potential to shift the diffusion strategy: journals would remain important to validate publications, but the relevance of a study should only be judged by many more readers than the typical two–four anonymous reviewers. With a shift in the diffusion strategy, the role of traditional journals and their editors would be to showcase scientific discoveries for specialized readership.Making publication easier can lead to the proliferation of studies of uneven quality. A trade-off between the intensity of the peer-review filtering and the benefits to science has been hypothesized


Unlike traditional journals, which rely largely on subscription revenue, many open-access publications earn their money through publication fees from authors. Profit is linked to volume, seemingly unlimited on the Internet. Although the open-access world includes many high-standard journals, abuse is prevalent, as an investigation by the journal Science recently established [Science journalist John Bohannon submitted fake papers with unmistakable scientific flaws to 304 open-access journals. It turned out that 157 of the journals had accepted the paper and 98 had rejected the paper. Of the remaining 49 journals, 29 seemed to be non-operational and 20 journals had yet to reply. Acceptance took 40 days on average, compared to 24 days for a rejection. Of the 255 papers that underwent the entire editing process to acceptance or rejection, about 60 % of the final decisions occurred with no sign of peer review. Of the 106 journals that evidently performed any review, 70 % ultimately accepted the paper. Most reviews focused exclusively on the paper’s layout, formatting, and language. Only 36 of the 304 submissions gave rise to review comments recognising any of the paper’s scientific problems, and 16 of those papers were accepted by the editors despite the poor reviews! To summarise, bogus research as concocted by Science can easily pass the threshold of publication in the open-access area; even 157 journals accepted the fake papers!In general, the current article-refereeing mechanism depends on trust in both the integrity of submissions and in peer reviewers. Nowadays, that trust is being tested by a disturbing change in scientific communication: ablished , 2. To tsick and collapsing under its own weight’ [the societal impact. The ability to publish papers and their underlying data in full on the Internet opens new possibilities to show true negative  results. In the past, papers showing that a drug had no favourable effects failed to see the light of day. On the other hand, disseminating certain scientific information could pose a threat to safety and security. Scientists in industry, too, are struggling to define the limits of openness when communicating patented research, and whether some kinds of patents may actually suppress innovation [With open-access journals booming, debate is needed about how to ensure the credibility of scientific literature. Open-access pioneer Vitek Tracz believes that anonymous peer review is ‘ weight’ . As a renovation .Science in Transition by five scientists/policymakers: Huub Dijstelbloem (Amsterdam), Frank Huisman (Utrecht), Frank Miedema (Utrecht), Jerry Ravetz (Oxford) and Wijnand Mijnhardt . These individuals voice a deeply-felt uncertainty and discontent on a number of aspects of the scientific system: the tools measuring scientific output, the publish-or-perish culture, the level of academic teaching, the scarcity of career opportunities for young scholars, the impact of science on policy, and the relationship between science, society and industry (www.scienceintransition.nl). Over the past years there has been an overemphasis on Hirsch indices and impact factors, even to such a point that these parameters became of crucial importance in awarding grants, career perspectives, and publication policies [Science in Transition advocate that science should be evaluated on the basis of its added value to society. The public should be given a better insight into the process of knowledge production: what parties play a role and what issues are at stake. Stakeholders from society should become more involved in this process, and have a bigger say in the allocation of research funding.How the dramatic shifts in scientific communication will affect the culture of research and processes for academic advancement and funding is far from clear. One thing becomes evident: science is becoming more of a public activity. Recently, this phenomenon has become a major issue in the Netherlands and has been coined as policies –7. Obviopolicies , 9. ConsAlthough the desired ‘reformation’ of the scientific system might be refreshing and challenging, there are many questions to be answered. How does one measure the ‘added value to society’? How should one directly involve the public in the scientific process? Is scientific research useful when there is no direct clinical, practical, or societal impact ? When ap


All scientific journals, including this one, are concerned about plagiarism. The Publications Committee of the International Organization of Medical Physics (IOMP) had prepared an editorial on plagiarism. The editorial is reproduced here (with permission from the IOMP) with slight modifications to enhance its relevance to the audience of this journal.plagiare”, meaning “to kidnap”) is defined as “the appropriation or imitation of the language, ideas and thoughts of another author and representation of them as one's original work” (The Random House Dictionary of the English Language - unabridged). Plagiarism is a serious breach of research ethics that, if committed intentionally, is considered research misconduct. Plagiarism may result in serious sanctions, including public disclosure, loss of research funding, loss of professional stature and termination of employment. Plagiarism undermines the authenticity of research manuscripts and the journals in which they are published and compromises the integrity of the scientific process and the public regard for science. Plagiarism violates the literary rights of individuals who are plagiarized and the property rights of copyright holders. Violation of literary or property rights' may result in legal action against the individual(s) committing plagiarism. Although plagiarism has existed since the beginning of science, it seems to be increasing because the World Wide Web (Internet) facilitates finding and copying the work of othersPlagiarism  article may be published in two journals, because the journals reach different audiences and the article is of interest to both. This practice must be approved by the editors of both journals, and the duplication must be acknowledged in each articleWhen there is a possibility of plagiarism , the journal's editor should act quickly. The editor should examine the original material and the publication alleged to constitute plagiarism. If the editor concludes that no plagiarism has occurred, the accuser should be notified, and no further action is necessary. If the evidence suggests that plagiarism may have occurred, the editor should contact the accused author(s), the author(s) whose work may have been plagiarized and the copyright holder of the original material if different from the author(s). The correspondence should include the alleged plagiarizing language and a copy of the original and suspected work. If all parties agree that plagiarism  has occurred, a written letter of apology should be sent promptly by the offending author(s) to the editor and to the author(s) and copyright holder whose work has been plagiarized. If the offending work has been published, a notice of plagiarism, citing both the plagiarized and the offending articles and containing the exact text that has been plagiarized, should be