Peer review: how to get it right – 10 tips


1) Be professional. It’s called peer review for a reason. You, putative reviewer, are the peer. If you don’t do it for them why should they do it for you? This is a core part of your job as an academic. It shows both that you are part of the academy and willing to engage in the interplay that makes the profession work. Reviewing is an excellent way to keep up with literature and a superb way to sharpen your own writing.

2) Be pleasant. If the paper is truly awful, suggest a reject but don’t engage in ad hominum remarks. Rejection should be a positive experience for all. Don’t say things in a peer review that you would not say to the person’s face in a presentation or in a bar after a conference.

3) Read the invite. When you receive an email inviting you to review a paper, most journals will provide a link to either accept and or reject. Don’t respond to the editor with a long apology about how you would love to do it but your cat has had kittens and you have a paper yourself to do, plus a class to teach.

4. Be helpful. Suggest to the authors how to overcome the shortcomings you identify. It’s the easiest thing in the world to poke holes in something. It is usually much harder to suggest how to fix them. A review is more than a suggestion to revise, reject or accept. It should be meaningful. It should guide the author on what is good and what is not so good as you see it. If it’s too short, then it probably isn’t going to do that. So be loquacious. Explain what is going on in your thinking. Suggest alternative approaches.

5) Be scientific. Your role is that of a scientific peer. It is not that of an editor in either the proofreading or decision-making sense. Don’t fall back on filling a review with editorial and typographic issues. If the paper is rife with errors, tell the editor and give examples. Concentrate rather on showing the added value of your scientific knowledge and not so much on missing commas etc. If as part of your revision you think that the paper should be professionally proof edited (as I sometimes do with my own), then say so. A caveat to this is that the paper (and indeed the review) is an act of communication. If it is so poorly constructed as to fail in its communication role, then tell me that. Remember that in the end the paper is not about style but substance, unless the style gets in the way.

6) Be timely. There is no point complaining about how slow the paper publication process is if you’re part of the problem. When you agree to review a paper with a timeline given (unless there is a really good reason), you should stick to it. Believe it or not, editors do track who is reviewing what and when. We have to balance the natural tendency to give more reviews to those who do most, with a realisation that people are doing this essentially pro bono and have limited time. So the timeframe we give is designed to be timely but mildly pressurising. Deadlines are good. Stick to them.

7) Be realistic. Be realistic about the work presented, changes you suggest and your role. You as a reviewer are part of the process. You don’t have final say on the determination of the manuscript. I, as editor, have that. Sometimes editors override the suggestions of reviewers (hopefully with good reasons). You can, and in that case engage, in a dialog with the editor as to why – ideally this is a learning opportunity for all. Sometimes this overriding is because the bar being set by the reviewer is too high for that paper. Data may not be available, a paradigm suggested not appropriate. These may be useful suggestions for another paper but each paper is, or should be, one main idea.

8) Be empathetic. Think of the best review you have gotten in terms of guiding a paper forward. Then think of the worst. Which would you rather get on average? Then put yourself into the shoes of the author whose paper you are reviewing. Where along the scale will your review fall? What goes around comes around and therefore ensuring that your reviews are scientific, helpful and courteous is a good idea.

9) Be open. Unless it’s a review for the Journal of Incredible Specialization, specialists and generalists both have a role to play. Editors, especially of general interest journals, will try to get both specialized and more general reviewers. Saying “it’s not my area” is rarely an excuse, especially when you have recently published a very closely related paper. Saying “I’m only one of the authors” in response, doesn’t cut it either. Editors try to balance reviews. That is why we ask for a number of reviewers. We may want a generalist, a subject specialist, someone with experience in the methodology and someone whose work is being critiqued. If we ask you then assume you have a valid and useful role to play.

10) Be organised. A review is, like a paper, a communication. It therefore requires structure and a logical flow. It is not possible to critique a paper for logical holes, grammatical howlers, poor structure etc if your critique is itself rife with these flaws. Draft the review as you go along, then redraft. Most publishers provide short guides on structuring a peer review on their website. Read some of these and follow the main principles. At the start, give a brief one or two sentence overview of your review. Then give feedback on the following: paper structure, the quality of data sources and methods of investigation used, specific issues on the methods and methodologies used (yes, there is a difference), logical flow of argument (or lack thereof), and validity of conclusions drawn. Then comment on style, voice and lexical concerns and choices, giving suggestions on how to improve.

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Posted in Journal article, Medical Writing, Peer Review, Peer-reviewed Journal, Scientific Journal, Scientific writing

Open access: six myths to put to rest

Open access to research is still held back by misunderstandings repeated by people who should know better, says reader

Open access to academic research has never been a hotter topic. But it’s still held back by myths and misunderstandings repeated by people who should know better. The good news is that open access has been successful enough to attract comment from beyond its circle of pioneers and experts. The bad news is that a disappointing number of policy-makers, journalists and academics opine in public without doing their homework.

opening access research

It’s time to unlock and put to rest the myths surrounding open access research, says reader

Here, at the start of the sixth global Open Access Week, are the six most common and harmful misunderstandings about open access:

1) The only way to provide open access to peer-reviewed journal articles is to publish in open access journals

Open access delivered by journals is called “gold” open access and open access delivered by repositories is called “green” open access. The myth asserts that all open access is gold , even for peer-reviewed articles. It has been false since the birth of open access, and yet it remains a tenacious and widespread misconception. Today most open access in medicine and biomedicine is gold, but in every other field it’s mostly green.

