aje best practices workshop usp
TRANSCRIPT
BEST PRACTICES FOR WRITING AND PUBLISHING YOUR RESEARCHAmy BeiselStrategic Partnerships Manager
www.aje.com
© AJE
MORNING SESSION9h30 – 10h: Opening and Scholarly Publishing Report
10h – 12h: Best Practices for Reading and Writing Scholarly Articles
• Keeping up with the literature• Best practices for writing each section:
Introduction, Materials and Methods, Results, Discussion• English editing basics• Avoiding plagiarism
AFTERNOON SESSION13h30 – 15h: Best Practices for Reporting Your Research
and Submitting Your Manuscript
• Selecting data and formatting figures• Writing a title and abstract• Choosing a journal• Writing a cover letter
15h20 – 16h20: Roundtable with Experts
• Cases, Questions, and Answers
16h20: Closing Remarks
WHO WE ARE
WHO WE ARE
We help researchers successfully communicate their work.
WHO WE ARE
• PhDs: 100 on staff and 2500 in expert network• Editors recruited from top US graduate programs• Subject-matter experts in 400 areas of study• Native English speakers• 60k manuscripts / year, 400k since 2004• Proprietary software matches manuscripts with
experts• Multilingual support staff• Partnerships with major publishers and societies
WHO YOU ARERaise your hand if you are…
• Principle Investigator / Faculty Member
• Post-Doctoral Researcher
• Graduate Student
• Undergraduate Student
WHO YOU ARE
Raise your hand if you have ever…• Been an author on a published paper• Written a manuscript• Formatted a manuscript• Created figures for a manuscript• Had a manuscript rejected…
so you had to start all over again!
PUBLISHING IS TIME CONSUMING
http://indico.cern.ch/event/332370/session/10/contribution/24
arc.aje.com
THE EXPERTSTheresa Anderson, PhD – Scientific IllustratorAriana Bevilacqua, MS – Editing Team ManagerPaul Klenk, MBA/PhD – Financial AnalystLuciana Leopold, PhD – Editing Team ManagerTony Macias, MA – Academic Translation AdvisorBen Mudrak, PhD – Communications ManagerMichaela Panter, PhD – Academic EditorSilvia Santos, PhD – Translation Team ManagerAshley Smith, PhD – Scientific IllustratorKurt Spurlock, MA – Quality ManagerApril Troester, PhD – Customer Service Director
AJE SCHOLARLY PUBLISHING REPORT 2015Trends around the world and in Brazil
PUBLISHING TRENDS 2015Publication output is rapidly increasingChina is contributing a larger share every year
TEN YEARS IN REVIEW: 2005-2015
84% increase in publications:• >900,000 more in 2015 than 2005
Emerging markets playing a large role:• 204% increase in Brazil’s output• 220% increase in India’s output• 191% increase in China’s output
Medical papers have skyrocketed, with over 266,000 more published in 2015 than in 2005
PUBLISHING TRENDS: BRAZILBrazil’s growth has been slower but steady:
>50,000 papers for 2 years running
PUBLISHING TRENDS: BRAZIL
www.scimagojr.com
Brazil’s research output has increased relative to Latin America: now the majority
PUBLISHING SNAPSHOT: BRAZIL 2015Brazil has an outsize influence on Agricultural fieldsFields represented here?
PUBLISHING SNAPSHOT: BRAZIL 2015Universidade de São Paulo was 2nd in the world in terms of publication output by a research institution (after Chinese Academy of Science)
SNAPSHOT: BRAZIL 2015
Brazilian researchers published most frequently in
• PLOS ONE • Espacios• Seminas: Ciências Agrárias• Ciência e Saúde Coletiva• Ciência Rural
LOOKING BACK: BRAZIL 2005-2015
• Overall, 204% increase in publications (over 26,000 more papers last year than 2015)
• Brazil has nearly doubled its share of publications worldwide, to ~3% of the total
• Brazil has maintained its position as the largest research producer in Latin America
BEST PRACTICES FOR READING AND WRITING SCHOLARLY ARTICLES
BEST PRACTICES: OVERVIEW
• Keeping up with the literature and evaluating credibility• Writing each section of your manuscript:
Introduction, Materials and Methods, Results, Discussion
• English editing basics• Plagiarism in academic papers
KEEPING UP WITH THE LITERATURE
KEEPING UP WITH THE LITERATURE
2 million articles28,000 journals
every year
…
How can I keep up with this amount of material?How can I be sure to read the most relevant articles for my
field?
1) LITERATURE-BASED SEARCH ENGINES
These return citation results based on
keywordsauthor names
article titlejournal type
Examples of free search engines:
PubMed: You can search 26 million biomedical citations from MEDLINE, life sciences journals, and online books. May include links to full-text content.
PubCrawler scans daily updates to the PubMed and GenBank databases and emails you an alert.
PubChase: You can search the biomedical literature, create libraries, and receive recommendations based on saved articles.
Agris is a search engine for agricultural science and technology.
Google Scholar is one of the most widely used academic search engines. It’s good for “free” versions but returns a lot of gray literature or irrelevant results.