published in the next available article of the journal in which the offending article was published. The plagiarizing authors must agree that all dissemination of the offending article will to be accompanied by the notice of plagiarismIf the accused author(s) deny that plagiarism has occurred, the editor must explore the accusation further, preferably through a mechanism already established by the journal to investigate allegations of scientific misconduct. All parties to the allegation should be encouraged to submit corroborating evidence, and the accused author(s) should be granted an opportunity  to testify in person in defense against the allegation. The investigation should be concluded within a reasonable period of time (e.g. 3 months)If the mechanism to investigate the allegation of plagiarism concludes in support of the allegation, then the process for the case in which plagiarism is admitted should be instituted. Further, the editor must decide whether the plagiarism should be reported to the guilty parties' supervisor, employer and/or professional organization. If the mechanism rules against the accusation of plagiarism, a letter stating this ruling should be provided to the accuser, the author(s) accused of plagiarism, the author(s) of the original work and the copyright holder if different from the author(s). In either case, these actions should constitute closure of the allegation of plagiarismAn allegation of plagiarism is a serious accusation and should never be taken lightly. On the other hand, self-policing is a major strength of the scientific community, and plagiarism should always be reported when it is suspected to have occurred


Ayurveda describes five ways to acquire knowledge and create an evidence base. It’s concept of Apta means an unbiased and intuitive acquisition of knowledge from the masters; Pratyaksha refers to observational data acquired through the senses or their extensions in the form of actual experimentation; Anumana is evidence derived from logical analysis leading to a deduction; Upamana concerns evidence generated by analogy (or similar association between variables); while Yukti treats facts ascertained from a planned intervention to test an idea or evaluate an observation. Together, these reflect the epistemology of Ayurveda and its robust approach to ensure evidence based rigor. Today, aet al.[Drosophila research in India, and Valiathan’s significant contributions in medicine and appreciation toward Ayurveda are well known. After receiving communications from these esteemed scientists, as Editor-in-Chief, I took immediate steps to consult the Executive Editor, authors and reviewers to obtain more information. We studied the history of the article and obtained responses from reviewers and authors. I also discussed the article in detail with the Editor, who was responsible for processing this particular manuscript. The editorial policies and circumstances, which led to its final acceptance, are given here. We attempt fairly rigorous due diligence at J-AIM for all papers presented for review. We take into account a background and importance of the study and unique contributions made by authors. J-AIM has a sufficiently large number of competent reviewers from diverse disciplines and in this case they contributed significantly to improvements in the article. The article had undergone nearly 5 months peer review process after its submission on October 20, 2009, until its final acceptance on April 5, 2010.In this light, correspondence published in this issue about the transdisciplinary article by Priyadarshini et al. has a spDrosophila. They claim that their data on specially formulated rasayanas have produced comparable results on all Drosophila melanogaster lines tested. Priyasarshini and her co-authors responded responsibly to the peer review process, agreeing to position their work as a “Preliminary Study”. Priyadarshini requested the Executive Editor to protect details of the rasayana formulation because she wanted to protect the intellectual property. According to the authors, formulating a rasayana acceptable to D. melanogaster was an achievement in itself.The first author, Vaidya Priyadarshini, has been teaching at Government Ayurveda College, Mysore, for many years. She initiated this work in 2007 in collaboration with Asha Devi, who worked at the Drosophila Stock Center of University of Mysore for 17 years. Vaidya Priyadarshini and her collaborators claim to have tested several rasayanas specially formulated for J-AIM is primarily a journal dedicated to transdisciplinary research on Ayurveda. The readership of J-AIM requires some background information, especially for biology related studies. This may justify the relatively long introduction, model description and information related to aging and Ayurveda. I personally agree that the article has many verbose expressions and the style is a little aggressive. But as an editorial policy, we do not impose a particular style on authors and we do give them reasonable freedom to express their point, provided there is sufficient evidence base and scientific support. As an editorial policy, we encourage authors to improve their manuscripts rather than rejecting them simply based on style or other such matters. This is strictly with the objective of providing opportunities for Ayurveda researchers to improve their skills, without compromising either the rigor of the review process or quality outcomes. We think that such hand-holding and encouragement is necessary in the Ayurveda and integrative medicine sector.http://apps.who.int/medicinedocs/en/d/Jwhozip42e/6.3.html). This has been addressed by publishing an Erratum in this issue. We are publishing a letter from Lakhotia along with a response from Priyadarshini et al. , along with a relevant letter from Madan Thangavelu . These communications are self-explanatory. This debate suggests a need for basic orientation to Ayurveda when researching its concepts, therapies or medicines. The same is applicable when researchers from Ayurveda use modern biology protocols. History shows that research that does not consider basic epistemological differences has rarely benefitted science or shastra.I must accept an editorial error of not mentioning this article as a “black box” experiment in accordance with “General Guidelines for Methodologies on Research and Evaluation of Traditional Medicine” (The experience of the last 9 months has led J-AIM to adopt a conscious policy of mentoring authors wherever necessary. We will soon announce a policy of special guidance for authors, under which individual assistance will be provided, e.g., for expert advice on protocols, professional help for correct identification and standardization of botanical materials, as well as for improving language and editing. J-AIM will also announce a new policy for transdisciplinary articles on Ayurveda, giving preference to those where at least one of the authors is an Ayurveda expert.We are still learning our trade, and our website is now beginning to function as it should. J-AIM’s editorial policy is not to reject submissions outright for the need of improved English, style or scientific refinement. Rather, editors and reviewers will offer advice on all such aspects of a paper until promising submissions are brought up to the requisite standard. However, we do encourage discussions, debates and healthy criticism between experts from Ayurveda and other transdisciplinary areas on relevance and scientific value. Longer times between submission and publication may be a necessary price to pay to ensure the scientific rigor without compromising the epistemological reflections. We thank our authors and reviewers for being tolerant and also for their enthusiastic cooperation.