The myth is due in part to the relative novelty of the green model. Most academics understand open access journals, more or less, because they understand journals. (I say “more or less” because the common understanding of open access journals is itself myth-ridden; more below.) By contrast, repositories are comparatively new in the scholarly landscape, making them easy to overlook or underestimate. Digital research repositories arose in the digital era, while peer-reviewed journals arose in the year that Isaac Newton earned his bachelor’s degree.

However, this excuse is wearing thin. Today the Registry of Open Access Repositories (ROAR) lists more than 250 subject-based open access repositories and more than 2,300 institutional open access repositories. The Cornell University arXiv for physics and mathematics is more than 20 years old – ancient in internet time. Several open access repositories, including arXiv, the Social Science Research Network (SSRN), andPubMed Central (PMC), dominate their respective subject fields.

Nearly every open access policy at a university or funding agency is a green policy, that is, a policy requiring deposit in an open access repository rather than submission to open access journals. Although open access repositories were novel a couple of decades ago, there’s no excuse for digital scholars not to know that they exist, that they differ from journals, and that they are effective options for the lawful distribution of articles published in peer-reviewed journals.

2) All or most open access journals charge publication fees

Charging publication fees (sometimes called author fees or article processing charges) is the best-known business model for open access journals, but it’s far far from the most common. We’ve known since 2006that most peer-reviewed open access journals charge no fees at all. Earlier this year the Directory of Open Access Journals (DOAJ) began providing its own tallies of open access journals that do and don’t charge fees. As of this week, the DOAJ reports that more than two-thirds (67%)of all peer-reviewed open access journals charge no fees.

We’ve also known since 2006 that most (75%) conventional or non-open access journals do charge author-side fees, on top of reader-side subscription fees. This matters because a close cousin to myth number two is the assumption that author-side fees corrupt peer review. If true, then this corruption affects the majority of conventional journals and only a minority of open access journals.

3) Most author-side fees are paid by the authors themselves

According to the comprehensive Study of Open Access Publishing (SOAP), when researchers publish in fee-based open access journals, the fees are paid by funders (59%) or by universities (24%). Only 12% of the time are they paid by authors out of pocket. This is a good reason to stop using the term “author fees” for publication fees, or the term “author pays” for the fee-based business model.

Scholars who make their work green open access rather than gold never pay a fee to do so. Even when they choose the gold route, only 33% of peer-reviewed open access journals charge author-side fees. It follows that only 4% of authors who publish in open access journals (12% of 33%) pay fees out of pocket. At the same time, about 50% of articles published in peer-reviewed open access journals are published in fee-based journals. If we count by article rather than by journal, then only 6% of authors who publish in open access journals (12% of 50%) pay fees out of pocket.

4) Publishing in a conventional journal closes the door on making the same work open access

Most conventional publishers give standing permission for author-initiated green open access. Many of the others will give permission on request. For authors unsure of a publisher’s position, check out the Sherpa RoMEO database of publisher policies, read the publishing contract, or ask an editor. It’s always worth asking, if only to register demand and show rising expectations.

Because this permission comes from publishers themselves, it makes green open access lawful even when authors have transferred all relevant rights to publishers. However, the permission needn’t come from publishers. Authors may retain relevant rights, on their own, throughauthor addenda (lawyer-drafted contract modifications), or through open access policies at their funding agency or employer. For example, since 2005 the Wellcome Trust has had a policy requiring Wellcome-funded researchers to retain the right to authorise open access, if the publisher doesn’t already permit or provide open access. The US National Institutions of Health (NIH) has had a similar policy since 2008. A new bill in Germany would allow authors to provide green open access to articles arising from publicly-funded research, regardless of their publishing contracts.

On the university side, departments in more than 40 universities around the world have adopted policies, inspired by those developed at Harvard, in which faculty grant their institution non-exclusive rights to make their future articles open access. Rights-retention policies like these assure that faculty may make their work open access even when they publish in a non-open access journal, even when the non-open access journal does not give standing permission for green open access, and even when faculty members have not negotiated special access terms or permissions with their publishers.

Bottom line: when the best journal in your field is not open access, and you’re good enough to be published there, then you can publish there and still make your peer-reviewed text open access through a repository.

5) Open access journals are intrinsically low in quality

As early as 2004, Thomson Scientific found that in every field of the sciences “there was at least one open access title that ranked at or near the top of its field” in citation impact. Of course the number of high-quality and high-impact open access journals has only grown since then. It’s not surprising that open access journals can be first-rate: the quality of a scholarly journal is a function of its authors, editors, and referees, not its business model or access policy. Even John Bohannon’s recent sting of the execrable bottom tier of open access publishers vindicated the excellent top tier (though without showing how good the best open access journals can be), and the vindicated publishers are among the largest open access publishers publishing the most open access journals and articles.

6) Open access mandates infringe academic freedom

This is true for gold open access but not for green. But if you believe that all open access is gold, then this myth follows as a lemma. Because only about one-third of peer-reviewed journals are open access, requiring researchers to submit new work to open access journals would severely limit their freedom to submit work to the journals of their choice. By contrast, green open access is compatible with publishing in non-open access journals, which means that green open access mandates can respect author freedom to publish where they please. That is why literally all university open access mandates are green, not gold. It’s also why the green/gold distinction is significant, not fussy, and why myths suppressing recognition of green open access are harmful, not merely false.

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Posted in Journal Selection, Open access, Peer-reviewed Journal, Science

Why we are not ready for radical changes in science publishing?

There are indeed concerns about the current science publishing model, but until major changes in grant funding are incorporated, researchers will continue to lust after publications in high-tier journals.