Visit Wikipedia’s “List of academic databases and search engines” for an extensive list, including discipline and access cost
2) RSS FEEDS
• Allow you to track particular websites by subscribing to automatic updates of web content
• Headlines and summaries / abstracts are listed via a feed reader
• Readers are available as add-ons in internet browsers
• After you download the RSS reader, you can subscribe to the RSS feed via journal webpages
3) TABLE OF CONTENT (TOC) ALERTS• Publishers offer TOC alerts for newly published journal
issues• Include Early View and online articles• Sign up at the publisher’s website
• SpringerAlerts, Wiley eTOC, Nature e-alert• JournalTOCs – aggregator for 28k journals including SciELO
4) LISTSERVS
• Receive journal TOCs, calls for papers, and dataset announcements via email distribution lists
• Listservs are often managed by universities and scientific organizations
• Search for associations in your discipline and ask if they offer a listserv
5) SOCIAL NETWORKS FOR ACADEMICS
Several benefits to engaging on academic networking sites:
• Identify relevant literature• Contact with researchers in your field• Building name recognition in your field• Create opportunities to collaborate
SOCIAL NETWORKS FOR ACADEMICS
How many of you have heard of the following services? How many of you use them?
• LinkedIn• Twitter• ResearchGate• Academia.edu• Google Scholar citation profile• ORCID
• Networking• Online CV• Controlling your image
• Instantaneous information
• Trading links• Public Q&A
RESEARCHGATE
• Networking• Sharing publications• Q&A with other members
ACADEMIA.EDU• Sharing full text• Discovering other articles• Searches that lead to you
GOOGLE SCHOLAR PROFILE
• Citations• Alerts for similar
articles• Largely automated
DISCUSSION
Turn to the person next to you and share one method that you often use to learn about relevant research articles.
What is a new method that you plan to try?
Any suggestions that we haven’t listed?
EVALUATING RESEARCH CREDIBILITY
You’ve read the literature
You’re ready to cite it
…
But how do you know if it’s credible?
COMMON ASSESSMENTS OF CREDIBILITY
1) Journal’s reputation
2) Author’s reputation
3) Number of article citations
CAVEAT: JOURNAL REPUTATION
Even if a journal is prominent in your field, peer reviewed, highly selective, and published by a well-regarded publisher, the article may be flawed
Journals with high impact factors have higher retraction rates
High quality research may be published in lesser-known journals, regional journals, specialized journals, or less selective journals
Other caveats?
CAVEAT: AUTHOR REPUTATION
An author’s seniority, reputation, publication record, education, affiliation with a prominent institution, or training by a prominent researcher do not guarantee that the article is credible
Why not? Your ideas?
CAVEAT: CITATION COUNT
Citation numbers can be inflated or deflated based on the factors we just mentioned:
readers’ perceptions of the journal’s reputation and author’s reputation
RISKS OF RELYING ON THESE ASSESSMENTS
1) Citing questionable studiesMay undermine the credibility of your study and perpetuate inaccuracies in the scholarly record
2) Omitting credible studies May weaken your study by overlooking findings that support or refute your work
ASSESSING CREDIBILITY
• Was the research design appropriate for the question? Were proper controls used?
• Is the work still relevant? Are there any retraction notices, errata, or negative citations?
• Are the references in the paper credible and properly interpreted?
• Is the reference list comprehensive?• How do the post-publication peer reviews evaluate the
quality of the study? (comments, PubPeer, PubMed Commons, Open Review)
ASSESSING CREDIBILITY
Taking a closer look at the research design and context will help you to become more familiar with the literature and more confident in the credibility of your sources.
DISCUSSION:Turn to the person next to you and describe an example of a research article you have read where the journal, author, or citation count was not an accurate indicator of the quality of the research.
Please share an example with the large group.
BEST PRACTICES FOR WRITING YOUR MANUSCRIPT
Keeping up with the literatureEvaluating research credibilityWriting Introduction, Materials and Methods, Results, Discussion
HOW TO TURN A LAB NOTEBOOK INTO A SCIENTIFIC MANUSCRIPTCarefully maintaining your lab notebook will make writing easier
For all experiments, record the following:• Objective• Materials and methods
• chemical reagents, analytical techniques, theoretical calculations, actual measurements, etc.
• Experimental procedure• Outcome / results• Any notable observations (especially if unexpected)
Do this for the 100th time for every procedure, not just the 1st – you never know which details will be significant
CHOOSING THE RIGHT STORY
1) Find all of your data and sort it – select the ones that tell this story
• You can put each experiment on a card or post-it so you can shuffle them around when planning
2) Next, create the figures for each point you want to make
3) Now, think about the narrative that connects each card – this will help you organize your arguments
Let’s look at some tips, section by section
ANATOMY OF A SCIENTIFIC RESEARCH ARTICLE1) Introduction2) Materials and Methods3) Results4) Discussion and Conclusions5) References6) Figures7) Title and Abstract
Cetin and Hackam (2005) Journal of Surgical Research
THE INTRODUCTIONSetting the stage
PURPOSE OF THE INTRODUCTION
Overview of the manuscript but distinct from the Abstract
• Abstract summarizes the entire paper• Introduction places the results in the context of the
larger field of study
QUESTIONS TO GUIDE YOUR INTRODUCTION
What is known about this topic?
What is not yet known?
How does this manuscript add to the body of literature in my field?
What was the purpose or hypothesis of the study?
