Author Archives: Vekky Repi

Hivebench: Electronic Laboratory Notebook for Modern Researchers

Hivebench

The scientific community is well aware of the pitfalls and challenges associated with keeping and storing data. While there may be other data management tools, the most commonly used one is the unambiguous lab notebook. This innocent tool for keeping data is far from perfect—data can be lost, degraded, or otherwise compromised. Enter Hivebench, an electronic laboratory notebook (ELN) built by scientists for scientists. Hivebench is the answer for researchers who wish to manage data, track protocols, and collaborate.

Introducing Hivebench

Elsevier acquired Hivebench from Shazino, a research application developer based in Lyon, France. Hivebench was set to be integrated into the existing Research Data Management portfolio maintained by Elsevier. In a nutshell, Hivebench is an ELN that helps researchers conduct and analyze experiments, prepare experiments, and store methods and protocols in one place. This saves the researcher’s time. In addition, Hivebench is the only ELN available on the desktop (OSX), mobile devices (iOS), and the web. Aside from these, Hivebench is linked to Mendeley Data and other Elsevier tools. Thus, researchers can export their results to Mendeley Data. The acquisition of Hivebench is set to benefit funders and institutions as well. Hivebench is to be integrated with the “funder compliance check” module, which will solidify the link between data posting requirements and laboratory data.

Hivebench – Unlocking the full potential of research data from Bob Hendriks on YouTube

Features and Benefits

Hivebench has a plethora of features and benefits as compared to traditional, paper-based laboratory notebooks. It provides researchers and their colleagues a way to share protocols and data, which is hard to do when using paper notebooks. In addition, Hivebench allows users to access all the protocols and data at the same time, anytime. The progress of experiments can be stored in real-time. Considering how fragile, risky, and limited paper notebooks are, Hivebench presents a novel and concrete solution. Researchers need to spend a lot of time writing in a laboratory notebook, which doesn’t have search features and requires deciphering; however, Hivebench can allow seamless sharing of work. Comments and conversations can also be tracked real-time.

When using paper notebooks, researchers need to rewrite sections of drafts and deal with security issues with respect to their data. Aside from this, paper laboratory notebooks cannot comply with funders/FDA. There is also no uniform format for sharing. In contrast to this, Hivebench uses universal templates to share results in a consistent manner. It also complies with FDA/funder requirements. Researchers who use Hivebench can securely share their work with their colleagues. Moreover, automatic sign-outs are a feature of Hivebench. Data can be preserved in a non-proprietary format.

How Helpful Is Hivebench?

Paper-based laboratory notebooks are surrounded by peril: it is too easy to lose, destroy, and misinterpret them. There are instances when paper-based laboratory notebooks proved to be a recipe for disaster. Hivebench can clearly address these problems and a lot more. For example, losing your laboratory notebook in a fire is not unheard of. When fires do occur in laboratories, everything is lost. All the precious data and protocols are gone. Another situation is not having a lab notebook at all. Taking notes is imperative in research and not having a notebook is a common cause of frustration. In addition, it is difficult to search for data required by reviewers in a lab notebook, wherein you have to look through a lot of data.

Aside from these, losing data files is not uncommon. For instance, storing pictures of cells or analyzing DNA sequences is commonplace. However, what if the computer malfunctions? Everything is then lost. Hivebench stores all data on the same platform, which means that they will be accessible for years. Information stored in multiple locations is a problem, which removes uniformity in data storage and encoding. Hivebench can address this because it is the same wherever you access it.

Hivebench: write your lab notebook from Team Shazino on Vimeo.

Key Aspects and Drawbacks

There are a number of key aspects that Hivebench is associated with:

  1. Improving sharing: Protocols are easier to access, common reagents and databases can be shared
  2. Increasing efficiency: Hivebench has an integrated notebook and calendar function that allows experiments to be scheduled so outcomes can be recorded
  3. Saving time: Protocols and previous results are easier to locate
  4. Reducing failure: It is easy to compare successful experiments with unsuccessful ones
  5. Signifying compliance with mandates: Funders are implementing mandates surrounding the sharing, storage, and capture of data.

There are, of course, some drawbacks to Hivebench:

  1. Protocol creation is rigid
  2. It doesn’t support the creation of tables
  3. Free Hivebench account is limited to 10 users
  4. Works only on iOS and OSX

There is no perfect system, however, Hivebench comes close. It’s still the best choice for researchers in terms of data collection and management.

We vs. They: Using the First & Third Person in Research Papers

first or third person

Writing in the first, second, or third person is referred to as the author’s point of view. When we write, our tendency is to personalize the text by writing in the first person. That is, we use pronouns such as “I” and “we”. This is acceptable when writing personal information, a journal, or a book. However, it is not common in academic writing.