Having had the honor of attending back-to-back lectures by Nobel awardees Dr James Rothman and Dr Randy Schekman at the recent American Society for Cell Biology meeting in New Orleans, it was Dr Rothman’s comments that struck the right chord – he specifically pointed out that the US National Institutes of Health (NIH) needs to allocate more money for basic research. Dr Rothman’s talk followed a lecture by Dr Jeremy Berg, former director of the NIH’s Institute for General Medical Science (NIGMS; the institute that promotes and funds basic research). In his lecture, Dr Berg noted that NIGMS receives only ~8% of the total NIH budget, yet about 60% of Nobel prizewinners are funded through this institute. Very telling, in my humble opinion.

science journals

The boycott of ‘super-journals’ with very high impact factors proposed by Nobel prizewinner Randy Sheckman misses the key point.

Dr Schekman also delivered an outstanding lecture, and he has recently made a case for changing the way in which science is published, here in the Guardian. Dr Schekman’s main beefs are with the overwhelming attention that scientists are paying to something known as the “impact factor”, and why this criterion is not a fair way to assess the merit or productivity of a researcher.

The impact factor is a number attributed to a journal that essentially quantifies the mean citations garnered by all of the papers published in that journal over time. It has long been recognised that there are serious concerns with such a system. For one, this is an average of all papers published in the journal, so a few highly cited papers considerably increase the overall impact factor of a journal, while many papers might not be cited at all.

Further complicating this method is that some journals publish reviews, perspectives, mini-reviews, commentaries, etc, and typically these tend to be very highly cited because they attract the attention of researchers outside a given field. On the other hand, other journals strictly publish research papers. And of course, some papers can also be highly cited, yet in a negative way. One such example is of the highly publicised Benveniste affair, in which it was claimed that water contains a memory of the antibodies that were diluted from it – raising cries of victory from homeopaths around the world.

So why has this impact factor become so established among today’s scientists? One reason is that the science itself is rapidly moving towards objective quantification – so there is a similar push to measure scientists’ productivity and careers in a similar manner. In years gone by, scientists would describe a phenotype – for example, a descriptive difference observed – and then provide examples of representative images to back their claims. Today, the gold standard has evolved to more than just show and tell, but providing actual numbers to back up the claims: graphs, tables and statistics. Overall, this is a good thing, as it forces researchers to use objective measures for evaluating scientific findings. But in other cases, the phenomenon may not have a measurable difference.

But there are other reasons why impact factors have become popular. Researchers are becoming squeezed by poor grant funding, bureaucracy and a host of other time-consuming responsibilities. Ideally, new faculty candidates should be examined by their scientific contributions and not by the journals in which they have published. But in the absence of time, impact factors have become an easy way to screen out candidates. This is wrong, but it won’t be easy to undo. The simple fact is that there are journals in which the peer review process is rigorous and thus the papers published can generally be trusted – and there are many other journals that are not worth the paper on which they are printed. Harsh? Perhaps, but also true.

I serve on a variety of editorial boards, and have reviewed scientific papers for many different journals. And I speak from experience when I say that some journals have non-existent standards. I have been asked to review manuscripts from such so-called peer reviewed journals, but when I recommended rejecting a paper for lack of controls and for claims by the authors that are either invalid, inaccurate or simply false, in some cases the editor went ahead and ultimately accepted the paper. Perhaps to collect the author’s publishing fee; I don’t know. In any case, from my perspective this rendered the review process useless, and I lost any respect for papers published in such a journal.

De facto, there is a journal hierarchy – and probably always will be. The question is how the system can be made better.

Some proponents of open access would basically abolish all journal distinctions. In this ideal world, everything should go up on the net – some even maintain that peer review is unnecessary. Although this is not the prevalent view, let me first explain why this model cannot work for biomedical sciences. Science today is highly specialised and scientists need to be able to build on published works – to trust that the peer review process has led to the publishing of reliable data. If anything and everything were to be published, scientists essentially could no longer use published data as the building blocks for continuing studies.

Researchers do not have the resources or time to repeat others’ experiments to test whether they are valid; and in many cases we rely on data coming from other fields – often data that we cannot easily evaluate on our own. As an example, my own cell biology research is often spurred on by new findings made by structural biologists. I can read and understand the conclusions drawn – and use them to test hypotheses concerning my research. But I would be unable to evaluate the actual x-ray data itself and decide if it’s convincing or even legitimate. That is the purpose of peer review.

However, the majority of those who seek to change the system of scientific publishing do not want to abolish peer review – in fact, a lot of the criticism is aimed at several of the most high-profile journals, in particular the trio of Cell, Science and Nature – considered by many to be the most influential journals for the careers of scientists. These journals are highly exclusive, and indeed send out only a fraction of the submitted manuscripts for peer review, as initial decisions are made by professional editors who work full-time for the journal. Criteria for acceptance – or even review in these journals – demands that the research papers address hot topics of “broad” interest to the research community. They are supposed to represent startling innovations or discoveries of high significance.

There are many solid journals that have outstanding peer review processes, but do not disqualify papers based on a lack of perceived appeal or considerations of whether the published paper will be highly cited. I strive to publish in such journals, not because of any impact factor attributed to them, but because I know that papers published in these journals are rigorously reviewed, and typically garner respect from others in the scientific community. Yes, there are always exceptions; a great paper could be published in a journal that has a poor review process, and occasionally lousy papers manage to filter through to the rigorously reviewed journals. But there is a clear hierarchy, and this is independent of impact factors.