THREE PARTS TO THE INTRODUCTION
1) Overview of previous researchWhat do we know?
2) Description of gaps in the current literatureWhat don’t we know?
3) Summary of the hypothesis underlying the studyWhat does this study contribute?
BE GENERAL FIRST, THEN SPECIFIC
“Individuals differ radically from one another in the degree to which they are willing and able to express their emotions.”
“Indeed, the popular view is that such emotional expressiveness is a central difference between men and women.... But the research evidence is mixed...”
“There is even some evidence that men may actually...”
“In this study, we recorded the emotional reactions of both men and women to filmed...”
(Bem 2003)
INTRODUCTION TIPSAssume that no one has read the Abstract
Define all abbreviations“Solid-state fermentation (SSF) is defined as the cultivation of microorganisms…”
Define key terms“surface-attached communities termed biofilms, in which the bacterial cells surround themselves with a self-produced matrix of sugar, protein, and DNA”“relative to planktonic (free-living) counterparts”
Connect the Title and Introduction
CITING PREVIOUS WORK:STRIKE A BALANCEProvide enough detail to place the results in context
…but not so much that you bore the readerPresent both sides of the previous literature
• Aim for an objective review• If you seem to be hiding some prior results,
reviewers may criticize it• Acknowledge different perspectives
CITE RECENT LITERATURERecent = past 5 years in most cases
Pitfalls of older literature:• The paper may have been disproven• The paper may not tell the whole story anymore• Readers may think you are not truly acquainted with the
field
Exception: citing historically important references or theories“Since the isolation of O139 Vibrio cholerae in 1993 [Smith et al.]”
HOW MANY REFERENCES?
Include enough references to support your hypothesis
The Introduction does not need to be an exhaustive review
Each reference should support a statement, not simply be an example
Avoid a string of references at the end of one sentence“have been examined using a variety of assays, mutagens, and strain backgrounds (31, 38, 41, 53, 56, 59).”
Many journals will allow the use of (e.g., [31] and [53])
NOTE “GAPS” IN THE LITERATURE
Each field has an infinite number of open questions –
mention a few that your manuscript answers
Don’t just mention a gap – explain why anyone should fill it
“Understanding how the P127 oncogene contributes to the transformation of epithelial cells could lead to the discovery of novel anticancer therapeutics.”
“GAPS”: OTHER THOUGHTS
If others have mentioned the question you’re answering, cite them:
this supports the importance of your project
Focus on gaps that are well defined“need to cure cancer” too broad“as yet, the portion of lipopolysaccharide bound by heat-labile enterotoxin is unknown” better
RECAP YOUR STUDY
Highlight what prompted you to perform the studyConnect your study to the gaps you defined earlier
“Because little is known about the types of V. cholerae that cause disease in non-epidemic settings, we investigated the infectious doses of several non-O1/non-O139 serogroups.”
HYPOTHESIS/PROBLEM QUESTIONHypothesis:
Specific prediction for results given current knowledgeProblem question:
Unanswered question or gap that you will fillHypotheses are encouraged
Otherwise, reviewers may think you were “fishing”Use clear, unambiguous language
“If competition lowers reproductive output, then we expect fruit size to be smaller when tree density increases.”
SUMMARIZE RESULTS BRIEFLY
Commonly, one sentence for methodsNo numerical data or statistics
“In the present study, a SUP4-o forward-mutation system was used to reexamine the relationship between MMR and Polη in preventing GO-associated mutagenesis in yeast.”
And one sentence for a major conclusion“The results reported here demonstrate that Polη can function independently of MMR to prevent GO-associated mutagenesis, presumably through its ability to bypass these lesions in an error-free manner.”
DON’T OVERSELL THE RESULTS
In mathematics proofs are common, but in biology, nothing is “proven”Use words that soften your text
likelyindicatescontributes to our understanding ofsuggestsfurther elucidates
INTRODUCTION: SUMMARY
Introduction provides context for your results:why did you write the paper?
Three parts:• Overview of results of previous studies• Description of key “gaps”• Summary of the current hypothesis and results
Be sure to include a hypothesis or problem question
INTRODUCTION: SUMMARYWhen your Introduction is written, ask yourself:
Have I described the context for my work and created a convincing narrative using references?
Your reader will look for an answer to the question:Why did the authors write this paper?
INTRODUCTION: CHECKLIST
MATERIALS AND METHODSWhat did you do? How did you do it?
WHY SPEND TIME ON THE MATERIALS AND METHODS SECTION?
The ultimate form of peer review is reproduction of published results
The importance of the results cannot be interpreted if the study methods are unclear
A good Methods section leads to reproducibility and credibility
WHY SPEND TIME ON THE MATERIALS AND METHODS SECTION?To keep the manuscript organized:
this is the framework for the Results sectionTo avoid rejection
“One of the more common reasons for rejection of a manuscript is that the reviewers cannot fully understand how the study was conducted.” Provenzale (2007) American Journal of Roentgenology
Other reasons?
WHEN IS IT BEST TO WRITE THE M&M?
