How to write a research paper...... Storytelling with rigid rules Steven R. Barthel, Ph.D. Google Images.com.

How to write a research paper......Storytelling with rigid rules

Steven R. Barthel, Ph.D.

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Writing can be challenging

Writing a scientific paper is not easy and does not come naturally to everyone. Procrastination is a real danger!

“It’s easier to embalm the dead than to write an article about it.” Paul Silvia, How to Write a Lot: A Practical Guide to Productive Academic Writing.

“It [writing] is a generative activity requiring motivation, and it is an intellectual activity requiring cognitive processes and

memory.”JR Hayes, A New Framework for Understanding Cognition and

Affect in Writing.

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Avoiding Procrastination – When to Write1) After every experiment, generate potentially publishable

figures.Immediacy/Urgency help to:-minimize error-focus the research

-saves time-saves money-saves pain by avoiding extra work

2) Compile the figures in Powerpoint, Illustrator or Photoshop in a logical sequence that tells an interesting story:

1. What is the topic of the paper?2. Why is this topic important?3. How can the hypothesis be formulated?4. What is the major finding, novelty or significance?

3) Begin writing even before the project is complete, generally as soon

as answers to 1-4) above are apparent (~50% of all data is compiled).

Avoiding Writer’s Block

Start with the easiest sections first! Materials and Methods Title Page

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Adapted from last year’s seminar by Dr. Charles J. Dimitroff

2009

Topics

B asic components of a research paper - Title, Abst, Intro, M&M, Results, Disc, Refs

A nnotate, repetitive and brevity - use outline for each section/focus on single

angle

S yntax and paper formatting - follow proper grammar and rigid

framework

I mpact of research paper - complete biological context

C o-authorship - recognition/career development

S ubmission and cover letter - appeal to editors and reviewers

TITLE

TITLE

a.) Provide a summary of study in one phrase or sentence

Phrase – “Analysis of the diet of summer students working in The Department of Dermatology ”

Sentence – “ Summer students working in The Department of Dermatology are major consumers of pizza. ”

Colonic – “ Pizza: a legendary food loved by all “

ABSTRACT

There is nothing abstract about the abstract!

a.) 2 sentences on background (Present)

b.) 1 sentence on gap in knowledge (Present)

c.) 1 sentence hypothesis or purpose of study (Present)

d.) 1-2 sentence description of methods/models/approach

(Past)e.) 3-5 sentences on results (Past)

f.) 1-2 sentences on how findings improve understanding

(Present)

Sentences = 10-13 ~200-250 words

INTRODUCTION

INTRODUCTION

a.) Define the gap in knowledge (Present) - Form known 1-2 thoughts (one paragraph/thought)

b.) Define straight path to the unknown or gap (one paragraph)

- State hypothesis or purpose of study (Present)

c.) Summarize plan of attack and overview of findings (one paragraph)

- Arrange as mini abstract with results (Past)

MATERIALS AND METHODS

MATERIALS AND METHODS

a.) List reagents (cells/proteins/chemicals) as individual categories and where they were purchased/obtained (Past)

b.) Describe how each bioassay/method was performed

using short recipe-like descriptions (Past)“ Pizza was cooked in an oven.“

vs.“ Pizza was cooked in an oven by heating to 350oC for 25 min. ”

Due to word limitations, authors increasingly place some Methods into the Supplemental Section to keep within word limitations

RESULTS

RESULTS (Figures)

a.) Create and outline a story based on logical flow of experimental observations (-layout Figures)

- Figures - Graphs, Summary Tables of Data, Photomicrographs of tissues, blots,

gels

- Simple, yet completely labeled axes - Viewer-friendly orientation and size

- Parallel structure (Font, alignment, size)

RESULTS

RESULTS (Figures)

a.) Create and outline a story based of logical flow of experimental observations (i.e. Figure order)

- Figures - Graphs, Summary Tables of Data, Photomicrographs of tissues, blots, gels

- Simple, yet completely labeled axes - Viewer-friendly orientation and size

- Parallel structure (Font, alignment, size)

b.) Describe all data shown in Figures and reveal any patterns (include statistics/group

numbers/controls) (Past)