The solution to the problem of the ramped-up “super-journals” is not trivial, and it is tied into our funding system in the US and in Europe. In reviewing grant proposals for the National Institutes of Health – the main source for funding of biomedical researchers in the US – there is simply not enough money to support science. With success rates dipping well below 10%, reviewers are forced to distinguish between outstanding grant proposals, knowing that only ~1/10 will be awarded funding. Since research topics vary widely, we reach a situation of comparing apples and oranges. And pineapples. Throw in mango, pears, peaches, papaya and even watermelon for good measure. So how does one compare? We come back to the “impact” – or more accurately – perceived impact. Reviewers are forced to make decisions based on their evaluation of the perceived impact of the research being proposed. And if one publishes in a super-journal with perceived high impact, does that not help make the case that one’s research is influential?

This is the crux of the matter: perceived impact is one of the most important criteria for funding, so unless researchers have a Nobel Prize – and are therefore immune to criticism of perceived impact – they will need to continue to strive to demonstrate the high impact of their studies.

I, too, signed and support DORA – the Declaration on Research Assessment – which states that scientists should be evaluated according to their scientific contributions, as opposed to an artificial and superficial numerical count of the impact factor of their publications. But a boycott of the “super-journals” with very high impact factors (Cell, Science and Nature), proposed by Dr Sheckman, misses the key point. I would therefore recommend to my fellow cell biologists and newly minted Nobel Laureate, Dr Schekman – for whom I have the greatest respect – that we first focus energies on securing sufficient funding to keep basic biomedical science afloat. I hope our outstanding Nobel winners will use their weighty influence and impact to lead the charge. Once we have managed to stem the damage to scientists’ careers, then it will be time to address the very complex issue of how to improve the science publication system.

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Posted in Case report, Impact Factor, Journal article, Journal Selection, Peer Review, Peer-reviewed Journal, Science, Scientific Journal

Why publish science in peer-reviewed journals?

Peer review is commonly accepted as an essential part of scientific publication. But the ways peer review is put into practice vary across journals and disciplines. What is the best method of peer review? Is it truly a value-adding process? What are the ethical concerns? And how can new technology be used to improve traditional models? The recent announcement of a new journal sponsored by the Howard Hughes Medical Institute, the Max Planck Society, and the Welcome Trust generated a bit of discussion about the issues in the scientific publishing process it is designed to address—arbitrary editorial decisions, slow and unhelpful peer review, and so on. Left unanswered, however, is a more fundamental question: why do we publish scientific articles in peer-reviewed journals to begin with? What value does the existence of these journals add? In this post, I will argue that cutting journals out of scientific publishing to a large extent would be unconditionally a good thing, and that the only thing keeping this from happening is the absence of a “killer app”.

The publishing process as it stands currently

As most readers here are aware, the path to publishing a scientific paper has two major obstacles: first, the editor of a journal has to decide that a paper is potentially “interesting” enough for publication in their journal; if it passes that threshold, it is then sent out for “peer review” by two to four people chosen by the editor. The reviewers make a recommendation about whether or not the journal should publish the paper – if they all like it, chances are it will be accepted (potentially after additional experiments); if one of them hates it, chances are it will be rejected; if the reviews are mixed, the editor makes a judgment call. In total, this process involves a handful of people at most, and takes around a few months to a year (of course, if the paper is rejected, you generally start all over again). The problems with this system have been pointed out ad nauseam; the most succinct statement of the issues I’ve seen this in a nice commentary by British Medical Journal editor. To summarize, peer review is costly (in terms of time and money), random (the correlation in perceived “publishability” of a paper between two groups of reviewers is little better than zero), ineffective at detecting errors, biased towards established groups and against originality, and sometimes abused (in that reviewers can steal ideas from papers they review or block the publication of competitors).

We can do better?

So why do we stick with this system, despite its many flaws? These days, there’s zero cost to self-publishing a paper online (for example, on a preprint server like arXiv or Nature Precedings), so going through a peer-reviewed journal for publication itself seems a bit silly. However, journals do perform a service of sorts: they filter papers, ostensibly based on interest to a community, and also ostensibly ensure that the details of an analysis are correct and clear enough to be replicated (though in practice, I doubt these filters work as intended).

So let’s take this goal–that of filtering papers based on quality, interest to a community, and reproducibility–as the legitimate service provided by peer-reviewed journals. When phrased like this, it’s simply absurd that our way of achieving this goal involves a handful of unaccountable, often anonymous, reviewers and editors, and takes so much time and money. Certainly the best judge of the interest of a paper to the community is, well, the community itself. Ditto for the best judge of the quality and reproducibility of a paper. So let’s imagine a different system. What features would this system have?

1. Immediate publication without peer review. This is simply a feature taken from preprint servers like arXiv, and addresses the issues of speed and cost of publication.

2. One-click recommendation of papers. Now we need to find a way to filter the papers in step 1. Imagine a feed of new papers (like the feed in reddit or Facebook); one simple and relatively effective filter is to allow individuals to express that they like a paper with a single click (again, like reddit, Facebook, or Google+). It seems stupid, but it’s little effort and extremely effective in some situations.

3. Connection to a social network. Of course, in some cases I don’t really care if a lot of people like a paper; instead, what I want to know is: do people I trust like the paper? If I’m trying to find the best recent papers on copy number variation, I don’t necessarily care if a thousand people like a paper, but I would probably take a second look at a paper recommended by (my GNZ colleague and copy number variation expert) Don Conrad.