While you are performing your experiments:
• Record key details
• Perform important controls
• Plan the next experiments logically
• Save time when you start writing manuscript(s)
PROPER ORDER
Order is important
Organize the section on two levels:Basic characteristics of the entire study … leading to details of individual experimentsMatch the order of methods and results reported
OVERALL FRAMEWORK
Study subjects • Human subjects, animals, bacterial strains, etc.• Approval and ethical statements
Interventions (for clinical trials)Experimental detailsData analysis
• Statistical methods
STUDY SUBJECTS AND ETHICSProvide all relevant information about study subjects
Humans: age, sex, how they were recruited, inclusion/exclusion criteria, medical conditions, control groups, sample size Animals: species, breed, housing/feeding, sample sizeMicroorganisms: species, strain, serotype
“Institutional review boards at the University of Manitoba in Winnipeg, Canada and St. John’s Medical College and Hospital in Bangalore, India approved the study and the verbal consent process. ”
INTERVENTIONS
For clinical trials or studies involving animals
• Drugs, hormones, antibiotics used (with manufacturer)• Method of administration (dose, route)
For studies involving microorganisms, list antibiotics used to maintain cultures
“All strains containing the inducible plasmid construct were grown in Luria-Bertani broth supplemented with ampicillin (100 µg/ml).”
EXPERIMENTAL DETAILSUsing the past tense, describe how each experiment was carried out and how data were measured
• Report methods in the same order as the corresponding results
• Make sure all results have methods described
• When using methods that are described in a previous paper, include a proper citation
• When modifying previous methods, include a citation and fully describe the changes
EXPERIMENTAL DETAILS WITH CITATIONS
Total sugar content was measured by a colorimetric method using phenol and sulfuric acid according to Taylor (1995).
“using the method of Taylor et al. (1995)”“as previously described (Taylor, 1995)”“using a previously described method (Taylor, 1995)”
“HESN status in the sexually exposed Colombian cohort was defined as previously described [9].”
PROVIDE SUFFICIENT DETAILS
Some terms (e.g., “analyzed”) can be vague – always state exactly what you measured or assessed
“Each fraction was analyzed for oxygen content”“Each fraction was assessed for the presence of oxygen”“The oxygen content in each fraction was measured”
Don’t confuse what was measured with what was performed“Cd binding capacity was performed”“Cd binding capacity was measured”“Measurement of Cd binding capacity was performed”
STATISTICAL ANALYSIS
Fully describe all statistical tests“An independent, two-tailed Student’s t-test for equal variance was used to compare the branch length in each group.”
If more than one test was used, specify when and how you decided to use one or the other
“Competition indices with a normal distribution, as determined by the Kolmogorov-Smirnov test, were tested for differences by Student’s t-test. Data sets without a normal distribution were tested for differences using the Mann-Whitney U test.”
Define the threshold for statistical significance“p-values < 0.05 were considered statistically significant.”
Materials and MethodsThis section is a common cause of rejection for lack of detail
Important questions:• Have I explained my methods sufficiently so that they can be reproduced
by others?
• Do I cite all previously described methods?
• Do I have too much text?
• Do I have the appropriate controls?
• Did my choice of methods introduce any bias into the results?
• Have I chosen the correct techniques to address my research question, and used the correct statistical analyses?
Materials and Methods: Final Considerations
Check journal requirements:• Animal studies (ARRIVE guidelines, IACUC approval)• Human subjects (CONSORT guidelines, IRB
approval) • Source of reagents
Consider: Do the results of the methods I chose answer my hypothesis?
RESULTS, DISCUSSION, CONCLUSIONClosing the case
RESULTS: KEY COMPONENTS
• The results should relate to the study objective
• Tie experiments together“Having shown that salamanders prefer cool water over warm water, we next determined whether water was preferred to other liquids.”
• Highlight important data, but include anything relevantPresent p-valuesTrim data that don’t fit your objective
• Follow the most logical order Not necessarily chronologicalReread for any gaps
DISCUSSION AND CONCLUSIONSLabel the final paragraph Conclusions
• Highlight major findings• Restate the study’s importance• Clarify the “takeaway message”
Address limitations• Balance with strengths• Don’t dwell on limitations that are outside of your control• End on a positive note
DISCUSSION AND CONCLUSION: FINAL CONSIDERATIONS
Base your conclusions only on the data• What do the results allow you to conclude?• Assumptions about what might be happening should be
clearly presented as speculationRemember that…
If your experimental design doesn’t answer your objective…If you generalize your results too far…If your conclusions are not supported by your data……the journal editor will not consider the work publishable
ENGLISH EDITING TIPS
BE CONCISEReaders focus on beginnings and ends
Longer sentences = larger “forgotten” middle
Rutgers University
LENGTHY SENTENCES
Take a moment to read this sentence:“On the tops of crinoids is a circle of plates called radials, which in some primitive crinoids is further divided into a lower inferradial and an upper superradial, and below the radials is a circlet of plates called basals.”
39 words(Carpenter, 2001)
LENGTHY SENTENCES
Now read the following:“On the tops of crinoids is a circle of plates called radials. In some primitive crinoids, these radials are divided into lower inferradials and upper superradials. Below the radials is a circlet of plates called basals.”
12, 14, and 13 words
(Carpenter, 2001)
LENGTHY SENTENCES
Long introductory dependent clause
Because…Because only certain proteins are transported into the nucleus of the cell, and many such proteins contain nuclear localization signals (NLSs) that are recognized by importins, we searched the primary sequences of the two novel proteins for homology to canonical NLSs.