Some writers find the use of first, second, or third person point of view a bit confusing while writing research papers. Since second person is avoided while writing in academic or scientific papers,the main confusion remains within first or third person.

In the following sections, we will discuss the usage and examples of the first, second, and third person point of view.

First Person

The first person point of view simply means that we use the pronouns that refer to ourselves in the text. These are as follows:

  • I
  • We
  • Me
  • My
  • Mine
  • Us
  • Our
  • Ours

Using these, we present the information based on what “we” found. In science and mathematics, this point of view is rarely used. It is often considered to be somewhat self-serving and arrogant. It is important to remember that when writing your research results, the focus of the communication is the research and not the persons who conducted the research. When you want to persuade the reader, it is best to avoid personal pronouns. In addition to sounding somewhat arrogant, the strength of your findings might be underestimated.

For example:

Based on my results, I concluded that A and B did not equal to C.

In this example, the entire meaning of the research could be misconstrued. The results discussed are not those of the author; they are generated from the experiment. To refer to the results in this context is incorrect and should be avoided. To make it more appropriate, the above sentence can be revised as follows:

Based on the results of the assay, A and B did not equal to C.

Second Person

The second person point of view uses pronouns that refer to the reader. These are as follows:

  • You
  • Your
  • Yours

This point of view is usually used in the context of providing instructions or advice, such as in “how to” manuals or recipe books. The reason behind using the second person is to engage the reader.

For example:

You will want to buy a turkey that is large enough to feed your extended family. Before cooking it, you must wash it first thoroughly with cold water.

Although this is a good technique for giving instructions, it is not appropriate in academic or scientific writing.

Third Person

The third person point of view uses both proper nouns, such as a person’s name, and pronouns that refer to individuals or groups (e.g., doctors, researchers) but not directly to the reader. The ones that refer to individuals are as follows:

  • She
  • Her
  • Hers (possessive form)
  • He
  • Him
  • His (possessive form)
  • It
  • Its (possessive form)
  • One
  • One’s (possessive form)

The third person point of view that refers to groups include the following:

  • Everyone
  • Anyone
  • Them
  • They
  • Their (possessive form)
  • Theirs (plural possessive form)

For example:

Everyone at the convention was interested in what Dr. Johnson presented.

The instructors decided that the students should help pay for lab supplies.

The researchers determined that there was not enough sample material to conduct the assay.

The third person point of view is generally used in scientific papers but, at times, the format can be difficult. We use indefinite pronouns to refer back to the subject but must avoid using masculine or feminine terminology. For example:

A researcher must ensure that he has enough material for his experiment.

The nurse must ensure that she has a large enough blood sample for her assay.

Many authors attempt to resolve this issue by using “he or she” or “him or her,” but this gets cumbersome and too many of these can distract the reader. For example:

A researcher must ensure that he or she has enough material for his or her experiment.

The nurse must ensure that he or she has a large enough blood sample for his or her assay.

These issues can easily be resolved by making the subjects plural as follows:

Researchers must ensure that they have enough material for their experiment.

Nurses must ensure that they have large enough blood samples for their assay.

Exceptions to the Rules

As mentioned earlier, the third person is generally used in scientific writing, but the rules are not quite as stringent anymore. It is now acceptable to use both the first and third person in some contexts, but this is still under controversy. 

In a February 2011 blog on Eloquent Science, Professor David M. Schultz presented several opinions on whether the author viewpoints differed. However, there appeared to be no consensus. Some believed that the old rules should stand to avoid subjectivity, while others believed that if the facts were valid, it didn’t matter which point of view was used.

First or Third Person: What Do The Journals Say

In general, it is acceptable in to use the first person point of view in abstracts, introductions, discussions, and conclusions, in some journals. Even then, avoid using “I” in these sections. Instead, use “we” to refer to the group of researchers that were part of the study. The third person point of view is used for writing methods and results sections. Consistency is the key and switching from one point of view to another within sections of a manuscript can be distracting and is discouraged. It is best to always check your author guidelines for that particular journal. Once that is done, make sure your manuscript is free from the above-mentioned or any other grammatical error.

Open Access Policies and Funding Agency Mandates

The open access (OA) model has changed the dynamics of traditional publishing by providing access to view, share, and reuse research findings. With the development of variants of OA such as gold APC, gold no-APC, and green OA, government organizations, research institutions, funders, and universities are not only promoting but also adopting OA policies. Moreover, several well-known funding bodies such as NIH, The Wellcome Trust, and the Bill & Melinda Gates Foundation have mandated open access to published materials.