GigaScience. One of the ways we have been doing this is by throwing light on the peer-review process and carrying out open peer-review as standard. In this editorial, we provide our rationale for undertaking this policy, give examples of our positive experiences to date, and encourage others to open up the normally opaque publication process.Fostering and promoting more open and transparent science is one of the goals of  Figshare, F1000 Research, eLife, PeerJ and of course GigaScience), 2012 has been talked of as the year of an “academic spring” that has started to shake up the centuries old, stuffy and closed system of scientific discourse [One of the big scientific trends of the past year has been the high profile that open-access and more open methods of performing science has received. With the Elsevier boycott, the Finch report in the UK, and the launch of a number of innovative new schemes in publishing open-access research and data (including Biology Direct and F1000 Research), pre-print servers, providing access to anonymized  or partial parts of the peer-review history (e.g. eLife), or encouraging reviewers to opt-into open peer-review .On top of changes to the way scientists and readers are demanding they can access and mine the literature and data, and with the new incentives and mechanisms to release and publish data, the process and deficiencies of peer-review has also come under the spotlight. Developing open source software is collaborative and interactive and so, if much of the scientific community are comfortable and find it constructive working in this manner, there is no reason why peer-review should not follow a similar process . Many neGigaScience, we have decided to take this process one step further and ask for open peer-review as default, and as our aims are to promote more open, reproducible and transparent-science, we feel it promotes accountability, fairness, and importantly gives credit to reviewers for their hard efforts. Our co-publisher BioMed Central is a pioneer in this area, and on top of the BMC Series medical journals having open peer-review since their launch in the year 2000, our stablemates and fellow data-focused journals, BioData Mining and Biology Direct, also have been following open models for a number of years as well.At GigaScience, it is now a good time to look back and highlight how it has gone so far. Last month provided an excellent example of this where we published an updated version of BGI’s popular SOAPdenovo software application, a state-of-the-art tool for de novo genome assembly [Tailoring our peer-review process to handle such data heavy articles has been a learning process, but now that sufficient examples of peer-reviewed  content have been published in assembly .GigaScience uses a much more transparent, accountable and open peer-review process. Tailoring the process for such data heavy studies, our criteria for publication is based more on the relative amount of data created or used, and transparency and availability more than subjective and unpredictable measures such as supposed “impact”.Stating that a software application can perform better than other computational tools with the same functionality is one thing, but to justify and prove this in review, testing by independent peers is needed, and the larger and more complicated a study and its associated data is, the more challenging this can be. In order to ease, throw light and credit the reviewers in this process, http://www.gigasciencejournal.com/content/1/1/18/prepub).During peer review, we can host all of the supporting information and data  and our curators make all of it available to the peer-reviewers from our FTP servers. In the case of SOAPdenovo2, we worked with several groups of expert reviewers who thoroughly tested the software against various tools and datasets to ensure the claims made by the authors were correct. In this case, all 8 reviewers consented for their names to be in their reports that are now available to view from the pre-publication history section associated with our published articles , as well as have the option to opt-out and have their name removed from reports if they have reasons to remain anonymous.One of the main arguments for the anonymous peer-review system is that “anonymity creates a safe place”, and more junior researchers may be reluctant to be critical of more senior authorities in their field for fear of comeback or to curry favour . To counDespite offering this opt-out, it is encouraging that none have asked to do this for all of the papers we have reviewed so far. The reports from our reviewers have generally been very constructive, and previous studies on open peer-review have also found that quality and courteousness of reviews were increased , with liGigaScience also carries this over to the publication process, of which this paper is also an excellent example. In addition to SOAPdenovo2 meeting our requirements of being open source and having its code hosted in a repository, the authors provide detailed pipelines with the tools including the commands and necessary utilities to reproduce the different tests carried out in the paper. The SOAPdenovo2 paper is associated with 78 GB of test data, tools and scripts, which is much larger than other journals are currently able to handle, and these have been made available from our http://gigadb.org database as separate citable DOIs.On top of improving transparency and reproducibility during the peer-review of data-heavy studies, We feel that it is important to credit methodology as well as data production, and whilst we have previously published data packages combining reference datasets and tools before, SOAPdenovo2 is the first paper that we have given separate DOIs to the tools  and dataAs this process is still evolving and being fine-tuned, we would welcome any feedback. Many journals are tentatively starting to experiment going down a partially more open route, but from our positive experiences so far we would encourage them and others to be bold and embrace full transparency.GigaScience and BGI Hong Kong.The author is employed by GigaScience.SCE wrote the editorial based on the editorial policies of


The following information is missing from the funding section: The charge for this publication was covered by the German Research Foundation (DFG) sponsorship "open access publication".


With comments provided by Terry Erwin, Eike Neubert and Lyubomir PenevZooKeys paper and to discuss broader issues relating to the editorial procedures used by this important journal. The paper of concern, titled “Two new species of Tornidae  from Espírito Santo, Brazil,” was published by Luiz Ricardo L. Simone in ZooKeys 238: 77–85 on 6 November 2012. Grammatical errors begin to appear in the first sentence of the abstract. Not only are sentences sometimes incomplete and improperly constructed, but there are some instances where their meaning cannot be determined. For example, what sense can be made of “since specimens with periostracum to eroded shells” (p. 78)? The language problem is most troubling in the descriptions of the shells where there are constructions such as “On aperture, region between ridge of superior carina and insertion of outer lip in adjacent preceding whorl a small region with ridge of peripheral ridge reabsorbed, forming anal notch with ~ 1/5 of aperture size” (p. 79). Simone is no newcomer to English language publication (see here1 for a list of his publications), but it appears that he used a machine translator for portions of this paper instead of relying on an English-speaking colleague.The purpose of this letter is to point out some shortcomings in the editing of a recent PageBreakComment:ZooKeys has well-defined policies for English language editing. During the submission process, authors are warned that manuscripts should be submitted only after being edited by a native English speaker. Authors have to confirm by checking a tick box that they have followed the above requirement. Unfortunately, it happens that some authors provide incorrect information on the language editing of their manuscripts.Involving outsourced language editing services by Pensoft would visibly increase the price of the open access fees charged by the journal, which shall become an additional obstacle for persons and institutions to publish in ZooKeys. Therefore we rely both on the conscience of our authors to provide stylistically proven texts and our editors to filter out badly written manuscripts.ZooKeys Author Guidelines are: “All papers should be in grammatically correct English. Non-native English speaking authors are required to have their manuscripts checked by a native English speaker prior to submission.” Surprisingly this is left to the author as the Guidelines state that “reviewers are not expected to provide a thorough linguistic editing or copyediting of a manuscript.” Removing that burden from reviewers is understandable, but the same wording appears in the instructions for Subject Editors.The first two sentences of the Comment:ZooKeys provides basic copy-editing but not linguistic editing of the manuscript. We do not expect that our reviewers and editors should spend their precious time in thorough editing of the English language. Nevertheless, many of them do this on voluntary basis and we greatly appreciate their efforts!Cyclostremiscus species described by Simone. However, it is not possible to determine exactly what is perisotracum in Figures 1–5 as there is no visible demarcation, or any indication of such, between shell and periostracum. The poor quality of this plate is compounded by the unintelligible description of the species which makes it difficult to understand why all of the shells in Figures 1–15 are treated as conspecific. In the Guidelines, ZooKeys lists six items under Focus & Scope. The second of these requires, for a new species, a thorough description with good quality images, neither of which is present in this paper, and the third requires a differential diagnosis. One may assume that Simone performed these tasks in an original Portuguese version of the manuscript, but it should have been properly translated. A fourth item required is an identification key. Keys are rarely used by malacologists and this requirement was obviously, and appropriately, waived for this paper.An unusual periostracum is an important feature of the Comment: PageBreak clear to me on the first sight, so there was no direct need to add something. I agree, in the caption this could have been mentioned again. However, I do not agree that this is a plate of poor quality, particularly if you consider the small size of the objects! We all know that it is quite difficult to take pictures of shells with a size of 2.5 mmIn his text, Simone describes the periostracum in a separate paragraph, and this structure can be clearly seen on