4. Effective search based on the collective opinion on a paper. Many times, I’m searching for the best papers in a field somewhat outside my own. One of the most useful features in Google Scholar in this regard is that it immediately tells you how many citations a paper has received; in general, this is highly correlated with the community opinion of a paper. This breaks down for new papers, all of which have zero citations. Often, I’d like to be able to search the relatively recent literature and sort based on the criteria in steps 2 and 3.

You can imagine additional sorts of features that would be useful in a system like this—comments, voting on comments themselves, encouragement of reproducible research via Sweave or some other mechanism—but the aspects above are probably essential.

Does a system like this perfectly address all of the issues with peer review mentioned above? No–my guess is that this sort of system would also be somewhat biased towards established research groups, just as peer review is. But for all other aspects, this sort of system seems superior.

How do we get there?

Many of the above ideas, of course, are not new (see, e.g., discussions by Cameron Neylon). And much of academia has bought into the “peer-reviewed journal” system for evaluation of individuals–that is, when evaluating an individual researcher for a grant or tenure, the quality of the journal in which a piece of work is published is often used as a proxy for the quality of the work itself. It’s easy to see how this system became entrenched, but it is obviously not compatible with the publishing model outlined above (nor is it an ideal system in its own right, unless you’re someone with a knack for getting crappy papers published in Nature). So what’s the way out?

One thing to note is that many of these ideas about community ranking could be incorporated into the “standard” publishing route. Indeed, some aspects of these ideas (comments, rating of articles) have been implemented by the innovative PLoS journals, but have been greeted with deafening yawns from the research community. Why is this? Certainly, it’s partially because these systems are non-trivial to use (you have to log in to some new system every time you want to rate a paper), but most importantly, there’s no sense of community—I’ll never see your comment on a paper, as relevant as it is, unless I come across it by chance, and there’s no mechanism to tell me when a paper is being read and liked by many people I trust. The current implementations of these ideas simply don’t perform the filtering mechanism that they’re designed to replace–if I see that a PLoS One paper is highly rated, this doesn’t help me at all; I’ve already found the paper!

This situation has created the perfect niche for a killer app—one that solves all of these issues and will actually be used. I’m not sure exactly what this will look like, but it will likely tap into already existing online identities and social networks (Google+? Facebook?), will require approximately no learning curve, and will be of genuine utility (i.e., it will deliver the good PLoS One papers to me, rather than waiting for me to find them). Once a system like this exists, and it can be shown that it’s possible to judge people (for grants, tenure, etc.) in this system based on the impact of their work, rather than the prestige of the journal in which the work is published, it’s an additional easy step to eliminate the journals altogether.


Before the internet, peer-reviewed journals and researchers had a happy symbiosis: scientists had no way of getting their best scientific results to the largest audience possible, and journals could perform that service while making a bit of profit. Now, that symbiosis has turned into parasitism: peer-reviewed journals actively prevent the best scientific results from being disseminated, siphoning off time and money that would be better spent doing other things. The funny thing is, somehow we have been convinced that this parasite is doing us a favor, and that we can’t survive any other way. It’s not, and we can.

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Posted in Journal article, Journal Selection, Peer Review, Peer-reviewed Journal, Science, Science and Technology, Scientific Journal

Making the most out of a conference: A practicable guide to writing and delivering a paper

Attending your first conference can be a nerve-wracking experience, and giving your first paper can be even more stressful. However, a little bit of forethought and preparation can make the whole experience much smoother and more enjoyable. For those who may be attending or presenting for the first time at a conference, here are some top tips on making sure you get the best out of the experience.

Writing the paper

  1. Make your argument obvious. Be absolutely clear about why your audience will benefit from listening to what you have to say. What is new and exciting about your research? Why are you changing the way people think? Make sure you clearly state your main point more frequently than you would in a written piece – this means your audience has multiple opportunities to absorb the information.
  2. Keep to the time limit. Your paper must fit into the time slot specified by the conference organizers.
  3. Remember that you are speaking, not writing. Keep your sentences shorter, more so than you would in your writing, as listeners will be able to follow your argument more easily.
  4. Practice reading your paper. Make sure you know the shape of each sentence, where the emphasis will fall and what direction the paper moves in. Listen for the places where you might rewrite passages to make them easier to say (and thus to understand).
  5. Make sure you begin and end your talk well. Begin with a couple of sentences to contextualize your work, and end with a clear summary of what you have said, so your audience knows you are rounding off your argument.

Delivering the paper

  1. Remember that you are giving a performance. Speak confidently and at a sensible speed. Whatever you do, remember to sound excited about what you’re saying – if you aren’t enthused about your subject, why should your audience be?
  2. Think about your body language. Try to establish eye contact with your audience as much as possible. Watch out for slips in your posture, like swaying from side to side or jumping from one foot to the other. Be aware of what your hands are doing.
  3. Be sensible about your presentation aides. PowerPoints are useful if you have images, figures, tables or site maps to display; if you will mainly be discussing texts, then handouts with margins for people to scribble their own notes on will be more useful.
  4. Don’t panic if you don’t get any questions. This doesn’t mean your paper was a failure – it means that you thoroughly convinced your audience of your point.
  5. Manage your crisis in advance. Back up your paper in something like Dropbox. Have a copy of your paper and handout or PowerPoint e-mailed to yourself. If you are travelling by plane, keep the paper copy of your talk in your hand luggage.