Searchable databases such as the Registry of Open Access Repository Mandates and Policies (ROARMAP) and SHERPA/Juliet provide updated information on the growth of OA policies and funders’ OA requirements for researchers, libraries, and more. As the number of OA policies and mandates continues to increase, it has become equally important to monitor the compliance to these mandates. This not only ensures fair use of public funds in research but also the wider dissemination of research findings for social benefits.

In this infographic, we present interesting statistics on the contribution to OA policies and mandates by different policymakers and regions.

Open Access

How Research Institutes Should Promote Ethical Behavior

Ethical Behavior

Research ethics is the essential code of conduct that governs academic research. It is a set of norms that define acceptable behavior. Unethical behavior often affects academic publishing. For instance, researchers may publish falsified data. However, many groups are now promoting research ethics. So how does a one maintain ethical conduct in academic research?

Ethics is Essential

Ethical research first requires honesty. This means that researchers should not falsify or misrepresent data. Each researcher must clearly report their data as is including the methods and results even if they are not favorable. They should not at any point change the data in order to deceive colleagues, funders, or the public.

Linked to honesty is objectivity. Studies must be designed to minimize bias. Researchers must also actively avoid bias in data analysis and interpretation as well. Any personal or financial interests should be disclosed along with the research. This will alert readers to any potential influences that may have affected your work.

In addition, all animals used in the research must be properly cared for. Experiments should be designed well. This means that the design must be statistically sound. This will help researchers to use only the number of animals that is necessary. A thorough literature search should be done to avoid repeating animal studies. It is wasteful to experiment on animals if conclusive published data exists.

When humans are the subjects of research they must be treated well. Every effort must be taken to minimize risks and maximize benefits. At every point, the rights to autonomy, privacy, and dignity must be respected. Special care must be taken when working with vulnerable populations.

Some believe that bad researchers behave unethically. The alternate theory says that misconduct happens because of external factors. These include the pressure to publish or win grants, incentives, or constraints. Misconduct can also occur because of poor supervision, career ambitions, or the pursuit of fame. Every researcher will face pressure at one time or another. What is the best way to ensure that they do the right thing?

Promoting Institutional Ethical Behavior

Ethical conduct is essential in inspiring trust. When scientists abide by research ethics, their work is trustworthy. Academic research institutions often wish to encourage their staff to behave ethically.

Institutions can promote ethical behavior by having formal and informal research ethics education. Formal education will expose researchers to ethical standards and policies. Using real-world examples can teach researchers about the importance and consequences of alternate responses to an ethical dilemma. Public discussions in an ethics course may discourage unethical behavior. This happens because participants talk about the potential harm that can result.

Institutions should do a few things to teach faculty and students research ethics.

  • Use specific examples as much as possible in the course. This is the best way to provide guidance.
  • Encourage more ethical behavior. There should be opportunities for experts to explain why certain ethical practices exist.
  • Use non-science fields to assist with rethinking controversial issues. Studies in moral philosophy or the social studies of science may help.
  • Chosen topics that are intellectually stimulating. They may be in a specific ethics course or part of a more general course.
  • Discuss institutional codes of conduct. This will help make everyone aware of what acceptable behavior is. It will also help staff and students learn how to address or report a breach of ethics.
  • Share and discuss unique ethical dilemmas among researchers. These talks should help them find the best ways to promote research ethics in their own niches.

Guidelines for Ethical Conduct

Fortunately, there are ethical guidelines available for various disciplines. For example, HEART has issued an ethics statement for publishers. (HEART is a group of editors of major cardiovascular journals). Medical laboratory staff can learn from the American Society for Clinical Laboratory Science’s code of ethics. Professors may adhere to the American Association of University Professors’ professional ethics statement.

Research ethics can be a very tricky subject. Ethical conduct is essential to researchers being trustworthy. Many institutions are now promoting research ethics. Academic research and academic publishing only have value when researchers behave ethically. You can get detailed guidance on the ethics of working with people here. Furthermore, if you are thinking about implementing an ethics course, you can read this for more tips.

Springer Journal Suggester: How to Identify an Appropriate Journal for Publishing

springer-journal-suggester

Finding the right academic journal is central to preventing the common mistake of editorial rejection of manuscripts, prior to peer review. The Springer Journal Suggester is an academic research tool that enables users to select the best-suited journal for their research. The automated process can enable journal selection from a database of over 2,600 Springer publications. The web-based semantics technology refines a list of relevant journals, based on inputs of manuscript title, abstract, and publishing model. The personalized recommendation process will search Springer and BioMed Central to find the best publication that suits the author’s choice. A refined list of potential journals can thereby assist authors to delineate a core publication for their final manuscript submission.