- Statistical analysis: GraphPad Prism, Excel, SPSS

RESULTS

RESULTS (Figures)

a.) Create and outline a story based of logical flow of experimental observations (i.e. Figure order)

- Figures - Graphs, Summary Tables of Data, Photomicrographs of tissues, blots, gels

- Simple, yet completely labeled axes - Viewer-friendly orientation and size

- Parallel structure (Font, alignment size)

b.) Describe all data shown in Figures and reveal any patterns (include statistics/group

numbers/controls) (Past)

- Statistical analysis: GraphPad Prism, Excel, SPSS

c.) Separate data sets into Subheading/Conclusive Sentence

e.g. Summer students love pizza. - Fig. 1 – Survey of students’ favorite food - Fig. 2 – Graph plotting number of students who eat pizza (#/day/week)

DISCUSSION

DISCUSSION

a.) Recap your data and provide any connections with your methods and results with other existing papers.

- If describing general knowledge/generalities (Present)

- If describing specific data from your study (Past)

DISCUSSION

DISCUSSION

a.) Recap your data and provide any connections with your methods and results with other existing papers.

- If describing general knowledge/generalities (Present)

- If describing specific data from your study (Past)

b.) Offer a proposal – conjecture, prediction, refined hypothesis, generalization, model or theory

(Present)

DISCUSSION

DISCUSSION

a.) Recap your data and provide any connections with your methods and results with other existing papers.

- If describing general knowledge/generalities (Present)

- If describing specific data from your study (Past)

b.) Offer a proposal – conjecture, prediction, refined hypothesis, generalization, model or theory

(Present)

- If possible, provide graphic/cartoon depiction of model

Taken from Goggle Images.com

REFERENCES

REFERENCES (Citations)

a.) Use ENDNOTE software

- Easiest method of managing, storing and inserting research papers as citations into your document

– Interfaces with Microsoft Word ; icons appear in the tool bar in Word document.

- Reference style needed for a specific Journal can be modified with a click of the button.

REFERENCES

REFERENCES (Citations)

a.) Use ENDNOTE software

- Easiest method of managing, storing and inserting research papers as citations into your document

– Interfaces with Microsoft Word ; icons appear in the tool bar in Word document.

- Reference style needed for a specific Journal can be modified with a click of the button.

b.) General Points

- When citing prior work, authors often reference their own work; lends credibility and building of reputation in the field. Also, advertises your

work!

- If citing a specific research finding, try to reference seminal research paper where discovery was made.

- If citing generalities, citing review papers is common.

REFERENCES

Taken from Goggle Images.com

WRITING PROCESS

a.) Always start with an outline (even for each section). - Familiarize yourself (become an expert) in your area

(Pubmed (updated daily), Wikipedia, Textbooks)

WRITING PROCESS

a.) Always start with an outline (even for each section). - Familiarize yourself (become an expert) in your area

(Pubmed (updated daily), Wikipedia, Textbooks)b.) Focus on a single research direction, purpose or definition

WRITING PROCESS

a.) Always start with an outline (even for each section). - Familiarize yourself (become an expert) in your area

(Pubmed (updated daily), Wikipedia, Textbooks)b.) Focus on a single research direction, purpose or definitionc.) Write as you experiment

- Keep written and computerized notebook - Form rough sentences– Use plural first person; “We” not “I”

WRITING PROCESS

a.) Always start with an outline (even for each section). - Familiarize yourself (become an expert) in your area

(Pubmed (updated daily), Wikipedia, Textbooks)b.) Focus on a single research direction, purpose or definitionc.) Write as you experiment

- Keep written and computerized notebook - Form rough sentences– Use plural first person; “We” not “I”

d.) Avoid euphemisms/vague expressions We “looked at” what summer students ate.

We analyzed the summer students’ diet.

WRITING PROCESS

a.) Always start with an outline (even for each section). - Familiarize yourself (become an expert) in your area

(Pubmed (updated daily), Wikipedia, Textbooks)b.) Focus on a single research direction, purpose or definitionc.) Write as you experiment

- Keep written and computerized notebook - Form rough sentences– Use plural first person; “We” not “I”

d.) Avoid euphemisms/vague expressions We “looked at” what summer students ate.