Attending the conference

  1. Do your preparation. Have a look at the conference program, find out who you know who is going, work out what you want to hear and who you want to catch up with.
  2. Be willing to experiment. Pick a panel you know absolutely nothing about that sounds interesting, and go along. You may hear something unexpectedly helpful for your own research.
  3. Take an interest in other people’s work. Think of questions for speakers, either during the discussion period or to follow up with them afterwards. The subject matter of papers also always gives you material to start up a conversation during the breaks.
  4. Network – and remember what networking is about. The primary goal of networking is to meet interesting people working on interesting things, not to engage in some kind of Machiavellian mind game. Be guided by your genuine curiosity and enthusiasm about your subject, and you’ll start meeting people who are as fascinated by your work as you are by theirs – which is the point.
  5. Remember that conferences are supposed to be fun! For all the pressure involved in preparing for conferences, they are great opportunities to meet interesting people, hear exciting new ideas and continue learning about your discipline. Try not to forget that once you’re actually on the ground.

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Posted in Communication, Education, Health Education, Scientific writing, Writing

What is a Peer Review article and it’s features?

What is Peer Review?

In academic publishing, the goal of peer review is to assess the quality of articles submitted for publication in a scholarly journal. Before an article is deemed appropriate to be published in a peer-reviewed journal, it must undergo the following process:

  • The author of the article must submit it to the journal editor who forwards the article to experts in the field. Because the reviewers specialize in the same scholarly area as the author, they are considered the author’s peers (hence “peer review”).
  •  These impartial reviewers are charged with carefully evaluating the quality of the submitted manuscript.
  •  The peer reviewers check the manuscript for accuracy and assess the validity of the research methodology and procedures.
  •  If appropriate, they suggest revisions. If they find the article lacking in scholarly validity and rigor, they reject it.

Because a peer-reviewed journal will not publish articles that fail to meet the standards established for a given discipline, peer-reviewed articles that are accepted for publication exemplify the best research practices in a field.

Features of a Peer-Reviewed Article

When you are determining whether or not the article your found is a peer-reviewed article, you should consider the following questions:

Is the journal in which you found the article published or sponsored by a professional scholarly society, professional association, or university academic department? Does it describe itself as a peer-reviewed publication? (To know that, check the journal’s website).

Did you find a citation for it in one of the  databases that includes scholarly publications? (Criminal Justice Abstracts, EBSCOhost Academic Search Complete, PsycINFO, etc.)?  Read the database description to see if it includes scholarly publications.

Did you limit your search to scholarly or peer-reviewed publications?

Is there an abstract (summary) at the beginning of the article?

Is the tone of the article thoughtful, restrained and serious?

Does the article have footnotes or citations of other sources?

Does the article have a bibliography or list of references at the end?

Are the author’s credentials listed?

Is the topic of the article narrowly focused and explored in depth?

Is the article based on either original research or authorities in the field (as opposed to personal opinion)?

Is the article written for readers with some prior knowledge of the subject?

If your field is social or natural science, is the article divided into sections with headings such as those listed below?

  • Introduction
  • Theory or Background
  • Methods
  • Discussion
  • Literature review
  • Subjects
  • Results
  • Conclusion

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Posted in Journal article, Peer Review, Scientific writing

Six things to do before writing your manuscript

A new study, “How to Prepare a Manuscript for International Journals” — a seasoned editor gives advice to boost your chances of acceptance

I think that sometimes researchers are not trained by their supervisors in writing scientific papers during the PhD period, which is the best time to learn the principles and discipline of publishing. For any author, it is also important to review papers from colleagues (I review an average of 45 to 50 papers per year, and I have reviewed for more than 65 different scientific journals), because this gives a broader view of the hot topics for publication. I’m also the editor of several journals.For these reasons, I think I can provide my particular view of how to increase your chances of having a paper accepted.

1. Think about why you want to publish your work – and whether it’s publishable

Writing a paper starts well in advance of the actual writing. In fact, you must to think about why you want to publish your work at the beginning of your research, when you question your hypothesis. You need to check then if the hypothesis and the survey/experiment design are publishable. Ask yourself:

  • Have I done something new and interesting?
  • Is there anything challenging in my work?
  • Is my work related directly to a current hot topic?
  • Have I provided solutions to some difficult problems?

If all answers are “yes,” then you can start preparations for your manuscript. If any of the responses are “no,” you can probably submit your paper to a local journal or one with lower Impact Factor.

When responding to these questions, you should keep in mind that reviewers are using questionnaires in which they must respond to questions such as:

  • Does the paper contain sufficient new material?
  • Is the topic within the scope of the journal?
  • Is it presented concisely and well organized?
  • Are the methods and experiments presented in the way that they can be replicated again?
  • Are the results presented adequately?
  • Is the discussion relevant, concise and well documented?
  • Are the conclusions supported by the data presented?
  • Is the language acceptable?
  • Are figures and tables adequate and well designed?, are there information duplicated? Are they too many?
  • Are all references cited in the text included in the references list?

2. Decide what type of the manuscript to write

You have at least three options on the type of manuscript:

  1. Full articles, or original articles, are the most important papers. Often they are substantial completed pieces of research that are of significance as original research.
  2. Letters/rapid communications/short communications are usually published for the quick and early communication of significant and original advances. They are much shorter than full articles (usually strictly limited in size, depending on each journal).
  3. Review papers or perspectives summarize recent developments on a specific hot topic, highlighting important points that have previously been reported and introduce no new information. Normally they are submitted on invitation by the editor of the journal.

When looking at your available information, you must self-evaluate your work: Is it sufficient for a full article, or are your results so thrilling that they should be shown as soon as possible?