Key Features

The web-based Journal Suggester is easily accessible, requiring only an abstract/description of the unpublished manuscript to find matching journals. When manually selecting the right journal for manuscript submission, stepwise instructions below, via Springer and BioMed Central can offer general guidance. Conversely, the online Journal Suggester automatically considers the same key points, during the process of personalized recommendations.

  1. Choosing the theme: Focus on the research discipline best suited for the unpublished manuscript. Consider the best fit of the study within research models of—applied science, clinical research, basic research, or translational research. Browse a list of journals by subject area.
  2. Choosing the audience: Consider the target audience. Choose a specialized journal or a broader publication covering a range of topics for accessibility of the study outlined.
  3. Type of article: Ensure the possibility of publishing the article in your journal of choice. Depending on the study and journal publication guidelines, submit the manuscript as an original research article, a review, or a case study.
  4. Impact Factor: This is not a key requisite for publication. However, enquire about the metrics as a measure of the journal’s reputation, in alignment with the quality of your impending publication.
  5. Publication timeline: Estimate the timeline for peer review and the turnaround time for publication in the journal of interest. To reach a broader audience, consider options from open access journals

You can further refine the web-based recommendations tool by including the following parameters to the semantics analysis:

  1. Minimum impact factor sought
  2. Article acceptance rate
  3. Time to first decision
  4. Indexing services
  5. View (choice of all journals, fully open access journals only, or subscription journals).

journalselector

For transparency, the entire database of Springer Open Access journals scanned during the automated refining process is also available online.

User Guide

The practice of research publication from proposal to journal article should align with best practices and codes of conduct. To begin with, therefore, publishing ethics highlight the researcher’s responsibility towards publication of the finalized manuscript. Selecting a journal via Journal Suggester depend on inputs of the unpublished manuscript’s abstract, research description, or a sample text. You can refine the results based on the defined parameters of 1) Publishing model, 2) Impact Factor and 3) Journal access. With a list of journals at hand for the manuscript of interest, the following user guide will assist in the publishing process:

  1. Manuscript preparation: Select a journal of your first choice from the refined list provided via Journal Suggester. Follow journal-specific guidelines on content style and the submission process—detailed as “Instructions for Authors”, on the individual journal’s homepage.
  2. Language: Ensure the manuscript clearly articulates its message in the English language. Should you require writing assistance in English consider the following options:

i) Ask a native English-speaking colleague to review your manuscript for clarity.

ii) Visit the English language tutorial designed to assist non-native English speaking scientists.

iii) Use a professional language editing service to help you refine your manuscript.

  1. Referencing style: Depending on the discipline refined via Journal Suggester, select the referencing style of your Springer journal of choice. Sample referencing styles are within your journal’s “Instructions for Authors”. Springer also provides output styles supporting the formats of both EndNote and LaTeX.
  2. Artwork: For Springer publications, all of your artwork requires submission in an electronic format. Next, the publication will meticulously produce the artwork to the highest standards, while directly reflecting its quality as provided.
  3. CrossCheck: The shortlisted Springer journal will crosscheck your manuscript for plagiarism detection and ensure originality of content.
  4. eSupplementary: It is possible to publish further dimensions of the article as electronic supplementary materials (animations, movies, audio, etc.). Springer accepts electronic files for publication in the online version only.
  5. Author helpdesk: For further assistance with article publication on the selected Springer journal, fill in the online helpdesk

journalselector_results

Benefits and Limitations for Users

Springer journals conveniently present a list of Springer Videos for user-friendly assistance on its online platform and on journal selection. When Journal Suggester provides a list of target journals, SpringerLink journal tutorials can guide the selection of your final choice. Automation offers a fast-track process for busy scientists to select a journal best suited for their research with ease. If you are keen to publish fast, Journal Suggester provides the option of deciding the ‘maximum time to first decision’. To strengthen your readership, it is possible to select open access exclusively during the journal refining process. After choosing the journal of interest, it is beneficial to identify a second and third choice of interest as well. This provides a broader range of alternatives for consideration should the first attempt at publication fail.

This automation process of Journal Suggester is beneficial overall for fast-paced and cutting-edge research publications. However, the portal’s limitations would be its influence on broader research; for example, additional experiments could increase the publication’s research impact. Furthermore, the manual process of browsing journals may provide you first-hand experience on relevant journals, albeit time-consumingly. The expected outcome of the automated Journal Suggester is to minimize editorial rejection of manuscripts prior to peer review. Overall, the benefits of this web-based academic research tool appear to outweigh its potential limitations.

