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FOR 694 Writing for Scientific Publication
Class Notes 2018

Jan 16: Why Publish?


Allison:  Working here on chestnut since 2006.  American chestnut, the blight, genetic transformation for disease resistance.  Developing procedures for rooting chestnut plants in different media.

Gretchen:  Forest Inventory and Analysis, history of US forest management.  Since 1930, a continuous forest inventory system.  Northern unit, 174 million acres.  Since 1998, annual surveys with a system for evaluating the field crews.  QC crews visit a subset of all plots.  List of variables.  Objectives: determine the rate of errors in different measurements.

Thu Ya: Rene Germain, Steve Stehman, Lindi Quackenbush.  Miyanmar, home of teak.  Objectives: detect forest cover change, using GIS, 200-2017. Interviews with local foresters.  Propose locations for community forestry projects. Forest cover declined by 56%!  Model areas suitable for teak plantations.

Shuai:  PhD student at SU with Charley Driscoll.  Developing critical loads of acidity for streams in the Adirondacks. Target ANC (acid neutralizing capacity), use a model, PnET-BGC (monthly timestep, forest and soil biogeochemistry) and historical deposition rates to determine pre-industrial ANC.  Describe soil acidification due to acid rain.

Joseph:  Biogeography of freshwater fish fauna in 10 countries in southern Africa. Biogeographic regions have been proposed but not tested with data.  Using published sources, digital atlas, approaches to data analysis.

Pu Ge (Jeff):  Water resources engineering, riparian buffers using remote sensing. Importance of riparian buffers in controlling bank erosion and pollution. Stockport Creek watershed.  He developed a technique to classify land cover at 1-m resolution.  Geospatial analysis techniques: hotspot, connectivity, land development intensity.  Recommend areas to target for restoration efforts.

Alex:  Sap flow is driven by transpiration, in the xylem of trees, controlled by stomates and environmental conditions (soil water and VPD).  Bartlett, NH, NxP additions to forest plots, Ca addition, too.  Two stands in this study, sugar maple and white birch, in 2017 and 2015.  Method involves two probes, how quickly heat moves away from a heated probe.  Questions:  Do N or P affect sap flux in these two species?

Why Publish?

Thu Ya: I need a publication as a credential to apply for PhD programs.

Gretchen:  I like to challenge myself, I don t really want to be published.  My major professor told me to.

Alex:  It s important to get my data out there.

Joseph: It helps to communicate with the broader scientific community.  And it will affect fish conservation.

Shuai:  This paper is going to be part of my dissertation.

Allison:  I need the ego boost when my papers are cited to combat my imposter syndrome.  Post-docs should be publishing, I need to maintain my track record.

Pu Ge:  Publish while you still remember what you did!

Thu Ya:  I want the experience, I haven t published before.

Alex:  I want to know what it takes to publish a paper, I will be doing it again.

Joseph:  The thrill and excitement of owning an idea and putting it across.

Shuai:  The review process can provide interesting questions.  Sometimes it can be hard.

Allison:  It s cool to see that people have taken my techniques and applied them to other species.

Pu Ge:  I need to publish for graduation.  I have been trying to publish for a while.

Intro to Getting Started

Autumn:  If I gave myself only 10 minutes it would have been better earlier.

Shuai:  I could divide my study into 2, based on data resolution.  Ruth: Then do the GSE twice!  It s easy compared to drafting the paper two different ways.

Jan 19: Getting Started Exercise

What s hard about your paper?  How can we help you?

Alex:  I don t have all of my results, so I don t have much to go off of.

Ruth:  Please ask each other for friendly review if you want feedback out of sync with the class.

Gretchen:  I used the graphs that I had been working on.  I tried to keep myself to 10 minutes, it took longer, but it helped me to be succinct.

Yang:  I have trouble with the importance of this paper.  Not all of my papers are super novel or important.

Gretchen:  What do other similar papers do?

Pu Ge:  I have a similar problem with novelty or importance. What do other papers do?  They relate to management.

Thu Ya:  My results are a map, so it was hard to write about it.

Pu Ge had a similar situation, and he marked key areas on his maps to describe in the text.

Allison:  There will be at least one person out there who really cares.  It s okay that most people in the world don t care.

Allison:  I tried not to give more background than necessary, but maybe it s too little.
Shuai:  I have the same problem with importance.  I have a modeling paper, and I am concerned about uncertainty in my results.  I want to write another paper with a full uncertainty analysis.  I m also thinking about a paper that includes climate change.

Joseph:  I am still working on my results, the exercise was interesting, because although I have a draft of my paper, I spent hours thinking about how to organize it.

Jan 23: Choosing your Journal

Factors to Consider

Subject matter, scope:  Where are similar articles published?  What is your target audience?

Regional journals, international journals.  Some journal names have geographical words in them, Australian Journal of Soil Science is now Soil Research.   Canadian Journal of Forest Research.  Regional journals are valuable to a restricted audience.

Acceptance rate:  Research Gate has a information on journals?  If you can t find it on the journal web site, you can contact them and ask.

Is the acceptance rate linked to the impact factor?  Let s find out.  Please find this information and we ll analyze it.