You should ask your supervisor (if you are a PhD student) or a colleague for advice on the manuscript type to be submitted. Remember also that sometimes outsiders – i.e., colleagues not involved in your research – can see things more clearly than you. Whatever type of article you write, plan to submit only one manuscript, not a series of manuscripts. (Normally editors hate this practice, since they have limited space in the journals and series of manuscripts consume too many pages for a single topic or an author/group of authors)

3. Choose the target journal

A common question is how to select the right journal for your work. Do not gamble by scattering your manuscript to many journals at the same time. Only submit once and wait for the response of the editor and the reviewers.

The most common way of selecting the right journal is to look at the articles you have consulted to prepare your manuscript. Probably most of them are concentrated in one or two journals. Read very recent publications in each candidate journal (even in press), and find out the hot topics and the types of articles accepted.

Also consider the high rejection rates of the journals (e.g., NatureScienceThe Lancet and Cell are >90 percent), and if your research is not very challenging, focus in more humble journals with lower Impact Factors. You can find a journal’s Impact Factor on its webpage or via Science Gateway.

4. Pay attention to journal requirements in the Guide for Authors

After selecting the journal for submission, go to the web page and download the Guide for Authors, print out it and read the guidelines again and again! They generally include detailed editorial guidelines, submission procedures, fees for publishing open access, and copyright and ethical guidelines. You must apply the Guide for Authors to your manuscript, even the first draft, using the proper text layout, references citation, nomenclature, figures and tables, etc. Following this simple tip will save your time – and the editor’s time. You must know that all editors hate wasting time on poorly prepared manuscripts. They may well think that the author shows no respect.

5. Pay attention to the structure of the paper

More and more journals have new types of structure for their articles, so it’s crucial to consult the Guide for Authors. However, in general, most of them follow the same structure:

  • A section that enables indexing and searching the topics, making the paper informative, attractive and effective. It consists of the Title, the Authors (and affiliations), the Abstract and the Keywords.
  • A section that includes the main text, which is usually divided into: Introduction, Methods, Results, Discussion and Conclusions.
  • A section that includes the Acknowledgements, References, and Supplementary Materials or annexes.

The general structure of a full article follows the IMRAD format, introduced as a standard by the American National Standards Institute in 1979, which responds to the questions below:

  • Introduction: What did you/others do? Why did you do it?
  • Methods: How did you do it?
  • Results: What did you find?
  • Discussion: What does it all mean?
  • Conclusions

6. Understand publication ethics to avoid violations

One of the worst things in science is plagiarism. Plagiarism and stealing work from colleagues can lead to serious consequences, both professionally and legally. Violations include data fabrication and falsification, improper use of human subjects and animals in research, and using another author’s ideas or wording without proper attribution. It’s also possible to commit ethics violations without intending to. Educational resources include the Publishing Ethics Resource Kit (PERK) from the Committee on Publication Ethics (COPE) and Elsevier’s Ethics in Publication & Research website.

Closing advice

As you prepare your manuscript, there are some basic principles you should always keep in mind:

  • Cherish your own work – if you do not take care, why should the journal?
  • There is no secret recipe for success – just some simple rules, dedication and hard work.
  • Editors and reviewers are all busy scientists, just like you. Make things easy to save them time.

Hence, if you are ready to learn more about preparing a manuscript, look for the next articles in this series and have good luck!

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Posted in Case report, Chicago Manual Style, Communication, Editing, Health Education, Impact Factor, Interdisciplinary research, Journal article, Journal Selection, Manuscript format, Medical Communication, Medical Writing, Peer Review, Proofreading, Review article, Scientific editing, Scientific writing, Writing

The open access journal Genomics Data helps researchers make the most of their data

In genomics, big data really is big. Genomic datasets quickly consume terabytes of computer storage with more information than we have the capacity to fully analyze or understand. As a result, scientists will often publish an article about only a small piece or particular aspect of their data, leaving the rest ripe for interpretation by others. In the words, “Information isn’t the bottleneck for discovery, interpretation is.”

Although this precious genomic data is uploaded into public repositories, sadly, few people dare to touch the data because it is too complicated to understand. Data files are often mislabeled, data may be raw or analyzed and analysis from dataset to dataset is highly variable, experimental subtleties are not mentioned, and software code used to filter through data is not available.

The lack of reproducibility has far-reaching consequences.

In a recent Nature news article, Dr. Francis CollinsDirector of the National Institutes of Health (NIH), and Lawrence Tabak, Deputy Director of the NIH, mention that there are “a troubling frequency of published reports that claim a significant result, but fail to be reproducible.”

Dr. John Greally, Professor at Albert Einstein College of Medicine in New York and Editor of the Genome Analysis and Tools Section of the journal Genomics, gave one example from his work. “It is impossible to truly review genomic research grant proposals,” he said, because there are so many variables in how genomic datasets are acquired, presented and analyzed. While research articles are an essential step forward in advancing science, they seem to fall short in being able to describe data well enough to make it reproducible.

That’s where Genomics Data, one of Elsevier’s new open access journals, comes in. It provides an avenue for researchers to bring their data – along with the details necessary to understand and reuse the data – to the forefront.

The journal’s signature “Data in Brief” articles describe publicly available genomic datasets thoroughly so the data can be easily found, reproduced, reused and reanalyzed. Data in Brief are intended to supplement a research article, describing all of the nitty-gritty details that are essential to understanding the data.

Now, these kinds of accompanying details must be documented in a Specifications table at the top of each Data in Brief. The journal’s Editorial Board also checks that any related software or programming code is submitted alongside the Data in Brief.

Because Data in Brief are reviewed by the editorial board, authors receive a decision quickly: the average time for a decision on the manuscript is one week. As a result, researchers can get the word out about their datasets quickly, driving more traffic to their data and to any research article that may discuss interpretations of that data.

