Eeny, meeny, miny, mo: Deciding where to submit a manuscript for publication

look-of-successI am one of the instructors for the MyResearch graduate seminar series, which just ended for the autumn semester. It will be offered again in the winter. Issues in scholarly publishing are one of the topics we discuss in MyResearch, such as which factors should we consider for determining the best journal to submit a manuscript.

I use the following multi-step approach for selecting a journal:

1- With the database search results I exported to EndNote, I sort the relevant references in my EndNote Library by the “Journal” column and pick out a few journals (usually 3-5) that published the most articles on my topic.  You can also click on “analyze results” in Web of Science and Scopus to see the list of journals in your results set, listed from the ones with the most articles to the least.

2- I visit each journal’s website, where I read about the scope of the journal and look at the instructions to the authors.  This helps me determine whether my article would be considered for publication by the journal.  If yes, I move on to the next step.

3- I search for the Journal Impact Factor in Journal Citation Reports (you can also click on the journal name for a result in Web of Science to view the Journal Impact Factor), and then I use the “Compare sources” option in Scopus to search for each journal, which will enable me to look at the journal’s SJR (Scimago Journal Rank) score, SNIP (the citation potential or the average times an article in that journal can expect to be cited in a given year) score, % not cited, and % reviews (review articles usually generate more citations, so if a journal publishes a lot of reviews, this might inflate its SJR and Journal Impact Factor scores).  All these metrics are calculated differently but viewed together they tell me a story of which journal has the higher impact, based on more than one criterion.

4- If the journals I’m comparing rank about the same, e.g., let’s say they both fall between the top 25-35% of highly cited journals, I consider other factors, such as:

i) How long will it take before I receive a decision about my manuscript, and what is the journal’s manuscript acceptance rate? (Look at the journal’s website for this information. If you’re short on time to meet a deadline that requires the work to be published, this factor might be very important because you want to give yourself enough time to resubmit to a second journal if the first journal rejects your manuscript.)

ii) In which databases is this journal indexed? (If there are more databases that provide references to articles in the journal, this increases the odds of someone finding a reference to your article and citing it.)

iii) Will the journal allow me to make, at least, a post-print (final text of your manuscript, incorporating changes from peer-review process) freely available on the web within 12 months after publication? (This will allow individuals without a personal or institutional subscription to the journal to be able to read your article without paying for it, and satisfy the Tri-Agency Open Access Policy on Publications for research funded by SSHRC, NSERC, and CIHR. Search the journal in Sherpa Romeo to find this information or look at the journal’s website).

5- By this stage, I have usually narrowed down my list of multiple journals to two journals.  At this step, I consider personal preferences.  Which of the two journals do I read or use the most, or which one would make me the most proud if I received a letter of acceptance?

This is the seventh in a series of posts about topics relating to research skills and ethics. Happy Halloween!

Image from the Laugh-Out-Loud Cats cartoon strip by Adam “Ape Lad” Koford (creative commons license)

Presenting with style: Mixing the arts of storytelling & teaching

In 3-minute thesis competitions, participants explain their research projects (the why, the how, and the implications for the real world) to non-experts in three minutes or less. The speaker of the best presentation wins. Great presenters will:

  • speak clearly and unhurriedly;
  • vary their pitch;
  • incorporate a story, include a metaphor from everyday life, and/or strike an emotional cord in the listener;
  • mention unexpected/interesting facts about their topics (e.g., Silver changes the color of your tongue to blue.); and
  • provide tangible examples.

The “CHEE 687: Research Skills and Ethics” class watched some 3-minute thesis competitors in action to prepare for their own presentations. My favourite 3-minute thesis talk was from Balarka Banerjee.showing lung capacityWe also discussed elements of a good PowerPoint presentation, which:

  • has minimal content on each slide;
  • contains descriptive/specific headings (rather than general and predictable headings like Introduction, Background, Results, Conclusions);
  • engages the audience at the beginning of the presentation with news headlines, statistics, or a story;
  • includes consistent formatting throughout;
  • utilizes a light background with dark text;
  • employs graphics to explain phenomena, processes, and/or concepts; and
  • includes citations for any images used (when not your own) on the slide itself.

This is the sixth in a series of weekly posts about topics relating to research skills and ethics. I will be taking a temporary hiatus from blogging and will resume writing this series later on in 2016. Happy holidays!