the figures cited. On the intermediate carina, these structures are obviously somewhat darker, which might be due to sand grains that adhere to the periostracal rods. He could probably have added an arrow to explicitly pinpoint these structures, however, the description of this peculiar feature was.Secondly, a differential diagnosis is present. Simone compares his new species to three other species, namely C. beauii, C. pentagonus and C. trilix, in the paragraph discussion.Cyclostremiscus mohicanus. Given the current state of knowledge of the Tornidae it is highly possible that this species may eventually be placed in a different genus. As mohicanus is not a Latin word, in the absence of its etymology it may present problems should it be placed in a feminine or neuter genus. The only Brazilian usage of this name located is for its use to describe the haircut style of a noted Brazilian football (= soccer) player. There can be no objection if that was the author’s intent, but is it an adjective (he had a mohican haircut) or a noun (he had a mohican)? How it would be used in Portuguese is not known. I encourage Simone to publish a note providing the etymology of mohicanus.The fifth required item under Focus & Scope of the Authors’ Guidelines is Etymology. Simone describes two new species in his paper. A complete etymology is given for one, but there is no etymology for the new species Comment:As explained to me by Dr Simone, the species epithet “mohicanus” is derived from the Indian tribe name “Mohican” and used here as a simple adjective. As the gender of the species epitheton is determined by the gender of the genus, the grammatical form “mohicanus” is correct, because Cyclostremiscus is of male gender. In case this species is transferred to another genus with a female or neuter gender, it turns to “mohicana” or “mohicanum”. In case this name would have been a noun in apposition, it would remain in its original form. This problem could have been avoided by publishing an etymology of the species epithet, and I am grateful to Mr. Petit for drawing our attention to this failure, for which I take responsibility.”Episcynia is misspelled as Episcinia in the abstract and twice on page 81. Also, “” appears in the text as “.” Neither this Bush paper nor a number of other cited papers are listed in the References. An omission of a listing in References of all cited items for a ZooKeys paper is strange as the instructions to authors stress the importance of cross-checking all entries “because all references will be linked electronically as completely as possible to the papers cited.” Failure to follow the guidelines, especially in this instance, reflects unfavorably on both the author and the editor and unnecessarily raises the question of whether or not the author ever actually saw a cited work.Every author has had a paper appear in print with typographical errors that should have been caught by him/her and were overlooked by reviewers and editors. Simone’s paper did not escape such error as ZooKeys that are on non-opisthobranch shelled marine gastropods .Implementing of thorough copy-editing services would visibly increase the open access fees. The authors would suffer from price increase the most, hence we are convinced that the authors, with the help of the editors, reviewers and journal’s Editorial Office should take proper care to bring their manuscripts into a shape corresponding to the journal’s style requirements.ZooKeys in the citation of references where authors’ initials not only lack periods, but are written together and without a comma after the family name. Thus a 1974 paper by R. T. Abbott is listed as “Abbott RT (1974).” Perhaps it is this usage that is responsible for the disconnect in the authorship of ZooKeys papers by authors with Spanish surnames. As an example, the paper by Caballer has as authors “Manuel Caballer, Jesus Ortea, Samuel Narcisco.” The abstract of this paper posted on the ZooKeys web site shows authors as “Manuel Caballer Gutierrez, Jesus Ortea, Samuel Narciso.” If Caballer Gutierrez did not wish for his full name to be used, how did it get on the abstract? The abstracts of other papers by Spanish authors are similarly treated with the names on the abstract not in agreement with the names on the paper.Another unfortunate editorial feature is the elimination of periods after abbreviations, the reason for which is not known. This is further compounded in Comment:PageBreakIt is a practice in many modern electronic journals to avoid periods after abbreviations and generally to simplify citation and reference style . Such a simplification makes the process of markup and text mining easier, which in turn facilitates the dissemination and use of the published information, to the benefit of the authors and science community as a whole.ZooKeys Subject Editors for most groups is impressive, with some groups and areas being quite restricted. For Mollusca there is one editor for “terrestrial slugs, Northern Hemisphere” (Andrzej Wiktor) and another for “terrestrial gastropods, Northern Hemisphere” (Eike Neubert). The latter is in addition to a listing of Anatoly A. Schileyko as editor for “terrestrial gastropods.” The editor for Opisthobranchia is Nathalie Yonow. The only other Mollusca editor is Bruce A. Marshall for “shelled marine mollusks.” Other categories  are listed without editors.The list of ZooKeys submissions have apparently not been assigned to the appropriate editor. Of the seven papers published on shelled marine mollusks, the only one on opisthobranchs was edited by “Guest Editor Herman Strack”, presumably as it was written by the Opisthobranchia Editor Nathalie Yonow. Of the three papers on marine bivalves, one was edited by Marshall and two by Yonow. The only three papers on shelled marine gastropods were all edited by Neubert. An eighth marine mollusk paper, on cephalopods, was edited by Marshall. Dr. Marshall advises  that he has no knowledge of the papers on shelled marine mollusks that were edited by others.These editors are detailed here because there is a serious question as to why, with such specific appointments, molluscan Comment:For some reasons, it was difficult to assemble an editorial group responsible for mollusks in ZooKeys. Probably this is due largely to the fact that the community studying this large group of animals has established specialized society journals, thus many active specialists on Mollusca are engaged elsewhere as editors.Currently, Global Editorial Networks (GENs)2 to extend the focus and scope of the journal to areas close to or beyond taxonomy in its narrow sense. Specialists who wish to serve as subject editors in various subject and taxa, Mollusca included, may apply using the following link3ZooKeys is undertaking an initiative, called .ZooKeys editor? As shown above, neither the editors nor reviewers for this journal are expected to correct English usage. A cynical conclusion would be that ZooKeys is a venue for publishing a paper in which the English is less than minimal as an editor can be selected whose first language is not English — simply pay minimal page charges and bypass editing. I am not alleging that this has happened, but it is a possibility that is hard to ignore.Are authors in some way allowed to choose a Comment:PageBreakguage editing in ZooKeys is a responsibility of the authors. It would be quite an exaggeration to generalize that “Zookeys is a venue for publishing a paper in which English is less than minimalAuthors have no influence on selecting the editors of their manuscripts. Editors are assigned by the journal’s Editorial Office. We stress again that the lan” based on a single or few examples of papers published in not properly edited English language.ZooKeys Bioinformatics Advisory Panel argues against any prejudice toward American authors. On the other hand, not only are there are no American Editors for Mollusca, the only two whose first language is English are Marshall and Yunow (inclusion of the latter is a guess based on her background—it is suspected that her English is superior to mine). Why were the only three papers on shelled marine non-opisthobranch gastropods edited by an editor (Neubert) whose first language is presumably German? As Dr. Neubert has published many papers in fluent English the core problem appears to be the failure of the Author Guidelines to require any supervision or correction of English. Indeed, the wording of the Guidelines is such that reviewers and editors are expected to expend their efforts on scientific quality and style. However, there is a provision that an editor can reject a manuscript for “poor English.”The presence of a number of American systematists on the Comment:There is no, nor has there ever been, prejudice against either American authors or editors, nor against such from any other nationality! Invitations to American malacologists to join the board of ZooKeys have been sent several times in the past, but unfortunately these have been declined.The presence of many native English speakers in the Editorial team of ZooKeys is understandable and has a great value for the journal. On the other side, there are also many other excellent editors from non English-speaking countries, which reflects the truly international character of the journal and of taxonomy as a discipline in general.It would be unrealistic to rely exclusively on the services of native English speakers as editors and reviewers, just because they are expected to correct the language of the submitted manuscripts.ZooKeys web site, as of 17 November 2012, lists by category the 1,014 papers it has published. Of that number 891 are on Arthropoda. These numbers may not be current as 22 papers on Mollusca are listed but 26 have been counted.The Comment:Numbers are derived from the articles’ metadata. The above figures will be checked and corrected.ZooKeys has become an important publication venue in systematic zoology, it would be advantageous for the journalto use editors who are familiar with the subject matter. There is also an obvious need to find some way to insure that English is used in a manner that can be understood. Minor grammatical errors can be accepted but wholesale misuse of the language should not be allowed. Unless the editing processPageBreak is tightened up, it is unlikely that the malacological community will make much use of the journal.Now that ZooKeys performed no favor for Simone by publishing his poorly presented paper. Accepting and publishing a work that is basically unintelligible was a disservice to Simone and to ZooKeys and detracts from the credibility of both.Comment:We fully agree with this general conclusion and thank you once again for raising the question. We are convinced that this case will be used to improve the control over the quality of English language editing of the manuscripts submitted to ZooKeys.