Only certain proteins are transported into the nucleus of the cell, and many such proteins contain nuclear localization signals (NLSs) that are recognized by importins. We therefore searched the primary sequences of the two novel proteins for homology to canonical NLSs.
40 words
24 and 16 words
LENGTHY SENTENCES
Flesch reading ease and Flesch-Kincaid grade level scores can be used to objectively evaluate readability.
Flesch reading easy guidelines: - 90.0-100.0 Easily understood by an 11-year-old student - 60.0-70.0 Easily understood by 13- to 15-year-old students - 0.0-30.0 Best understood by university students
https://en.wikipedia.org/wiki/Flesch%E2%80%93Kincaid_readability_tests#cite_note-7
CUT OUT EXTRANEOUS WORDS
Short, clear sentences are easier to digest and make the point stronger
As seenCurrentlyBecauseToWhether
Shorter versionLengthy versionAs can be seenAt the present timeDue to the fact thatIn order toWhether or not
REDUNDANT PHRASES
Avoid extra words that add no meaning
Absolutely essential essentialAggregate together aggregateCompletely filled filledEnd result resultFewer in number fewerThroughout the entire study throughout the study
FORMAL TONEScientific writing does not really involve English as we normally speak it
Jargon (transfect)
Specialized meanings (transform)
Unique conventions (gender vs. sex)
Deviating from this tone will stand out to reviewers and readers –
It’s important to maintain formality
FORMAL TONE – THINGS TO AVOID
Possessive formsThe material’s melting point was…The melting point of the material was…
ContractionsCan’t Isn’tIt’s Haven’t
“Ghost quotes”Nicknames (e.g., calling oncogenes “time bombs”)Quotation marks are appropriate for direct quotes.
FORMAL SYNONYMS
AddressesApproximatelyLargeCurrentlyPerformed/conductedSuch asObserved
Formal synonymInformal termDeals withAbout/aroundBigNowadaysDoneLikeSeen/saw
WORDS WITH LITTLE MEANINGHas/is
Cd nephrotoxicity is tubular dysfunctionCd nephrotoxicity manifests as tubular dysfunction
The species has three toxinsThe species secretes three toxins
InterestingOne of its interesting functions is…One of its relevant functions is… One unique function of this protein is…
WORDS WITH LITTLE MEANINGImportant
Rice is one of the most important cropsRice is one of the most commonly consumed crops OR Rice is a critical food source for billions
SuperiorThis method is superior to previous protocolsThis method is faster than previous protocols ORThis method requires less starting material than previous protocols
PRONOUN USAGEAvoid ambiguity with demonstrative pronouns
This, that, these, those
These correspond to…These features of the cells correspond to…
And other pronounsIt was not active in the absence of Mg2+.The enzyme was not active in the absence of Mg2+.
PRONOUN USAGE
Who vs. thatUse ‘who’ to introduce information about human beingsUse ‘that’ or ‘which’ to introduce information about inanimate objects or other nouns
Patients who presented with three of the following symptoms were included.The final two subjects, who were recruited from the same site, both tested negative.
PRONOUN USAGE
That vs. which
‘That’ introduces essential information“The car that is parked next to mine has a bird painted on it.” “The cells that were transfected glowed green.”
‘Which’ introduces additional nonessential information“Uruguay, which won the first FIFA world cup, will play against Venezuela later this summer.”“Vibrio cholerae, which causes the deadly diarrheal disease cholera, is endemic to many tropical regions.”
ANTHROPOMORPHISM
Human emotions or behaviors projected onto other animals or to inanimate objects
It is unclear why cows in the US choose to face north when they eat.It is unclear why cows in the US only eat when facing north.Bacteria in rich soil regularly attack each other.Bacteria in rich soil frequently secrete compounds that kill neighboring bacteria.
MISPLACED MODIFIERSPut explanatory phrases near what they modify
The patient experienced severe pain in his right arm when lifting objects for three months.
For three months, the patient experienced severe pain in his right arm upon lifting objects.
Copper enters the environment in high concentrations due to agricultural activity in the form of copper sulfate.
PARALLEL STRUCTUREMatch elements in a series so that they serve the same grammatical purpose
WordsPhrasesClausesSentences
• Possible therapeutic approaches include surgery, undergoing radiation therapy, and to give chemotherapy.
• Better: Possible therapeutic approaches include surgery, radiation therapy, and chemotherapy.
noun
passive voice/ gerund
infinitive
AVOIDING PLAGIARISMGiving credit where it is due
WHAT IS PLAGIARISM?
U.S. Office of Research Integrity defines plagiarism as “the appropriation of another person’s ideas, processes, results, or words without giving appropriate credit”
Academic misconduct that can result in• Diminished credibility• Rejection / retraction from a journal• Dismissal from a university or research
MAIN TYPES OF PLAGIARISM
Verbatim plagiarism:
Copying text word for word from someone else’s work without citing the source
Plagiarism of ideas:
Mentioning someone else’s unique idea – theory, interpretation, data, method, opinion, or new terminology – without citing the source
OTHER TYPES OF PLAGIARISMLoose paraphrasingParaphrasing someone else’s work with only slight changes, maintaining the author’s logic and ideas, without citing the source
Plagiarism from alternate sourcesFailing to cite the source of publicly available knowledge, such as websites, blogs, lectures
Self-plagiarism and duplicate publicationRecycling your own previously published text, whether a paragraph or a whole article
WHY PLAGIARIZE?Discussion: turn to the person next to you and discuss why someone may purposely or accidentally plagiarize
Your thoughts?