Image from the Laugh-Out-Loud Cats cartoon strip by Adam “Ape Lad” Koford (creative commons license)

Lab notebooks: Are they written in stone?

Researchers use lab notebooks to keep a daily record of their work, exactly as it happened. Lab notebooks are treated as if they are written in stone since you are not supposed to change a previous entry in any way. The lab notebook serves as proof and a complete permanent record of what was done, enabling researchers to write up their work, defend authorship and patents, remain organized, and teach others.notes everywhereBest practices for recording information in lab notebooks were discussed in a “CHEE 687: Research Skills and Ethics” lecture, and consist of:

  • Employing a bound notebook made with acid-free paper;
  • Writing in permanent ink;
  • Dating your entries and signing them at the end of the day;
  • Recording hypotheses, the plan for experiments, step-by-step procedures, all results observed, the use and location of materials, the calibration of instruments if applicable, etc., basically including as many details as possible so that another person can understand and reproduce your work;
  • Never removing pages, rather drawing a line through blank pages if you skipped some, and drawing lines through errors made when writing and initializing the strikethroughs;
  • Consecutively numbering the pages of your notebook;
  • Organizing content using headings and dividing it into sections when appropriate;
  • Attaching images and printouts of raw data to a notebook using glue;
  • Summarizing what you have done periodically; and
  • Reporting discussions with others about your work, including the names of the individuals.

This is the fifth in a series of weekly posts about topics relating to research skills and ethics. Stay tuned for the next post in the series, which will be about effective presentation styles for explaining your work to different audiences.

Image from the Laugh-Out-Loud Cats cartoon strip by Adam “Ape Lad” Koford (creative commons license)

Scientific misconduct: What is the link between cured sausage and dishonest authorship practices?

Salami, especially homemade, is one of my favourite cold cuts. I enjoy eating this type of cured sausage for lunch every once in a while. Some people say the taste of salami is different depending on the thickness of the slices. Salami is also a word used to describe papers in which the authors present very little original content since these papers are mostly a duplication of work already published by the authors. These are called salami publications. Instead of presenting the complete story of the research they conducted in the first article they wrote, the authors may have withheld some details to be able to write a second, third, fourth paper, etc. on essentially the same topic, or the authors may publish multiple papers employing similar methodologies to answer similar research questions. The authors are salami slicing or diluting the presentation of their research work to obtain more publications out of it. Regardless of whether the slicing is thin or thick, this is an example of a dishonest authorship practice that the class discussed in “CHEE 687: Research Skills and Ethics.”

We also talked about other improper authorship practices, such as:

  • manipulating data and/or images so that they look better but misrepresent what was found;
  • stretching the truth about research progress;
  • collecting or reporting data in a sloppy manner that leads to the presentation of inaccurate results;
  • sharing others’ ideas or data that you learned about in a confidential setting;
  • plagiarizing, whether including ideas or text from another’s work or your own previous work without properly citing it;
  • publishing the same work in different journals;
  • having another individual write the paper for you while you take credit for being the author; and
  • listing individuals as co-authors of a paper solely due to their reputations or authoritative ranks, even though they did not make a significant contribution to the research.keyword exposure

Just as you would do on a witness stand in the courtroom, behaving ethically as an author means reporting “the truth [i.e., the real data], the whole truth [making no changes to the real data], and nothing but the truth [not including additional information that is not based on the real data].”

Scientific misconduct encompasses all of the improper authorship practices described above since it includes engaging in any activities that are dishonest or involve lying in the data collection and reporting stages, like fabricating and falsifying data or results. The consequences for misconduct can be disastrous to a person’s career (e.g., student expelled, researcher fired, funding lost).

This is the fourth in a series of weekly posts about topics relating to research skills and ethics. Stay tuned for the next post in the series, which will be about best practices for recording and storing laboratory data.

Image from the Laugh-Out-Loud Cats cartoon strip by Adam “Ape Lad” Koford (creative commons license)

Peer review process: Confidential or not?

The peer review process is a method of assessing the quality of an individual (in the case of a grant application, for example) or evaluating the quality of a scholarly work (for instance, in the case of a journal article manuscript). It needs impartial reviewers who are experts in the research area for the process to work properly.