Endocrine Connections, a new Open Access journal offering authors the highest possible visibility for their work and stimulating cross-discipline collaboration. The journal is brought to you by the European Society of Endocrinology (ESE) and the Society for Endocrinology (SfE), working together to further research, education and clinical practice in endocrinology.Welcome to Endocrine Connections allows free permanent access to endocrine research on a global scale, ensuring wide dissemination. Work published in Endocrine Connections can be freely accessed by all, providing a unique opportunity to connect with your colleagues in intersecting disciplines. This is something that may not be possible when publishing in traditional endocrinology journals.The journal will publish original quality research and reviews in all areas of endocrinology, with a focus on papers that have relevance to its related and intersecting disciplines and the wider biomedical community. The endocrine system influences a myriad of cells and tissues within the body. As such endocrine research is often of relevance to other biomedical fields, with examples including, but not limited to, cardiology, dermatology, immunology, neurology and oncology. As an Open Access journal, As an Open Access journal, papers are published under the Creative Commons Licence 3.0. This means authors retain full copyright of their work and users are free to copy, distribute, transmit and adapt the work for commercial or other purposes, provided the work is properly attributed. It also means authors who are mandated by a funding body to make the paper Open Access can easily comply.Endocrine Connections will assess papers for broad appeal.An international editorial board has been appointed, which includes a world-class team of senior editors with a broad range of expertise, who are responsible for handling submissions within their subject area. A broader editorial board is committed to acting as expert reviewers. This editorial structure will allow us to provide rapid responses to authors; we aim to return a decision within 15 days of receipt whilst still maintaining high-quality peer review. Papers will be assessed on the quality and originality of the work presented; a judgement on the perceived level of interest will not be made, as is often traditionally the case. Instead, Unedited manuscripts will be published within 24 hours of acceptance and the journal also has a continuous publication model, meaning the final version of record is published as soon as it is ready, without having to wait for assignment to an issue. Together, these factors will ensure that papers will be citable immediately.We strive to encourage collaboration for the benefit of biomedical science as a whole and, as endocrinologists, we are keenly aware of the need for an interdisciplinary approach to clinical work as well as to clinical and basic research. Please submit your work to the journal and show your support for this new endeavour from ESE and SfE. In return, we will provide fast, high-quality peer review and rapid, instantly citable publication at the same high-quality standards employed by the other official ESE and SfE journals.We look forward to receiving your submissions.


Medicine and medical journalism are both noble professions. Those who are infected with the materialistic virus and want to make quick money should not take up these as professional careers. Editing a good quality peer reviewed medical journal in a developing third world country is extremely frustrating. An editor has to work under considerable stress and strain, and face numerous pressures. However, it is a joy and pleasure to be a successful medical editor. The mere fact that one can help so many authors and influence decision makers in the medical profession, health officials, pharmaceutical trade and industry and all others connected with the health sector gives tremendous professional satisfaction, which is invaluable and keeps one motivated. I have always believed that medicine as well as journalism are both noble professions and anyone who wishes to make quick money should never take up these fields as professional careers. In the practice of medicine, one gets the prayers and blessings of patients who are looked after; and seeing some one overcome disease to become a useful healthy member of society once again is, indeed, satisfying. These feelings of professional satisfaction - whether one successfully treats a patient, teaches and trains students and juniors, or gets involved in useful research - keeps one stimulated and motivated.My entry in the field of medical journalism was a pleasant accident. I was keen to become a doctor but ended up becoming a medical editor. Even otherwise, for people like me who come from a lower middle-class background, planning a career is a luxury we can ill afford, as one is at the mercy of circumstances. However, sincerity to one's selected field and devotion pays; and the end result is a precious diamond well cut out from a rough edged stone. God Almighty has always been very kind to me and my wish to be a doctor was fulfilled to a great extent through all of my three children who became doctors, and are currently practicing in the fields of Medicine, Surgery and Psychiatry.Medical journalism is a highly specialized field. Editing a quality peer reviewed medical journal in a developing Third World country is at times frustrating and a highly stressful job. It is just like giving birth to a baby, a very painful but equally pleasurable activity. Anyone going through this exercise once eventually relishes it so much that one keeps on doing it again and again.Editors of peer reviewed medical journals face enormous problems . Since tThe problems one faces while editing a medical journal are as outlined below.Instructions to Authors. They are not aware of Uniform Requirements for Submission of Manuscripts to Biomedical Journals as approved by International Committee of Medical Journal Editors . Hence it is not uncommon to find that at times the total of numbers in tables, abstract and the manuscript differ, percentages calculated are wrong, legends of figures, illustrations are missing, or references are not cited in the manuscript. Some even do not know how to write a structured abstract. Presentation itself is extremely poor, hence not suitable to be sent for peer review. Poor English in some of the manuscripts, incorrect statistical analysis, failure to respond to queries in time or communicating change in address, incomplete references where even the editors and reviewers cannot do much, are some of the other problems which make the life of an editor miserable.Most of the contributors do not read One has to be a good writer before one can review a manuscript, and finding good quality reviewers is not easy. Co-ordination between authors and reviewers is an uphill task. Keeping track of manuscripts, sending reminders to reviewers, satisfying authors is equally difficult. At times, the quality of the review may not be satisfactory, or the reviewer may fail to give clear guidance as regards approval or rejection of the manuscript, necessitating it to be sent to another reviewer. One has to be constantly on the look out to update the reviewer's database. Editing a journal is a team-work. A journal is as good as its Editorial Board helped by the reviewers. Since most of the reviewers do this job honorary, editors cannot be strict with them to keep to the deadlines.Medline is not easy for many journals. At present, only three out of about forty medical and dental journals published from Pakistan are included in Medline. However, over a dozen are covered by EMBASE, while quite a few are covered by ExtraMED, the Index Medicus of the WHO EMRO region. Some authors are always eager to get manuscripts published in journals covered by Medline as it ensures greater citations; hence attracting good quality manuscripts is a problem.Getting indexed in Medline. My interaction with many Indian authors and researchers gives me an impression that they are imbibed with a nationalistic spirit; hence they feel proud to publish their research work in their own journals. We expect similar practices in Pakistan. Unless authors publish good quality manuscripts in their own journals, how is their quality going to improve?The situation in India appears to be much better with a large number of journals covered by During the last ten years, the situation has changed a lot. Now authors are required to disclose their source of funding, if any, and also get their manuscript approved by the Institutional Ethics Committee and Institutional Review Boards (IRBs). If no such body exists, approval from any regional or national body is considered a must. However, in many cases, investigators do not meet these requirements, creating lot of ethical problems for editors while reviewing and editing such manuscripts.A vast majority of healthcare professionals have not developed a habit of reading, hence they never subscribe to a journal, and particularly so from their own countries. Libraries have no funds to subscribe to journals, either because institutions do not give it any priority, or no funds are allocated for this purpose. Advertising remains the major source of income but the pharmaceutical industry is more inclined to influence the doctors′ prescribing habits by looking after them in so many other ways, including all sort