We analyzed the summer students’ diet. e.) Be precise/concise “An effort was made to see how many pizzas that the

students’ ate during their summer internship.” “We studied the rate at which summer students ate

pizza.”

WRITING PROCESS

a.) Always start with an outline (even for each section). - Familiarize yourself (become an expert) in your area

(Pubmed (updated daily), Wikipedia, Textbooks)b.) Focus on a single research direction, purpose or

definitionc.) Write as you experiment

- Keep written and computerized notebook - Form rough sentences– Use plural first person; “We” not “I”

d.) Avoid euphemisms/vague expressions We “looked at” what summer students ate.

We analyzed the summer students’ diet. e.) Be precise “An effort was made to see how many pizzas that the

students’ ate during their summer internship.” “We studied the rate at which summer students ate

pizza.”f.) Evolving -Take suggestions and do not take criticism

personally

WRITING PROCESS

a.) Always start with an outline (even for each section). - Familiarize yourself (become an expert) in your area

(Pubmed (updated daily), Wikipedia, Textbooks)b.) Focus on a single research direction, purpose or definitionc.) Write as you experiment

- Keep written and computerized notebook - Form rough sentences– Use plural first person; “We” not “I”

d.) Avoid euphemisms/vague expressions We “looked at” what summer students ate.

We analyzed the summer students’ diet. e.) Be precise “An effort was made to see how many pizzas that the

students’ ate during their summer internship.” “We studied the rate at which summer students ate

pizza.”f.) Evolving -Take suggestions and do not take criticism

personallyg.) No contractions – “We are”, not We’re

IMPACT AND IMPACT FACTOR

Impact Factor -often used as a proxy for the relative importance of a

journal within its field.

- journals with higher impact factors are often deemed more important than those with lower ones.

IMPACT AND IMPACT FACTOR

Impact Factor -often used as a proxy for the relative importance of a

journal within its field.

- journals with higher impact factors are often deemed more important than those with lower ones.

Impact Factor = the average number of citations received per paper

published in that journal during the two preceding years.

Example: If a journal has an impact factor of 3 in 2012, then its papers

published in 2010 and 2011 received 3 citations each on average in 2012.

IMPACT AND IMPACT FACTOR

Impact Factor -often used as a proxy for the relative importance of a

journal within its field.

- journals with higher impact factors are often deemed more important than those with lower ones.

Impact Factor = the average number of citations received per paper

published in that journal during the two preceding years.

Example: If a journal has an impact factor of 3 in 2012, then its papers

published in 2010 and 2011 received 3 citations each on average in 2012.

Impact Factor is important for obtaining grants, for career progression and as a barometer by peers on the importance/novelty of your work. However, great manuscripts are often rejected from high impact journals. Conversely, erroneous manuscripts may be published in high impact journals. I.F.s can be manipulated!

IMPACT AND IMPACT FACTOR

a.) NOVELTY (Is pizza a newly-discovered food?)

b.) DEPTH of research assessment- Number of bioassays/determinants identified e.g. Why is pizza so desirable? Cheese, sauce,

pepperoni? e.g. Is there a nutritional aspect? Which metabolites? - controls

c.) SPECIES/MODEL - Observations in cell lines- Observations in humans- Observations in animal models (mouse summer

students)

d.) REPUTATION of peer-reviewed JOURNAL The Journal of Clinical Investigation (16)

vs. Scandinavian Journal of Clinical Laboratory Investigation (0.9)

e.) Number of viewers accessing the published paper

IMPACT AND IMPACT FACTOR

a.) NOVELTY (Is pizza a newly-discovered food?)

b.) DEPTH of research assessment- Number of bioassays/determinants identified e.g. Why is pizza so desirable? Cheese, sauce,

pepperoni? e.g. Is there a nutritional aspect? Which metabolites? - controls

c.) SPECIES/MODEL - Observations in cell lines- Observations in humans- Observations in animal models (mouse summer

students)

d.) REPUTATION of peer-reviewed JOURNAL The Journal of Clinical Investigation (16)

vs. Scandinavian Journal of Clinical Laboratory Investigation (0.9)

e.) Number of viewers accessing the published paper

IMPACT AND IMPACT FACTOR

a.) NOVELTY (Is pizza a newly-discovered food?)