I used to think tanonymoushat the journal peer review process was always double-blinded, i.e., the authors did not know who the reviewers of their manuscripts were and the reviewers, in turn, did not know who the authors were. I learned that some journals have a double-blinded peer review process while others have one-sided blinding, i.e., the authors do not know the names of their reviewers but the reviewers know who the authors are. Blinding on one side should not be a problem if the reviewers perform their task objectively and critically.

What are the responsibilities of a peer reviewer and author towards each other? This was a topic discussed in a “CHEE 687: Research Skills and Ethics” class, the content of which is summarized below.

The peer reviewer should:

  • keep the contents of the grant application or manuscript confidential by not sharing it with others;
  • submit his/her comments to the funding agency or journal editor within the allotted time;
  • refuse the assignment if there are any conflicts of interest that can bias his/her assessment of the work;
  • not use any ideas or methods contained in the document (if relevant to his/her own research) until after the reviewed researcher’s work is published; and
  • conscientiously apply any evaluation criteria (supplied by the funding agency or journal editor) to the work being reviewed.

After receiving comments from the reviewers and being invited to resubmit the manuscript, the authors should:

  • respond to each of the comments made by the reviewers with diplomacy and respect;
  • do some further work if additional experiments are requested, since just altering the text in the manuscript will not be enough in most of these cases;
  • be prepared to rewrite sentences or entire sections if the reviewers did not understand the purpose of the research; and
  • consider the reviewers’ comments as an opportunity to improve the manuscript and make it the best it can be.

The peer review process is not infallible (see Nature article about peer review frauds as an example). However, when it is conducted correctly, I believe that peer review improves the quality of the submitted work before it is published.

This is the third in a series of weekly posts about topics relating to research skills and ethics. Stay tuned for the next post in the series, which will be about scientific misconduct and questionable authorship practices.

Image from the Laugh-Out-Loud Cats cartoon strip by Adam “Ape Lad” Koford (creative commons license)

Another puzzle completed

Sometimes we just need a little amusing distraction. We have a Puzzle Corner in the library to help individuals take a break from their work. It is located on the main floor of the Schulich Library of Science & Engineering, walk past the elevators and turn to your left. Below is the 1,000 piece puzzle that was just completed (minus a few pieces that went missing and which I will have fun recreating).

boat puzzleA new puzzle was set out today and is waiting to be assembled. Enjoy!

Being responsible for research work: Who should be a co-author?

I often see multiple individuals listed as authors for a single journal article in the sciences and engineering. While teamwork is expected in these fields, I wonder who did what for the research discussed in the article when the list of authors is long, e.g., exceeds five. Perhaps, some names were included on the paper for political reasons rather than intellectual contribution to the work. In the “CHEE 687 Research Skills and Ethics” graduate course that I am attending this semester, the class discussed criteria or guidelines to consider when determining who should be a co-author on a paper.

meet the authorsCo-authorship is not automatic; it is earned. An individual would be offered co-authorship on a journal article or would ask to be a co-author. To be a co-author, a person should have done the following:
1) made a significant intellectual contribution to the work by participating in the creation of the research question and plan, the data collection, and/or the analysis and interpretation of the results;
2) agree to be accountable for the entire content in the article (not just for his/her contribution), which means that all authors must communicate with each other so that everyone understands exactly what was done and said in the article;
3) participate in drafting the article; and
4) critically evaluate and double check the content of the final draft.

If someone does not do all of the above, one could successfully argue that the person should not be a co-author but, rather, can be listed in the acknowledgements section if he/she helped in some way. Just communicating ideas to the lead author, providing feedback, editing, or helping with a task does not automatically make a person a co-author.

thought experimentThis is the second in a series of weekly posts about topics relating to research skills and ethics. Stay tuned for the next post in the series, which will be about the peer-review process.

Images from the Laugh-Out-Loud Cats cartoon strip by Adam “Ape Lad” Koford (creative commons license)

Reading and writing research: What makes a good scientific paper?

I am fortunate this semester to be able to participate in a new graduate Chemical Engineering course called “CHEE 687 Research Skills and Ethics,” taught by Professor Nathalie Tufenkji. This course covers a wide range of topics dealing with how to conduct research as a graduate student and professional, such as best practices for keeping a lab notebook, how to recognize and manage conflicts of interest, what elements to include when writing a scientific paper, how to determine who should be a co-author on a paper, etc. I find the classes very engaging and practical, thereby inspiring me to write about some of the topics presented with the belief that it might be of interest to readers doing their own research.