of unethical marketing practices. Hence advertising in journals is not on their priority list, either. At times, even if they do advertise, they try to influence the editorial policy despite the fact that advertisements placed by the pharmaceutical industry in medical publications all over the world is considered a legitimate support which is to the mutual advantage of industry as well as medical publishers. Hence an editor has to be extremely careful not to compromise on the credibility of the journal by succumbing to any of such pressures. I have had my share of such problems, but God Almighty gave me the courage and inner strength to face such situations.The Lancet published similar findings , we were told that this case report was earlier sent to an Indexed journal which had rejected it. Hence, we should not publish it. However, we went ahead with the peer review process and both the reviewers recommended its publication. While the journal was still under publication, one of the reviewers informed us that his own uncle, who was a cardiac patient, had died due to this antimalarial which was prescribed to him by their family physician. Had he not reviewed this case report, he wouldn't have known about it. He felt that this case report be published as soon as possible to save more lives. Its publication  spoiled Most standard peer reviewed journals insist that authors give a written undertaking regarding exclusive submission and confirm that the manuscript submitted is an unpublished material. Even after giving such a written undertaking, some authors do indulge in simultaneous submission to more than one journal. Editors have to trust the authors and they cannot act as policemen. Sometimes, such duplicate submissions are detected before the manuscript is published. But in other cases, it may escape the attention of reviewers as well as the editor.When I had to take action of black listing such authors and also decided to convey the decision to their employers as well as concerned government agencies, departments, regulatory bodies like Pakistan Medical and Dental Council, it was a very unpleasant experience. In such situations, an editor should be prepared to face the wrath of such unethical authors. It could even pose a serious threat of physical assault, including security of life. Here again I had my share of such episodes .Dr. A had submitted a manuscript for publication and also gave a written undertaking regarding exclusive submission to our journal. He was helped by the reviewers to re-write and revise the manuscript. However, he got it published in another journal without withdrawing it from our journal. We came to know about it while the journal was being printed. We had to delete that manuscript, re-number the pages before printing, all at a great financial loss. We wrote to the author who stated that he had never sent this manuscript to the other journal and he was not at all aware of its publication. He was obviously lying: how could the other journal get a manuscript unless the author provided it? We informed about this unethical practice to his employers, the institution head, Pakistan Medical and Dental Council as well as the Higher Education Commission. The author wrote us a letter stating that his professional career was at stake and if anything happened, he wouldn't spare us. We were prepared to face the consequences but luckily there were no further developments.In yet another case, a faculty member submitted a manuscript and wanted to get it published quickly. He was worried since his retirement was due within a couple of months, his wife had already been promoted as Professor and he did not want to retire as Associate Professor. He even approached about half a dozen senior professors to ensure that his manuscript was accommodated early. As a special case, we got it reviewed and processed on a priority basis and published it after due peer review process. However, soon we were informed that two of the tables and a paragraph were copied from another article published by another author some years ago. Somehow we could not detect that fraud during the peer review process. We retracted that article and also informed about it to the author, his institution head, provincial health department and the Pakistan Medical and Dental Council. The author suffered a severe myocardial infarction and was admitted to the Coronary Care Unit. His wife made a threatening phone call saying that if anything went wrong with her husband, she would sue us. Luckily he survived and eventually retired as Associate Professor.Nothing could be more frustrating for an editor than to find out that after an author has been helped to revise and improve his/her manuscript, the authors send it to some other journal just to get it published early. Or for them to ask that their manuscript be withdrawn at such a late stage that the paper has already been scheduled to be included in a forthcoming issue, or is already in the press.As an editor, I am not happy, in fact, it is always painful to reject a paper that fails to meet the minimum required standard, or suffers from serious deficiencies. But I believe rejection of a manuscript is just like amputation, which can be life saving. It acts as a barrier to dissemination of wrong information. I believe an editor, who is not knowledgeable and is inexperienced, can be a very dangerous person; he can mislead and misguide many, and that can have serious repercussions.British Medical Journal (1947–1965) had stated:Hugh Clegg, Editor of the A medical editor has to be the keeper of the conscience of a profession and if he or she tries to live up to this ideal, he/she will always be getting into trouble . - all these have helped me achieve the present position.For an editor, financial considerations should never come in his way while performing his duties. Even in today's materialistic world, it is my firm belief that one can earn a decent living while keeping up professional ethics. One has only to be a contented person and carefully watch the dividing line between Pharmaceutical industry is the major source of revenue for medical journals through advertising. At times the journals are faced with a dilemma when the industry tries to influence the editorial policy as regards publication of clinical trials or adverse drug reactions. What course should medical journals pursue to ensure an independent policy while at the same time ensuring sustained continued publication?Local dose finding studies are now compulsory in many countries before registration of a new drug. If any healthcare professional observes some unwanted side effects even after local dose finding studies have declared the drug to be safe, should it be discarded, or it is better to have another look at the safety of the drug and earlier dose finding studies?Simultaneous submission of manuscripts to more than one periodical by authors is a serious problem faced by medical journals. Editors cannot act as policemen and they have to trust the authors when they give a written undertaking regarding exclusive submission. Even after giving a written undertaking, if an author indulges in unethical practice of simultaneous submission, what can the editors do to discourage this practice apart from black listing such authors and conveying this to their employers, institutions they are affiliated with, as well as concerned government agencies?If a manuscript is rejected by an indexed journal, it does not mean this does not merit publication. If the authors submit this manuscript to another journal, should it be entertained and published after proper peer review? Secondly, is it essential for the authors to disclose that this manuscript was earlier submitted to another journal and the reasons why it was rejected? Thirdly, will such a disclosure affect the decision of the editors to accept or reject the manuscript?Doctors in developing third world countries are usually afraid to report any adverse drug reactions because they fear losing the cozy relationship they enjoy with the pharma industry which offers them many benefits. This is an important reason why setting up ADR Monitoring Centers has not been a success. What measures should be taken to encourage and convince them that such adverse drug reactions are regularly reported to concerned ADR monitoring centers and agencies so as to save the patients unnecessary side effects which increase morbidity, and at times could prove fatal?Shaukat Ali Jawaid is one of the senior most medical journalists of Pakistan active in the field of medical journalism since 1966. Currently he is Chief Editor, Pulse International, a fortnightly medical newspaper, and Managing Editor, Pakistan Journal of Medical Sciences, a peer reviewed medical journal. He is former Founder President of Pakistan Medical Journalists Association, Member British Medical Journalists Association, and Vice President at large of Eastern Mediterranean Association of Medical Editors (EMAME). He is also General Secretary of Pakistan Aspirin Foundation and Member, National Bioethics Committee constituted by Government of Pakistan. He has authored thirteen books on topics like Medical Writing, Medical Ethics in Contemporary Era, Aspirin- the life saving miracle drug, Medical Men and Women of Pakistan etc. He is regularly invited as facilitator at workshops and seminars on Medical Writing and Medical Ethics. He has thirty scientific papers to his credit.