Some possibilities:• Pressure to publish• Desire to advance in career• Anxiety about writing original work in English• Struggle to express complex ideas in their own words• Carelessness while writing• Heavy reliance on few sources• Belief that “imitation is the sincerest form of flattery”• Lack of understanding of norms around plagiarism
HOW TO AVOID PLAGIARISM IN YOUR WRITING
1) As you read the literature, keep careful records of your sources
Citation software can help: Zotero, ReadCube, EndNote
HOW TO AVOID PLAGIARISM IN YOUR WRITING2) Draw on multiple sources to ensure content diversity, and err on the side of citation
3) After writing, review your manuscript and reference list to ensure that all appropriate citations are included
Plagiarism software can help: Turnitin, iThenticate, eTBLAST (free)
HOW TO AVOID PLAGIARISM IN YOUR WRITING
WHEN TO CITE
When including verbatim text• Also place it inside quotation marks
When paraphrasing unique ideas, logic, information – regardless of the source
When mentioning your previously published work
When reproducing / adapting others’ graphs or tables • Request permission first
WHEN NOT TO CITE
When describing your own work for the first time
When mentioning common knowledge• Information in general reference texts• If you are not sure, cite it
MORNING SESSION9h30 – 10h: Opening and Scholarly Publishing Report
10h – 12h: Best Practices for Reading and Writing Scholarly Articles
• Keeping up with the literature• Best practices for writing each section:
Introduction, Materials and Methods, Results, Discussion
• English editing basics• Avoiding plagiarism in academic papers
QUESTIONS / DISCUSSION
BREAK
AFTERNOON SESSION13h30 – 15h: Best Practices for Reporting Your Research
and Submitting Your Manuscript
• Data and figures• Finishing touches: title and abstract• Choosing a journal• Writing a cover letter
15h20 – 16h20: Roundtable with Experts: Cases, Questions, and Answers
16h20: Closing, Questions, and Final Observations
BEST PRACTICES FOR REPORTING YOUR RESEARCH
DATA AND FIGURES
Ashley Smith, PhDScientific Illustrator
AFTERNOON SESSION13h30 – 15h: Best Practices for Reporting Your Research
and Submitting Your Manuscript
• Selecting data and formatting figures• Writing a title and abstract• Choosing a journal• Writing a cover letter
15h20 – 16h20: Roundtable with Experts
• Cases, Questions, and Answers
16h20: Closing Remarks
FINISHING TOUCHESTips for writing a strong title and abstract
CHOOSING A TITLE
Most important part of the paper• Many readers will only see the title• First chance to make a good impression
How do I write a good, appropriate title?
KEEP IT SHORT…
Lengthy titles will not be completely read• Research shows that papers with shorter titles are viewed
and cited more frequently (Paiva et al., 2012)
• 16 words is sufficient (Knight, 1996)
Remove filler terms• ‘effects of’• ‘comparison of’• ‘a case of’/ ‘a study on’
Do not use abbreviations to save space
…BUT DON’T MAKE IT TOO SHORT
Too little information means readers will skip your paper
• They may not know it is relevant to them• “Novel cancer biomarker” is short but not
informativeInclude enough information to make your study unique
“Compensatory evolution of net-charge in influenza A virus hemagglutinin”
AVOID QUESTIONS AND LENGTHY CONSTRUCTIONS• Choose a descriptive phrase – no filler words• Questions do not make good titles for scientific manuscripts
• You should be providing an answer
• Complete sentences often add excess words
“Red hens undergo spontaneous chromosome rearrangement when exposed to ultraviolet light” vs.“Ultraviolet light-induced chromosome rearrangement in red hens”
DON’T OVERSELL THE MANUSCRIPT
Avoid bold terms unless they are absolutely true – reviewers will be skeptical
• “novel”• “first time”
TITLE TIPS
Make sure your paper relates to your title
“Molecular mechanism of chromosome rearrangement in red hens” should provide a full mechanism
You may need to temper the language: “Protein X contributes to chromosome rearrangement in red hens”
Only mention methods if they are the paper’s focusPapers with methods-based titles are read less frequently (Paiva et al., 2012)
KEYWORDS
Use keywords that a reader would search for• Organism name• Most common name for a gene• Name of key technique
Place most important terms at the beginning and end
TITLE: FINAL THOUGHTS
Get your colleagues’ help!• Offer three or four choices and see which grabs
their attention
Reevaluate the title after any revisions or resubmissions
THE ABSTRACT: FIRST AND LAST
The Abstract is found at the beginning…but write it last
Always select a journal first• Word count• Differences in format and other
requirements
WRITING THE ABSTRACT
Summarize key points from every section• Reason for the study• Hypothesis• Primary methods used• Key results• Importance of the study
WRITING THE ABSTRACT: WHAT TO AVOID
Never refer to the text• “will be discussed further in the text”
Avoid citations if at all possible• Citations clutter the abstract and draw attention away
from your workLeave out numbers and statistics
• Focus on conclusions from data/overall resultsMinimize abbreviations
• But always define the ones you use
UNNECESSARY INFORMATION
Make every word count:• Remember to stay on topic. Avoid mentioning
interesting findings or experiments if they aren’t relevant to this story.