Processing time:  How can we find that information?  Elsevier has a tool that will suggest journals based on your abstract?  The report processing time that varies by journal.  You can also look at published papers, which give the date submitted, accepted, and published.  There are possible delays in the review process (Yang has a paper that has yet to be assigned to an editor after 5 months in PLOS One).  There can be additional delays in getting it to publication.  Frequency of publication might matter.  Some journals will make your paper available electronically as soon as it s accepted, even if the print version is not out yet.

Cost of publication, cost for Open Access:  see below.

How important is Open Access?  They are more accessible and more often cited.  Ask if this is in your budget.

If not Open Access, who has subscriptions?  How can you tell how accessible your paper will be?

Your co-authors have to agree.  They can be a resource for suggestions.

Have you published with them previously?  Do you co-authors have relationships with the journal?

Journals you chose

Joseph: African Journal of Aquatic Sciences, where it will be read by the people who care and have an influence on policy and management decisions.  7500 words.  200 abstract.

Shuai:  Ecological Applications or maybe Atmospheric Environment, depending on what is included in the paper (model performance would go to Ecological Applications).  They don t specify word limits.  They do require code in supplemental material.

Allison:  Depending on PI decision on cost, IF of 4.6 vs. 0.3 but it costs twice as much.  Abstract could be 350 or 200 words.

Thu Ya: Remote Sensing (fast and high acceptance rate) or Restoration Ecology.  Around 300 words for the abstract.

Pu Ge:  Restoration Ecology publishes more of this type of paper than the nearest contender.  <7000 words.

Alex:  Forest Ecology and Management (34% acceptance rate), rather than Environmental and Experimental Botany (14%), and it more often publishes papers like mine.  400 word abstract.

Yang:  Bulletin of Environmental Contamination and Toxicology, it s lower impact but I want to get it published.  150 words abstract.

Gretchen: Forest Ecology and Management.  Requires highlights, funding sources, lots of guidelines.  How to label your figures.

Read the Instructions

You don t want any unpleasant surprises when you finally submit your paper!

Required sections:  Allison is looking at significance to the horticultural industry

Pu Ge: A section on implications of no more than 120 words.

Results and Discussion may or may not be combined.

Shuai has to provide his computer code.

Allison has to provide her data.

Acknowledge funding sources.

Does anyone here have patents?

Highlights: 3-5 bullet points, up to 85 characters each

International Journal of Applied Earth Observation and Geoinformation: Open Access $3200

Journal of Environmental Horticulture:  All papers are Open Acess, $1200.  It used to be a page fee.

Ecological Applications:  $75/page.  $3000 for non-members, $2250
African Journal of Aquatic Sciences:  175 Rand for African researchers, $30 for non-African researchers, per page.  If you can t afford the page fees, you can apply to the editor.

Forest Ecology and Management: free unless you want it to be Open Access $3800.

Bulletin of Environmental Contamination and Toxicology:  Free, on-line only, Open Access $1000

Environmental and Experimental Botany: Free, $3000 for Open Access.

Restoration Ecology: $3000 for Open Access.  Page charges $150/page, $35/page if you have limited support, $10/page if you have no support.

Note:  The Research Office at ESF might be able to pick up your publication costs if your grant has closed out.

Last year s data on acceptance rate:  32% Science of the Total Environment, 65% Journal of Great Lakes Research IF=1.9, Ecological Indicators 44%, 3.19,  Remote Sensing of the Environment 29% 5.8, 21% for Building and Environment IF 3.4,

Figures and Tables

Print 4 copies at the size you expect the journal to reproduce them.

Please number your figures and tables so we can refer to them.

If you have multiple alternatives for a graph, show us the options!

We like the dotted line but it needs to be explained in the figure caption.

Order the legend to match the observations.

What about putting the top, mid and bottom of the tree on the y axis.  Soils people do this all the time, even though it means the response variable goes on the x.

Figure axis labels should have units in parentheses at the end.

Avoid acronyms.

Are figures usually labeled with sans serif fonts?  Does your journal have a particular style?

Order of treatments!  Alphabetical is rarely the best order.

Don t use the same fill pattern to mean the same thing across different graphs, if you can afford it.

Table of data sources--need to decide whether this is better than a paragraph of text.

Don t include tables redundant with figures (or text).

How do you decide how many digits to report?

For P values: report to 0.01 or the first significant digit, whichever comes first.

Think about how many digits are meaningful.  Probably elevation of a lake is not precise to 0.01 m.

You can also look at the variability.  1622 plus or minus 50?

You may decide to include insignificant digits up to the 1 place.  1600 kg/ha

Align numbers on the decimal (or make sure the journal does it for you)

What s in rows vs. columns?  Numbers are easier to compare in columns than rows.

Beware of defaults.  Do you want the gray background, the gridlines, etc.

Maps:  You need a north arrow if it s not up.

Choose your base map--for example, are political boundaries helpful?

Consider an inset map for context.

Scale bar.

Specify the meaning of your error bars (SD, SE, CI)

Specify the parts of your box plots.

Spell out conventions in other types of figures; you will enlarge the audience who can understand your paper.