Biological Procedures Online has been transferred to the open access publisher BioMed Central, a powerhouse for the timely publishing of articles in online journals.We are excited to inform all previous and future contributors, as well as readers, that I am honored to continue to act as Editor-in-Chief, serving alongside editorial board members from various well-renowned institutions. In joining BioMed Central, we are confident that the journal will have a much stronger impact in the near future. Based on the many high quality publications published in 2009 and 2010, it is our belief that our impact factor will make a strong recovery next year.Biological Procedures Online is an open access, peer-reviewed journal which publishes articles that improve access to techniques and methods in the medical and biological sciences. Articles feature step-by-step protocols that allow researchers to implement methods in "cookbook" fashion at the bench top.Biological Procedures Online is interested in any small or large technical innovation in the field of biology, with an emphasis on biomedical science. Our special interests include: technological innovation related to stem cells, siRNA, genomics, genome sequencing, nanomedicine, drug delivery and experimental protocols. We welcome research articles, case reports, reviews, commentaries, methodology articles and short reports.Biological Procedures Online will be freely available for anyone to view. Biological Procedures Online defrays the cost of the publication process via article-processing charges because it does not have subscription charges for its content. This policy allows open access journals to reach a much larger audience than subscription-based journals [Biological Procedures Online is also indexed by a number of prominent services, including Thomson Reuters (ISI), BIOSIS, CABI, CAS, EmBase, Scopus and the Zoological Record.By continuing to publish as an open access journal, all articles published in journals , with thjournals ,3. The jjournals , complyijournals -8. BioloBiological Procedures Online will be subjected to a quick and impartial closed peer-review process. The Editor-in-Chief/assigned editors will initially examine the manuscripts to check the animal assurance and proper handling of human tissues. Based on a review of the results, and the recommendations from the assigned editors, the Editor-in-Chief will inform authors regarding acceptance of their manuscripts. Upon acceptance, the articles will appear online immediately and be posted on PubMed soon after.All manuscripts submitted to Biological Procedures Online forward with BioMed Central and look forward to receiving research articles, methodology articles and protocols for consideration.We are delighted to be taking


Over many years, EAACI have focused on publishing two major journals, Allergy as well as Pediatric Allergy and Immunology (PAI). However, these two excellent journals alone are limited in their ability to publish a considerable number of articles despite their quality, and therefore are insufficient to provide the required platform for communication of many high quality scientific papers for the EAACI community. Consequently, in the last years it has become evident that new journals need to be established by the Academy. It was also felt that Open Access was crucial for any new EAACI journal, as many funding bodies today require the research to be published in this way, and open access makes published research available to the general public, without any need for subscriptions. A key principle for CTA will be to provide a very rapid and fair review process for all submission, and we hope the journal becomes a favourite for your, and the allergy, asthma and immunology community as a whole. Further, all manuscripts accepted for publication in CTA will be immediately published online, as the publication date is not at all dependent on publication of a printed issue, as is the case for print journals.It is with the greatest satisfaction and pride that the European Academy of Allergy and Clinical Immunology (EAACI) today can launch its first open access scientific journal, CTA is to provide a platform for the dissemination of original allergy-immunology research, exciting reviews as well as EAACI-developed position papers. Today, at the launch of the journal, one position paper and three exciting reviews are published, and several recently submitted original research papers are under consideration. Firstly, a very long-term effort in developing an EAACI position paper on diagnostic tools in rhinology is published in CTA [CTA will publish. Beyond clinical experimental research and epidemiology, CTA will certainly also accept any studies using animal models of any allergic process, and immunological research related to allergic disease.The aim of d in CTA . This pud in CTA , discussd in CTA , consided in CTA , examineThe field of allergy concerns the most common group of diseases globally. Allergic diseases have grown rapidly in prevalence in the industrialized world, and are now rapidly growing in developing countries. It is considered that diseases of the immune system, such as allergic diseases, are best explained through a clear grasp of normal immune mechanisms and the ways by which these processes become dysfunctional. This is one of the explanations of selecting the name of the journal, including the key word "translational", since it is likely that the most interesting future results will evolve from truly translational research. Therefore, manuscripts describing research that utilises several techniques to prove a key biological process, or explaining effect of a treatment, will receive extra attention by the journal.CTA will be externally peer reviewed, to achieve independent input on the quality of the research, the appropriateness of any review, and the quality of the research presented. The written English will also need to be of very high quality for any manuscript to be considered by the journal. Importantly, the Editor's decisions remain independent, and are not only based on reviewer's comments and suggestions, but also on priorities made by the Editors. The current editorial board of CTA has primarily been recruited among leaders within the EAACI community . However, applications for membership in the Editorial Board are welcome by e-mail, including an attached Curriculum Vitae and specified field of interest.Each manuscript submitted to CTA will charge a nominal fee for any article published, which will have to be covered by the authors of the article. This is becoming a common approach for many scientists preferably publishing in Open Access journals, and the total cost for publishing in CTA is lower than for subscriptions to other journals. The nominal fee for publishing in CTA is currently £1095 (€1250). As for all BioMed Central journals, authors from countries listed in the World Bank low or lower-middle income bracket are automatically granted a waiver of the publication charges, to ensure that inability to pay is not a barrier to publication [One advantage with the open access system is the availability of the published research online. However, any publication process costs money, and since there is no subscription income to open access journals, the cost will have to be covered by the publishing authors. Therefore, CTA is established not only for the benefit of EAACI, but for the good of the global allergy community. Again this is well illustrated by the first published reviews [Last, but not least,  reviews -4, incluClinical and Translational Allergy, Current EAACI PresidentJan Lötvall, Editor-in-Chief - Clinical and Translational Allergy, Current EAACI Vice President Communication and MembershipVictoria Cardona, Managing Editor -