• Choose effective verbs• Critically examine each word/phrase: does it
convey important information?
TELLING READERS THEY ARE READING A PAPER
Is it necessary to remind readers that you are describing your results?
We found that neither group showed a statistically significant increase over the course of the experiment.Our results indicate that protein X is not functional in the absence of magnesium.
Note: this is okay when contrasting with others’ findings in the Introduction and Conclusion
XX
TELLING READERS THEY ARE IN THE PRESENT
Is it necessary to remind your readers that you are describing current knowledge?
In the present day, numerous archaeal genomes have been fully sequenced.There are currently known to be seven components of the ATC complex.
Note: this is okay if you are directly contrasting the findings with what was previously thought
XX
EXAMPLES OF WORDINESS
There were several subjects who completed…
Several subjects completed…
Copper, which is one of the most harmful heavy metals,
Copper, one of the most harmful heavy metals,
X
X
CHECKLIST – TITLE AND ABSTRACT
SAMPLE ABSTRACT
180 words
REVISED ABSTRACT
136 words
SAMPLE ABSTRACT
Original:At this time, very little is known about the family of proteins called editins.
More concise version:Little is known about the editin family of proteins.
14 words
9 words
SAMPLE ABSTRACT
Original:While it has previously been shown that editins can promote the progression of the cell cycle in various cell types, the exact role that this family of proteins plays is not clear.
More concise version:While editins promote cell cycle progression in various cell types, the exact role they play is unknown.
33 words
17 words
SAMPLE ABSTRACT
Original:In this study, we isolated two editin proteins, EDT1 and EDT2, from the yeast Saccharomyces cerevisiae and characterized some basic biochemical properties, such as molecular weight, isoelectric point, and multimerization status.
More concise version:Here, we isolated two editins, EDT1 and EDT2, from the yeast Saccharomyces cerevisiae and characterized several basic biochemical properties…
32 words
28 words
SAMPLE ABSTRACT
Original:It was found that both editins were present as dimers.
More concise version:Both editins were found as dimers.
10 words
6 words
SAMPLE ABSTRACT
Original:EDT1 as a monomer is 52 kDa with a pI of 5.4, and EDT2 as a monomer is 54 kDa with a pI of 5.7.
More concise version:Monomeric EDT1 is 52 kDa with a pI of 5.4, and monomeric EDT2 is 54 kDa with a pI of 5.7.
25 words
21 words
SAMPLE ABSTRACT
Original:Epitope tagging studies further demonstrated that heterodimers of EDT1 and EDT2 could also be isolated, but it is unknown whether or not heterodimers are functionally equivalent to homodimers of EDT1 or EDT2.
More concise version:Epitope tagging demonstrated that heterodimers of EDT1 and EDT2 also exist, but it is unknown whether heterodimers are functionally equivalent to EDT1 or EDT2 homodimers.
32 words
21 words
SAMPLE ABSTRACT
Original:Here, we describe the basic properties of two editins from Saccharomyces cerevisiae as well as a protocol for their purification.
More concise version:We report the basic properties of two yeast editins and a protocol for their purification.
21 words
15 words
SAMPLE ABSTRACT
Original:Additional future studies will be needed to determine how these editins contribute to cell cycle progression.
More concise version:Future studies will be needed to determine how these editins contribute to cell cycle progression.
16 words
15 words
CHOOSING THE BEST JOURNALFOR YOUR PAPER
THE GOAL: PUBLISH QUICKLY
Publication – still the primary goal of most researchers in an academic setting
Investigate
Present
Review
Publish
Read
Teach
Mentor
THE GOAL: PUBLISH QUICKLY
Every time you get rejected, it can cost you months of time or more
Find a journal that fits your work closely – take your best shot first
SCHOLARLY JOURNALSGlobal market:
2,000 journal publishersOver 30,000 active, peer-reviewed scholarly journals
At least 10,000 open access journals
English-language journals:680 publishers11,550 journalsAnnual revenues of $9 to $10 billion
Growing 7-8% per yearThomson Reuters; Directory of Open Access Journals (www.doaj.org)
PUBLICATION TRENDS
Over 1.5 million articles a year are published Growing at 3% annually (for 200 years!)
Many more are submitted to journals each year
IDENTIFYING YOUR TARGET JOURNALS
1) Find articles similar to the one you want to publish2) Collect a list of journals that publish those articles3) Research those journals4) Make a prioritized list of target journals
EXAMPLE SEARCH ENGINES
jane.biosemantics.orgwww.ncbi.nlm.nih.gov/pubmed
scholar.google.com www.journalguide.com
SEARCH
Use your draft title and abstract (finding a journal)
Use keywords (more general searches)
PROS AND CONS
PubMed All peer-reviewed Advanced search capabilities Restricted to certain
biomedical journals
Google Scholar Good at finding free versions Expansive Includes gray literature and
junk
JANE Easy interface
Layered over Medline, so no extra coverage
JournalGuide Standardized layout for finding
and comparing journals Coverage beyond PubMed while
still restricted to peer-reviewed literature
Still growing and expanding functions
ADVANCED SEARCH STRATEGIES
Use “advanced search” options if availableLimit your search to the years 2011-2016
(expand to earlier articles only if needed)Include recent articles or articles in pressNote the name of the publisher to investigate later
SAVE YOUR SEARCHES TO RUN LATER!
