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.

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.

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.

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.

2. 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.

3. Consider the reference style of the journal of interest and ensure you comply with the citation system for re-submission.

4. 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.

5. 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.

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.

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.