Recently, Enago Academy launched Open Access Journal Finder (OAJF) that aims at enabling research scholars to find open access journals relevant to their manuscript. OAJF uses a validated journal index provided by Directory of Open Access Journals (DOAJ) – the most trusted non-predatory open access journal directory in its search results. Moreover, the tool displays vital journal details to the scholars including publisher details, peer review process, confidence index (indicates similarity between matching keywords in the published articles across all journals indexed by DOAJ), and publication speed.

Discussion Vs. Conclusion: Know the Difference Before Drafting Manuscripts

Discussion Vs. Conclusion

The discussion section of your manuscript can be one of the hardest to write as it requires you to think about the meaning of the research you have done. An effective discussion section tells the reader what your study means and why it is important. In this article, we will cover some pointers for writing a clear, well-organized discussion and conclusion sections and discuss what should NOT be part of these sections.

What Should be in Discussion Section?

Your discussion is, in short, the answer to the question “what do my results mean?” The discussion section of the manuscript should come after methods and results section and before the conclusion. It should relate back directly to the questions posed in your introduction, and contextualize your results within the literature you have covered in your literature review. In order to explain to your reader, you should include the following information:

  • The major findings of your study
  • The meaning of those findings
  • How these findings relate to what others have done
  • Limitations of your findings
  • An explanation for any surprising, unexpected, or inconclusive results
  • Suggestions for further research

Your discussion should NOT include any of the following information:

  • New results or data not presented previously in the paper
  • Unwarranted speculation
  • Tangential issues
  • Conclusions not supported by the data

How to Make Discussion Section Effective?

There are several ways to make the discussion section of your manuscript effective, interesting, and relevant. Most writing guides recommend listing the findings of your study in order from most to least important. You would not want your reader to lose sight of the key results that you found. Therefore, put the most important finding front and center.

Imagine that you conduct a study aimed at evaluating the effectiveness of stent placement in patients with partially blocked arteries. You find that despite this being a common first-line treatment, stents are not effective for patients with partially blocked arteries. The study also discovers that patients treated with a stent tend to develop asthma at slightly higher rates than those who receive no such treatment.

Which sentence would you choose to begin your discussion?

Our findings suggest that patients who had partially blocked arteries and were treated with a stent as the first line of intervention had no better outcomes than patients who were not given any surgical treatments.

Our findings noted that patients who received stents demonstrated slightly higher rates of asthma than those who did not. In addition, the placement of a stent did not impact their rates of cardiac events in a statistically significant way.

If you chose the first example, you are correct. If you aren’t sure which results are the most important, go back to your research question and start from there. The most important result is the one that answers your research question.

It is also necessary to contextualize the meaning of your findings for the reader. What does previous literature say, and do your results agree? Do your results elaborate on previous findings, or differ significantly?

In our stent example, if previous literature found that stents were an effective line of treatment for patients with partially blocked arteries, you should explore why your results are different in the discussion. Did your methodology differ? Was your study broader in scope and larger in scale than the previous studies? Were there any limitations to previous studies that your study overcame? Alternatively, is it possible that your own study could be incorrect due to some difficulties you had in carrying it out? Think of your discussion as telling the story of your research.

Finally, remember that your discussion is not the time to introduce any new data, or speculate wildly as to the possible future implications of your study. However, considering alternative explanations for your results is encouraged.

Discussion and Conclusion

Avoiding Confusion in your Conclusion!

Many writers confuse the information they should include in their discussion with the information they should place in their conclusion. One easy way to avoid this confusion is to think of your conclusion as a summary of everything that you have said thus far. In the conclusion section, you remind the reader exactly what they have just read. Your conclusion should:

  • Restate your hypothesis or research question
  • Restate your major findings
  • Tell the reader what contribution your study has made to the literature
  • Highlight any limitations of your study
  • State future directions for research/recommendations

Your conclusion should NOT:

  • Introduce new arguments
  • Introduce new data
  • Fail to include your research question
  • Fail to state your major results

An appropriate conclusion to our hypothetical stent study might read as follows:

In this study, we examined the effectiveness of stent placement in patients with partially blocked arteries compared with non-surgical interventions. After examining the five-year medical outcomes of 19,457 patients in the greater Dallas area, our statistical analysis concluded that the placement of a stent resulted in outcomes that were no better than non-surgical interventions such as diet and exercise. Although previous findings indicated that stent placement improved patient outcomes, our study followed a greater number of patients than the major studies previously conducted. It is possible that outcomes would vary if measured over a ten or fifteen year period, and future researchers should consider investigating the impact of stent placement in these patients over a longer period of time than five years. Regardless, our results point to the need for medical practitioners to reconsider the placement of a stent as the first line of treatment as non-surgical interventions may have equally positive outcomes for patients.