Theoretical biology encompasses a broad range of biological disciplines ranging from mathematical biology and biomathematics to philosophy of biology. Adopting a broad definition of "biology", Theoretical Biology and Medical Modelling, an open access journal, considers original research studies that focus on theoretical ideas and models associated with developments in biology and medicine. Theoretical Biology and Medical Modelling (TBioMed), a 10 year old online journal, has steadily grown since its first launch in late 2003 as an independent journal of BioMed Central (BMC). Included in PubMed and PubMed Central and indexed by SCI for an impact factor, the journal has increasingly attracted a broad scientific audience, who are interested in mathematical modelling studies in biology and medicine [TBioMed, from June 2013, on behalf of all scholars in the community. We act as successors of Dr. Paul Agutter, a medical expert and mathematical modeller, who has made a respected effort to cultivate the field, grow TBioMed and let the journal be recognized across the world.TBioMed which we regard as advantageous for the authors and readers and we aim for these to remain unchanged. First, as an independent journal of BMC, TBioMed has continuously been an open access journal. The open access journal can permit all scientists across the world to have unrestricted and unlimited access to every single study in the field of theoretical biology and medicine. Instead of printing and selling the journal, the authors pay an article processing charge, thereby allowing all readers to download via internet and print the article at free of charge. Second, the online journal has another advantage for submitting authors, in that authors do not to have any limitation on the number of pages or figures and data that can be included, per article. For instance, the authors can decide whether a rigorous mathematical proof should be included in the main text or in the online only supporting material. Third, TBioMed makes a difference from other journals, in fulfilling the scope of the latter half of the title “Medical Modelling”, and attracting medical studies that are useful in applications to diagnosis, treatment and prevention. In fact, many published studies have been operational and directly applicable to existing medical problems. Fourth, the length of peer review is kept shorter than those of other journals in theoretical biology and medicine. We make an effort to ensure a fast review process, as we understand that operational studies cannot wait for months and years to reach publication, even when the study involves rigorous mathematical and analytical exercises.There have been four notable characteristics of PLoS Computational Biology or Journal of Theoretical Biology. Otherwise, original modelling studies are frequently considered by interdisciplinary journals, that remain to be rather broad and have very little restriction in the content (e.g. PLoS ONE). In relation to this point, we believe that TBioMed can beautifully fill its biomedical modelling niche, and indeed, the scope and standpoint of TBioMed are in line with this notion. We aim to offer a platform to publish, read and discuss relatively unrestricted studies, at the same time as having good quality control of the scientific content.In the field of theoretical biology and medicine, publications of new studies have tended to be restricted to those with an explicit methodological advancement and those significantly improving our understanding in biology. These types of publications, in particular, are seen in other good journals that have restricted scopes, such as TBioMed[Under the Open Access publishing model, authors need to consider the financial support available to them to cover the article processing charge for publication in TBioMed. For autTBioMed and authTBioMed is low to moderate, i.e., 1.46 in 2012, and other citation metrics are not substantially high (e.g. Eigenfactor is 0.00182). One of the most important roles for us during the next few years is to ensure greater impact and better metrics of the journal. Not only to recover and improve the impact factor, but we also aim to compete with and replace the aforementioned journals in the same subject category. We plan to promote special issues on topical subject areas and publish other special materials including award lectures. Moreover, we aim to contribute to education among students and early career researchers, and we will also consider a series of solicited review articles, written by invited leading scholars.Presently, the impact factor of Cancer Cell International. Dr. Agutter has worked on a broad range of studies in theoretical biology, including the aetiology of deep venous thrombosis and chronic venous insufficiency, allometric scaling of metabolic rate, mechanisms of intracellular transport and history and philosophy of medicine and biology. We must emphasize that Dr. Agutter has spent a substantial fraction of his personal time in handling the manuscripts published in the journal to date, and we also thank him for his voluntary editing of submitted manuscripts written by authors in non-English speaking countries. Dr. Wheatley and Dr. Agutter are not only friends but also collaborators [TBioMed. To deal with the broad range of subjects covered by the journal, new associate editors (who help manage peer-review) and editorial board members, who represent different subject areas, have been recruited. Moreover, we feel very confident in having Drs’ Wheatley and Agutter remain involved with the journal as associate editors. Splitting editorial responsibility into three, whilst supported by our strong colleagues on the board, we are taking over with a belief that TBioMed can be further strengthened and take the lead in its subject category.As we prepare to lead the journal, we would like to acknowledge the efforts that have been made by the founding editor, Dr. Denys Wheatley and former Editor-in-Chief, Dr. Paul Agutter in establishing the journal. Dr. Wheatley has worked on cell biology to better understand the mechanism of cancer, and most notably, he has been successful in raising and growing important journals in his professional areas including borators . Dr. Ed borators -7, shariTBioMed when submitting your original studies in the area of theoretical biology and medicine. We adopt a broad definition of "biology" and all original research studies that focus on theoretical ideas and models associated with developments in biology and medicine are considered. Submissions that are not only technically sound, but contributing to the field by offering either improved understanding in biology or progress in theory or methods will be highly welcomed.We invite all authors in the community to consider The authors declare that they have no competing interests.This editorial was based on editorial meetings among all authors. HN drafted the manuscript. ER and RW gave comments on the earlier version of the manuscript. All authors read and approved the final manuscript.


Cardiovascular Journal of Africa has recently experienced a dramatic increase in the number of articles submitted to this journal. The articles emanate from authors in many diverse countries. As a consequence of the volume of articles, we are experiencing delays in the length of time to publish them.The office of the To obviate this, we have now made available an additional option for authors to advance publish their articles online. We must charge for this option as it involves additional expense. Local authors in Africa will pay R1 000 and those overseas R2 500. This amount could be budgeted for in the research grant if one knows beforehand that the article needs to be advance published.Authors will now have the immediate benefit of having their article appear online on PubMed, but will have to wait as usual for the article to appear in the printed journal. We trust that this will be of help in getting your important research to the immediate attention of other interested researchers and readers.Please contact Elsabé Burmeister at elsabe@cvja.co.za for more information. Fig. 1.