COLLECT “HITS” INTO JOURNAL LIST
DEALING WITH THE RESULTS
• A good number of results is 100 – 300If you recover < 30 or > 300 results, expand or restrict your search• Make a list of your top journal choices• Find out more about these journals
INFORMATION TO GATHER
Find the journal’s website, and pull out key pieces of information:
• ISSN (unique identifier for every journal)• Publisher/affiliated societies• Contact information (in case of questions)• Aims and scope• Publication frequency
INFORMATION TO GATHER
Look for additional information that can help you make a more informed decision:
• Acceptance rate• Speed
Time to first decision, time to publication online• Costs
Page fees, publication fees, color image fees• Open access policies
Is self-archiving allowed?Is full open access available?
JOURNALGUIDE.COMFind most of the information you need in one place with a standardized layout:
• ISSN• Publisher/affiliated
societies• Aims and scope• Types of submissions
accepted• Indexing• Acceptance rate• Publication
frequency• Contact info
JOURNALGUIDE.COMFind most of the information you need in one place with a standardized layout:
• Time to publication/first response
• Submission/page fees
• Color image fees• Open Access
policy
COLLEAGUES’ EXPERIENCE
One of the most valuable pieces of data about a journal is the experience of real researchers. Ask around!
Advisor/committeeLabmates (past and present)Collaborators
BENEFITS AND RISKS
High impact factor = stronger “stamp of approval”
High risk of rejection and lost time
Is it more important to get this research out quickly or to maximize the prestige of the journal?
Is this project a primary focus of your lab’s efforts or is it a side project that might be nice to wrap up?
BENEFITS AND RISKS
Multidisciplinary journal = more readers, broader impact
Need to rewrite paper to appeal to readers with less context and background
Is your work relevant to a broad audience or will its most interested readers be within your field?
Can you easily contextualize your research for a multidisciplinary audience?
BENEFITS AND RISKS
Specialized journal with fewer submissions = higher chance of acceptance
Risk of “walling off” your research within your field
Is getting the research accepted quickly an important consideration?
Will a specialized journal be visible enough to researchers in other fields?
BENEFITS AND RISKS
Open access journal = greater exposure and (perhaps) more citations
May not be the most prestigious journal in your field
Chance of running into questionable publishers
Is open access an important motivation for you?
Will you be concerned if only researchers with subscriptions can see your work?
SOUND RESEARCH “MEGAJOURNALS”
What is a megajournal?Review for soundness of research results and interpretation, not perceived importance/impactBroad subject scopePublishes any and all articles that meet criteria
PLOS ONE
2007 2013Binfield, 2013
All megajournals
MEGAJOURNALS Increasing number of journals focusing on rigor of research, not perceived
interested/novelty Usually include broad subject areas
Fast and often simpler route to publication
More effort on your part in other areas: Polishing the language Sharing the paper post-publication Demonstrating the value of the paper without relying on the journal
“brand”
THE FINAL DECISION
Weigh the pros and cons for each journal, then make an ordered list
Start with journal #1 and move down the list only if needed
Remember that the best fit is not the only thing that affects your paper’s chances:
• Edit your paper carefully• Spend time creating strong figures• Write an effective cover letter
WRITING A COMPELLINGCOVER LETTERMake your case to the journal editor
TAKE CARE WITH THE COVER LETTER
• The cover letter is your opportunity to convince the journal editor to send your manuscript out for peer review
• It highlights your most important findings
• It explains why your manuscript is a good fit for the journal
COVER LETTER: INTRO
1) Address the journal editor formally by name, if possible
2) Include your contact information
This information may also appear in the journal’s online submission system, but it is appropriate to include in the letter
COVER LETTER: OPENING PARAGRAPHS
1) State the manuscript title and author names
2) Mention what type of article it is: research article, review, case study, etc.
3) Describe your study’s rationale and major findings
COVER LETTER: MIDDLE PARAGRAPH
1) Briefly explain how your manuscript fits the journal’s Aims & Scope
2) Don’t simply state the the findings are “novel” or “of interest to the field – include specific aspects relevant to the journal
COVER LETTER: FINAL PARAGRAPH
Close with a brief paragraph indicating the following:
1) The manuscript is original work2) No part of the manuscript has been published before3) The manuscript is not under consideration at any other
journal4) There are no conflicts of interest to disclose5) A list of potential reviewers – only if journal requests this6) Any researchers who should not review your manuscript
due to potential conflicts / bias
COVER LETTER: CLOSING THOUGHTS
A well-written cover letter assures the journal editor that • your manuscript should be considered• it is a good fit for the journal
Good research may be reviewed regardless of the cover letter’s quality, but a great cover letter can help your manuscript stand out
EXPERT ROUNDTABLEQuestions & answers with AJE’s team of experts in the United States
arc.aje.com
THANK YOU AND BEST WISHESFROM THE AJE TEAM
Flavia Jaszczak [email protected] [email protected]
© AJE