How Sharing Peer Review Data Helps Counter Scientific Misconduct

https://www.enago.com/academy/wp-content/uploads/2018/01/Peer-Review-Data.jpg

Life science research is going through a reproducibility crisis. Indeed, 70% of researchers have tried and failed to reproduce another scientist’s experiments. This has prompted scientists to question peer review models and promote the sharing of peer review data. All of this has come as an effort to promote scientific integrity and effectively minimize instances of scientific fraud.

Analyses in psychology and cancer biology have revealed shocking facts about experimental reproducibility. According to a recent study, only 40% of the reports from psychology and 10% from cancer biology are reproducible. This lack of reproducibility is largely due to the selective reporting of data, pressure to publish, low statistical power/poor analysis, insufficient replication, poor experimental design, or unavailability of raw data. One way to address this is to promote the peer review of manuscript data. This will significantly facilitate the assessment of data accuracy.

Sharing Raw Data
Efforts to promote data sharing have been increasing. Nevertheless, only a few journals have actually implemented policies to meet the goals of establishing transparency.

Some journals review data sets, but they do not share such data sets. Furthermore, peer review itself has not been systematically reviewed for efficacy (perhaps, this has consequences for reproducibility too). There continue to be discussions on enhancing resources that are available to editors and researchers. One possible solution is to work with meta-researchers and create experimental peer review systems that can be validated easily. Incorporating plagiarism detection software for detecting copied data sets could also help to some extent.

Peer Review of Shared Data Sets
Currently, several journals require that authors submit data sets for peer review. Journals then perform a technical and subject-area review of data sets, which includes an assessment of the following:

– Data logic
– Consistency
– Formatting
– Open access plausibility
– Quality
– Handling/reuse
– Units of measurement
– Quality of collection methods
– Presence of any anomalies

Meanwhile, several researchers still hesitate to share data sets, presumably because of the extreme competition and reduced research funding.

Journals Should Share Peer Review Data
Sharing all aspects of peer review could help promote transparency. PEERE, a large European cohort, worked with Elsevier, Springer Nature, and Wiley to develop a protocol to do so. Ultimately, their efforts seek to develop a normalized system for publishing peer-reviewed data sets.

In addition to the PEERE initiative, several peer review models need modifications to enhance the transparency of manuscripts and experimental data sets. In summary, the peer review of shared data sets is expected to decrease instances of scientific misconduct.

Tips on Manuscript Resubmission: How to Write a Good Rebuttal Letter

Rebuttal letter

Following from ‘Five Tips for Writing a Good Rebuttal Letter’, we revisit the theme of manuscript resubmission to academic journals. The initial feedback from editors and reviewer’s about one’s work can trigger a variety of reactions based on its analysis. While authors seek positive feedback in general, the more realistic expectation is to address the reviewer’s requests for revision. Methods of writing a rebuttal letter can determine if manuscript revision is likely to be successful or a futile attempt at resubmission. Should the editorial outcome be negative with equally critical referees, the recommendation is to provide an appeal letter first. However, authors who receive positive feedback can revise in compliance with comments, and submit revisions along with a rebuttal letter.

A Writing Guide – Do’s and Don’ts

A rebuttal letter offers authors an opportunity to address reviewer’s concerns directly, defend aspects of work, and eliminate contextual misunderstandings. This stepwise breakdown of writing a rebuttal letter aims to assist authors during the revision to ensure grant of appeal.

Step 1: Say Thank You

Acknowledge the reviewers time, comments and expertise. Thanking the reviewers sets a positive tone to begin with, providing the basis for an ongoing amicable exchange. Do not insinuate reviewer bias or incompetence. Prudent statements from the author cannot result in a positive re-evaluation of the work.

Step 2: Be Modest

Acknowledge any misunderstandings on your part including a poor presentation that may have led to reviewer’s confusion. Do not imply reviewer incompetence or lack of expertise in the phrasing of your rebuttal. Be clear, avoiding ambiguous and blank statements.

Step 3: Keep it Short

Respond to each reviewer’s individual comments, by copying the full text within your rebuttal letter. Strive to keep answers brief, succinct and well versed. Explain how you intend to revise the concerns either experimentally or editorially. Do not plead for reconsideration based on lack of funding as one of the reasons surrounding your inability to complete key experiments. Original scientific articles require the full spectrum of research, and the inability to meet reviewer requests experimentally is not viable.