b.) DEPTH of research assessment- Number of bioassays/determinants identified e.g. Why is pizza so desirable? Cheese, sauce,

pepperoni? e.g. Is there a nutritional aspect? Which metabolites? - controls

c.) SPECIES/MODEL - Observations in cell lines- Observations in humans- Observations in animal models (mouse summer

students)

d.) REPUTATION of peer-reviewed JOURNAL The Journal of Clinical Investigation (16)

vs. Scandinavian Journal of Clinical Laboratory Investigation (0.9)

e.) Number of viewers accessing the published paper

IMPACT AND IMPACT FACTOR

a.) NOVELTY (Is pizza a newly-discovered food?)

b.) DEPTH of research assessment- Number of bioassays/determinants identified e.g. Why is pizza so desirable? Cheese, sauce,

pepperoni? e.g. Is there a nutritional aspect? Which metabolites? - controls

c.) SPECIES/MODEL - Observations in cell lines- Observations in humans- Observations in animal models (mouse summer

students)

d.) REPUTATION of peer-reviewed JOURNAL The Journal of Clinical Investigation (16)

vs. Scandinavian Journal of Clinical Laboratory Investigation (0.9)

e.) Number of viewers accessing the published paper

IMPACT AND IMPACT FACTOR

a.) NOVELTY (Is pizza a newly-discovered food?)

b.) DEPTH of research assessment- Number of bioassays/determinants identified e.g. Why is pizza so desirable? Cheese, sauce,

pepperoni? e.g. Is there a nutritional aspect? Which metabolites? - controls

c.) SPECIES/MODEL - Observations in cell lines- Observations in humans- Observations in animal models (mouse summer

students)

d.) REPUTATION of peer-reviewed JOURNAL The Journal of Clinical Investigation (16)

vs. Scandinavian Journal of Clinical Laboratory Investigation (0.9)

e.) Number of viewers accessing the published paper

AUTHORSHIP

Example: Steven Barthel, Danielle Hays, Erika Yazawa, Matt Opperman,

KC Walley, Charles Dimitroff

Criteria of contributions: 1.) Conceive study 2.) Design experiments 3.) Conduct

experiments 4.) Analyze data 5.) Write paper 6.) Provide material 7.) Supervise all experimentation

A. First author – Writes the majority of the paper and usually contributes the most data sets

B. Middle authors – Contribute in criteria 2.) - 6.) or provide material* - Individual who contributes to most data sets is closest to 1o

author - Senior investigators are typically closest to last author - Second from last author contributes the most if multiple senior

PIs * Not all investigators who provide material ask to be included as co-

author

C. Corresponding author – All 7 criteria apply; plus, fund majority of study

SUBMISSION AND COVER LETTER

a.) Pick an appropriate journal based on journal relevance, mission, impact factor

SUBMISSION AND COVER LETTER

b.) Journal Guidelines

- Each Journal has their own regulations and guidelines e.g. length restrictions (e.g. 200words/abstract; 6 figures)

- Manuscript needs to adhere to these restrictions or will be returned

a.) Pick an appropriate journal based on journal relevance, mission, impact factor

SUBMISSION AND COVER LETTER

b.) Journal Guidelines

- Each Journal has their own regulations and guidelines e.g. length restrictions (e.g. 200words/abstract; 6 figures)

- Manuscript needs to adhere to these restrictions or will be returned c.) Cover letter

- Define the gap in knowledge and outline how your work fills the gap

- Emphasize how your work will appeal to the readership of that particular Journal; Make sure your work fits into mission of Journal

- Recommend potential reviewers as well as reveal those reviewers who you believe will not view your work fairly (conflict of interest)

a.) Pick an appropriate journal based on journal relevance, mission, impact factor

Conclusions-Begin writing early

-Don’t procrastinate: Write easiest sections first

-Aim for novelty and importance

-Pick an appropriate journal

-Write a good cover letter, title, abstract and intro to catch the attention of the editor

-Take your scientific papers seriously: quality over quantity

The End But his beginning!