The first topic I would like to discuss is about scientific writing. We may have a sense when we are reading a research article that it is difficult to read or that there is something quite not right with the article, but we may not always be able to articulate the reasons why.

middle of nowhereWhat are the characteristics of a good scientific paper? What should we look for when reading a paper and what elements should we consider including when writing one? We tackled this topic in class by discussing what should be in each section of a research article, which is summarized in the points below:

  • Introduction/Background section: Publishing a journal article is a method of communicating research findings and helps build a researcher’s professional reputation. However, Professor Tufenkji also reminded us that one of the purposes of a research article is to educate readers. Imagine that one of the article’s readers is a beginning graduate student in this area. Therefore, the introduction/background section of the article is where the authors should explain the context of the research by summarizing and citing previous work in the area, describing how this study builds on previous publications or is different from them, stating the motivation of the study (the “why”), and presenting the research question/hypothesis (the “what”). This section usually starts from the general (the summary of previous work) and moves to the specific (the research question/hypothesis).
  • Methods section: Includes a detailed description of the steps the authors took to conduct the experiment/study (the “how”) so that readers can reproduce the study if they wish. The more details the authors can provide to help the reader understand and replicate what was done, the better (e.g., state the pH of a sample, the volume of the sample, how or where it was obtained, etc.).
  • Results section: Simply describes what was found. The results section should be presented in the same order as the methods section to make it easier for readers to follow. For example, if the authors conducted two experiments and described the steps for Experiment 1 first in the methods section, then the reader would also expect the results for Experiment 1 to appear first in the results section.
  • Discussion & conclusion sections: Interpret the results by explaining to the reader what the data means and comparing this data to previous published literature on the topic. This is also where the authors use the data to make appropriate and logical conclusions (without generalizing or over interpreting the results) and describe directions for future research.

The authors should write the paper in a way that makes the greatest impact on its readers, such as writing an article title that describes the major finding of the article and writing the article in a language that is as clear as possible (see a list of wordy phrases to avoid using when writing a manuscript).

lol titleRemember that while the article is written in the order that the authors went about conducting the experiment/study (i.e., Introduction/Background – Methods – Results – Discussion/Conclusion), this does not mean that you need to read the article in this order. I frequently skim a research article in the following order to quickly extract the main points: after reading the abstract, I jump to the discussion and conclusion sections to find out what the research all means, then back track to the introduction/background to get the context for the research, look at the results for more details of what was found, paying attention to any figures or tables that summarize the main findings of the article, and finally examine the details in the methods section. If the article is relevant for my own research or impacts my professional practice, I will read it thoroughly, otherwise I will put it aside.

This is the first in a series of weekly posts about topics relating to research skills and ethics. Stay tuned for the next post in the series, which will be about determining authorship for a scientific paper.

Images from the Laugh-Out-Loud Cats cartoon strip by Adam “Ape Lad” Koford (creative commons license)

Natural Disasters: Live from the MOOC’s Epicentre!

350-public-mooc-natural-disasterAs you may have already heard, there is a MOOC currently being offered on Natural Disasters, which is taught by Professor John Gyakum and Professor John Stix. Related to this, the professors will be giving a talk about natural disasters in the Montreal area. This will include why certain disasters would not happen here and how we can mitigate the impact of natural disasters on our daily lives. They will also be answering your questions about natural disasters.

This event will be held on Tuesday, July 15th from 6:30-8:30pm in the Schulich Library of Science and Engineering. Refreshments will be served.

All are welcome to attend. Registration is required. Please visit http://bit.ly/montrealepicentre to register. I hope to see you there!

Plant regrowth after 1,600 years

Spring is here and my parents have started planning their garden by growing tomato seeds indoors.  In about a month’s time, these seeds will have grown into small plants that will be transplanted to the earth outside when the weather is warmer.  There was an interesting article published in the March 17th issue of Current Biology that discusses how scientists were able to regrow a moss plant that had been frozen for 1,600 years.  They just let it thaw and watered it.  According to the authors, it is the first study to report the revival of a frozen plant or animal after such a long period of time.