Step 4: Explain Everything

If data required is available as a supplementary article, which the reviewer may have missed, explain this in your rebuttal for clarity. If you are unable to address a point raised in the reviewer comments, explain your reasons for evasion. Do not blatantly ignore reviewer comments, while selectively answering a few.

Step 5: Major Comments and Minor Comments

Often authors receive feedback on their manuscript from the editorial and reviewers as ‘Major’ and ‘Minor’ comments. If reviewer comments deviate from the typical format, categorize the comments provided relative to your work, as major and minor:

  • Major comments: delineate major comments based on its relevance to the integral scientific or academic content of your manuscript.
  • Minor comments: concern data presentation, table formatting, suggested changes to figures and citation errors, including comments on syntax errors.

Wrapping It Up

The five key opinions stated above, point authors in the right direction of writing an effective rebuttal letter. However, a few considerations remain to refine and wrap-up the final framework.

  1. Most journals require individual acknowledgment of the work completed by co-authors in a multiple-author manuscript, up-front, prior to submission. The process allows due validation of the author’s contributions, regardless of the order in which they appear on the manuscript.
  1. For structural clarity, consider numbering the comments, breaking them apart in paragraphs, using different fonts or colors. This enables reviewers to distinguish your response relative to the comments provided in the initial feedback, immediately. Avoid the urge to write a single reply to an entire review.
  1. Consider the reference style of the journal of interest and ensure you comply with the citation system for re-submission.
  1. Upon addition of data, i.e., tables or figures, provide page numbers of inclusion as they appear within the manuscript. If the required information exceeds recommended word limits, provide the new information within Supplementary materials. Include figure panels and table numbers/positions as they appear on the revised manuscript, to distinguish the revised content. If you cannot provide the required additional information in the revised manuscript, clearly state your reasons.
  1. If referees have raised similar concerns, redirect the response to the earlier mentioned comment. Bear in mind that all referees can view all comments and replies, therefore, address each of them respectfully. Do not paraphrase a reviewer’s comments in your own response for convenience. Take time and effort to ensure your rebuttal effectively concludes the revision of your research work, for manuscript resubmission.

A quick guide sheds further light on the process of preparing your rebuttal letter in response to reviewers. Researchers can also seek support externally, to integrate a straightforward review and response process.

Predatory Publishers: How to Stop Them from Hurting Us!

Predatory Publishers

There is a constant rise in the number of articles published in predatory journals. Young, inexperienced researchers are the main target of a growing group of dubious publishers that is willing to accept almost any manuscript (regardless of the quality or authenticity) for a fee. These supposedly academic companies do not offer any services, such as peer review or archiving, and have no problem in publishing low-quality papers if the authors pay for the same. Their websites are usually unstable/poorly designed and the articles they publish are not indexed by Medline or similar databases.

Who Publishes in Predatory Journals?

According to a survey that was carried out at the beginning of the year, researchers working in developing countries (those with insufficient funds, poor research infrastructure, and limited training) are more susceptible to submitting their work to predatory journals. The idea of getting something published quickly can be quite appealing to some researchers, and receiving invitations from journals or having their papers accepted easily can give them a (false) feeling of success.

A recent study published in Nature shows that researchers from wealthy nations also fall prey to predatory publishing. David Moher, an epidemiologist at the Ottawa Hospital Research Institute in Ontario, Canada, and several colleagues spent 12 months analyzing almost 2,000 articles from about 200 suspected predatory journals. They found that more than half of the corresponding authors came from high- and upper-middle-income countries and that many articles had been submitted from institutions in the United States. Interestingly, the US National Institutes of Health (NIH) was frequently named as one of the funding agencies.

An Urgent Problem

The authors point out that “the problem of predatory journals is more urgent than many realize.” In their study, they also assessed the quality of papers published in those journals and found that most experiments could not be reproduced or evaluated properly because of missing information. Additionally, only 40% of the studies carried out on humans and animals mentioned something about seeking approval from an ethics committee, whereas in regular journals, such approval is reported for more than 90% of the animal and 70% of the human investigations.

Based on their results, Moher and colleagues estimate that at least 18,000 funded biomedical research studies end up in dubious, obscure, and poorly indexed journals. These publications do not advance science at all as they are usually of low quality and are also difficult to locate.

Global Predation

An evaluation of over 1,900 papers published in potentially predatory journals (based on Beall’s list, which was taken offline at the beginning of this year) showed that the corresponding authors of all such publications mainly originated from India (27%), the United States (15%), Nigeria (5%), Iran (4%), and Japan (4%). However, to understand these numbers, it is important to consider the total scientific output per nation (last year, the United States produced about five times more biomedical articles than India and 80 times more than Nigeria).