We hope Data in Brief will be a big step forward in making genomic data sharing and reproduction a reality.

Data in Brief — how it works

Two essential components of genomic research are:

  1. The data, available in a public repository: supports your research article but is not published or copyrighted as a part of that research article.
  2. The Research Article: an interpretation of the data.

The Data in Brief articles support these elements by providing a thorough description of the data, including quality-control checks and base-level analysis.

Data in Brief Chart

Data in Brief articles:

  • Thoroughly describe data, facilitating reproducibility.
  • Make deposited genomic data easier to find.
  • Increase traffic towards associated research articles and data, leading to more citations.
  • Open up doors for new collaborations.

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Posted in Interdisciplinary research, Journal article, Peer Review, Science

Appearance of Lyme disease rash can help predict how bacteria spreads through body

Lyme disease is often evident by a rash on the skin, but infections do not always produce similar rashes. This can make it difficult to detect the disease early, when antibiotic treatment is most effective. In today’s issue of the Biophysical Journal, published by Elsevier’s Cell Press, researchers describe a new mathematical model that captures the interactions between disease-causing bacteria and the host immune response that affect the appearance of a rash and the spread of infection.

“The findings are important because they connect how the rash looks with the behavior of the bacteria in our body,” said the researcher of Physics and Cellular and Molecular Biology at the University of Arizona in Tucson. The research team developed a fairly simple mathematical model that can account for the growth and appearance of a Lyme disease rash and might be used to predict the densities of the disease-causing bacteria in relationship to the rash as a function of time during spreading.

In many cases, patients with Lyme disease develop a rash with a bull’s-eye appearance. The model reveals that in these cases, the rash begins as a small and uniform rash. Activation of the immune response is strongest at the center of the rash and clears most, but not all, of the bacteria from the center within about one week; however, bacteria at the edge of the rash continue to spread outward, further activating the immune response away from the edge. Therefore, the rash grows, but the center becomes less inflamed. As time progresses, though, the bacteria re-surge at the center, leading to the characteristic bull’s-eye pattern.


Dynamics of the Lyme disease rash

By revealing that the bacteria and immune cell populations change as a rash progresses, the model may help guide Lyme disease treatment. “The model that we have developed can be used to predict how the bacteria move through our bodies and how they are affected by therapeutics,” explained the researcher.

To that end, the researchers simulated the progression of different rash types over the course of antibiotic treatment. They found that for all types of Lyme disease rashes, bacteria were cleared from the skin within roughly the first week; however, the dynamics of disappearance of the rash varied depending on the type of rash with which the patient presented. For example, while bull’s-eye rashes resolved within a week of treatment, uniform rashes tended to be present even after four weeks, likely due to prolonged inflammation. Such differences suggest that there may not be a one-size-fits-all treatment regimen for resolving Lyme disease and its effects on the body. The researcher also notes that there are a number of similarities between the bacterium that causes Lyme disease and the bacterium that causes syphilis, and that “therefore, it is likely that this model will also be applicable to understanding syphilis, as well as potentially other bacterial infections.

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Posted in Biology, Biotechnology, Case report, Chemistry, Communication, Editing, Education, Health Education, Journal article, Medical Communication, Medical Writing, Medicine, Molecular Biology, Neurology, Peer Review, Physics, Proofreading, Review article, Science

Electrical brain stimulation may spark a person’s ‘will to persevere’

What gives some people the ability to persevere through difficult situations that others may find insurmountable?

The answer is no doubt a complicated one that may be beyond our full understanding, but new research published online today in the Cell Press journal Neuron provides some intriguing insights. The study pinpoints a region of the brain that, when stimulated, causes an individual to anticipate a challenge and possess a strong motivation to overcome it.

The researcher of the Department of Neurology and Neurological Sciences at Stanford University commented on the significance of the findings:

That few electrical pulses delivered to a population of brain cells in conscious human individuals give rise to such a high level set of emotions and thoughts we associate with a human virtue such as perseverance tells us that our unique human qualities are anchored dearly in the operation of our brain cells.

The study involved two individuals with epilepsy who had electrodes implanted in their brains to help doctors learn about the source of their seizures. The electrodes were situated in the anterior midcingulate cortex, a brain region that is thought to be involved in emotions, pain, and decision making.

When electrical charge was delivered to a location within this region, both patients described feeling the expectation of an imminent challenge coupled with a determined attitude to surmount it. This was accompanied by increased heart rate and physical sensations in the chest and neck. They did not experience any of these psychological or physical effects when they thought that their brains were being stimulated but no electrical charge was delivered. The same effects did not occur with stimulation of nearby regions only 5 mm away.

Imaging experiments revealed that the site of stimulation in both patients was at the core of a network linking the anterior midcingulate cortex to other regions of the brain. “Our study pinpoints the precise anatomical coordinates of neuronal populations, and their associated network, that support complex psychological and behavioral states associated with perseverance,” the researcher explained. The findings suggest that differences in the structure and function of this network may be linked with innate differences in our abilities to cope during tough situations. The results may even pertain to psychopathological conditions in which people experience a significantly reduced capacity to endure psychological or physical distress.

“These innate differences might potentially be identified in childhood and be modified by behavioral therapy, medication or, as suggested here, electrical stimulation,” the researcher said.

Download and watch a patient’s experience with electrical brain stimulation

The term “sham trial” refers to the instances when the electrical current was set at zero but the patient thought he was being stimulated.

Protogenist, Neuron_ Supplemental

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Posted in Biology, Health Education, Journal article, Neurology, Neuroscience, Science, Science and Technology
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