Stop the Plague!

Kelly Cobey, a publications officer at the Ottawa Hospital Research Institute in Canada (and one of the authors of the Nature study), is in charge of educating researchers and guiding them in their journal submission. She also helps them identify and avoid predatory journals. Unfortunately, many research institutions do not have staff members with similar roles, so what else can we do to stop the plague of predatory publishers in academic publishing?

One thing is clear: we must act immediately! To start with, it is important to tell the public what these dubious publishers are doing and warn authors (especially the inexperienced researchers) about the consequences of publishing their work in shady journals. Funding agencies, research institutions, and reputed publishers should work together to issue clear warnings against illegitimate journals and introduce recommendations on publication integrity.

Moher, Cobey, and colleagues also suggest that funders and research institutions should increase the amount of money available for open-access publishing, ensure that researchers are able to identify questionable journals and prohibit the use of funds for submitting papers to predatory journals. They should also monitor where exactly all the grantees and staff members publish their funded work (developing automated tools to achieve this would be immensely valuable).

Manuscripts published in predatory journals should not be considered for granting promotions, appraisals, tenure, or subsequent funding. Moher et al. even suggest that scientists wanting to advance in their careers or looking for research funding should be asked to include a declaration that they have never published in predatory journals (and that they do not intend to do so). Publication lists could then be checked against the Directory of Open Access Journals (DOAJ) or the Journal Citation Reports, the researchers say.

How to Publish Symposium-Based Research Presentations

symposium

Presenting your research in a conference or professional meeting symposium is a prestigious accomplishment. In a symposium talk, you present a review of your research and demonstrate how it contributes to the overall symposium topic. Preparing a symposium-based research talk is a major undertaking. However, after presenting symposium talks, many researchers move on to other tasks. All that is left of their effort and contribution is a note on their curriculum vitae that they were a speaker. The scientific content is lost to the memories of the participants and audience. However, by publishing your symposium-based research talk you create a permanent record of your participation. Through publication you also reach a wider target audience than those that were physically present. To foster your publication record, it is good practice to commit your spoken words to writing. With a little more effort, you can publish a paper as well as participate in the symposium.

What is a Symposium-Based Research Article?

A symposium-based research article is a formal document that summarizes the information presented during a symposium at a conference or professional meeting. It typically is a mini-review of a research topic, especially that of a single author or a principal investigator.

Many journals publish symposium-based research articles. There are some publishers who specialize in these types of articles. However, the pathway to publication generally follows two forms: proceedings and independently submitted articles.

Proceedings

The symposium or conference organizers may decide to collectively publish the information presented. This is done in a format called a proceeding. Proceedings report the content of symposium talks in a collection of papers which may take up an entire edition of a journal. It is the responsibility of the organizers to solicit and collect manuscripts from the speakers and to deliver them to the publisher. The decision to publish a proceeding is generally made before the symposium convenes. Authors should be notified at the time of invitation that they would need to produce a manuscript after the meeting. In these cases, it is best to organize the talk with ultimate publication in mind.

Independently Submitted Papers

If the organizers do not plan to publish the symposium in a formal proceeding, you can still publish your talk. In this case, you (the author) will be responsible for locating a suitable journal to submit your manuscript. Many, but not all, journals accept these types of papers. Some journals publish mini-reviews which are a suitable format for your symposium-based research articles. If you are invited to participate in a symposium in which the organizers do not plan to publish proceeding, you should begin exploring how and where you can publish your talk as you develop it; plan ahead. Basically, your paper will be a mini-review of a research topic. This is an excellent means to further your publication track record and reach a wider audience.  Note, it is considered unethical to submit a manuscript for publication before participating in the symposium.

Format of the Symposium-Based Research Article

The specific format will be determined by the journal to which you are submitting your paper. Unlike a normal review, the symposium-based research article is much shorter in length and limited in scope. The length will be determined by the journal with 3,000-6,000 words being typical. Your paper should include tables and figures if appropriate. Generally, the paper will follow a review format and have the following or similar sections:

  • Abstract
  • Introduction
  • Main Body of Topics (with headings and sub-headings)
  • Conclusions
  • References

Symposium-based research articles are based on lengthy, in depth symposium talks, not the typical short 10-minute journal papers given at meetings.  The latter normally present a single experiment/project which is often not finished or published.

As a researcher, you should always seek out and accept opportunities to participate in conference symposia. These are excellent ways to reach your audience and further your career. The talks you give are also opportunities which can lead to publications. As you develop your presentation, think about how to get a publication out of your efforts. Begin planning and writing your symposium-based research article as you prepare your talk.