Site names:  Don t ask your readers to memorize the meaning of your site names (don t ask them to learn any unnecessary vocabulary)

Consider using color, if it won t cost you more.  Use colors that can be distinguished in black and white.

Close up space between panels if the axis labels are redundant and can be removed.

When should your axes start at zero?  Is the magnitude of the effect relevant to zero?

Font sizes (bigger)

When do you connect the dots?  When do you use a curve to connect them?

Feb 1: Outline, Objectives

Alex:  It challenged me to think about my discussion points, but I don t have all my results yet.

Gretchen:  I really want to write my Introduction.  I don t have all my results yet either.  Now I can work on other parts of my paper.

Yang:  I finished my Intro, Methods, and Results yesterday--this is a small paper.  I have my objectives, not just as bullet points, but explaining the importance.  Something like that.

Thu Ya:  My major issue is deciding how to present results from 100 sites.  GIS plus interiews of experts.

Yang:  You could pick some, like case studies.

Shuai:  How to organize my information, put it into 2 papers.  I finished the Methods and Introductions and part of the Results, as one combined report.  This outline is for the paper that reports all the streams.  Some parts may belong in the other paper.

Ruth:  Seeing outlines for both papers at once may help you.  If you want more review, ask someone!

Joseph:  The exercise was interesting because it gave me a template, a more detailed look at what to focus on.  It got me thinking about the focus and my title.  I wasn t initially focused on endemism, but those are the most striking results.  I expected more from the quantitative results.

Feb 6:  Results

What do you want help with?

Shuai:  methods are okay.  They might be too long (3800 words).

Joseph sighs.  I had a brief discussion with my major professor about the results.  He said that it s common to identify outliers and then search again on a reduced data set for patterns.  Now I have very different results that I need to begin to understand.

For methods, how much detail is needed?

Thu Ya:  The GIS covers only 10% of my study area.  I talked with my professor, what about the other areas?  There are some teak plantations already established, but they are not accessible by road.  I may need to change my methodology, and my results will change.  I can compare the two methods.

Yang:  I have too few results, just 14 lines.  10 sentences.  I m thinking thinking about adding a search of the literature and adding an analysis of other studies.  Does this belong in Discussion or Results?

Ruth:  Put it where we can review it sooner!  Ultimately, if the methods are complicated, but them in Methods and Results.

Gretchen is off to a good start.  Her results are still coming in; Ruth suggested that she write the narrative with blanks for the missing results.  Figures and tables have been updated and improved.  Does the table make sense or is it superfluous?

Alex is still doing analyses.  It s taking time to gather environmental factors.  If the results are not significant, papers on the individual elements are not likely to be publishable on their own.  A combined paper could be more attractive.

Joseph:  Sometimes I feel that what I put on paper is not enough.  My word limit is 7500, and my paper may be half of that.

Feb 8:  Methods

Alex:  My methods are choppy.  They don t flow very well.  I may have to describe different methods for different collection dates.

Ordering rules:  chronological, general to detail.

Gretchen:  I didn t feel like mine was clunky.  I felt like mine was a good first draft.  I don t know what I might be missing.  But does it make sense to a reader who might not be familiar with my methodology.

Yang:  In general it s good but I might be missing some details.

Thu Ya:  I ve written a lot, there might be things that don t need to be here.

Shuai:  My methods section is long and I need to add more to it.  When I wrote the Results I realized that I didn t explain in enough detail the methods for the critical loads and how to extrapolate to the region.

For my results, I have too much information in each figure and I m not sure which part to focus on.  If I have 4 panels for 4 solutes, I want to describe them in one paragraph.

Joseph:  Is the title a guide to what s important in your paper?

Joseph:  I m having a difficult time with my statistics.  I might have to get help from an expert in multivariate analysis.  I m applying it to presence-absence data.

Feb 13: Peer Review

Review Criteria

Some of the questions will be more relevant when we review the full draft:

Does the title of the paper clearly reflect its contents?

Is the information new and exciting?  (we might not know this until we see the introduction)

Are the conclusions supported by the data?

Are the references up to date?  Are they necessary?  Is the number suitable to the length and subject of the text?

Are the design and analysis appropriate and correct?

Are the methods described in sufficient detail that the work could be repeated by someone else?

Are the tables and figures necessary?  Are they of publication quality?  Are all the figures and tables referenced?

Is the manuscript logically organized?

Do the paragraphs flow smoothly?

Is the writing clear?

Is it understandable to someone not a specialist in the field?

Length: Are there portions of the paper that should be condensed, expanded, or deleted?

Are scientific names given for plants and animals when they are first introduced?

Some questions we saw are specific to the type of journal, e.g. metric units, number of tables and figures, and international vs. regional.

What makes a good review?

When the journal editor selects reviewers, they will be specialists in the field.  You may want to communicate to the editor that you are not an expert in this field.

Details are important.  Read the manuscript carefully.  You may have to read parts of it more than once.

Pu Ge:  The first time, I look for general issues with the writing.  Kind of scratching the surface.  Then I read it again and try to dig deeper.

Ruth:  You can give a marked up copy to the author directly (electronic or paper).  The journal editor needs your review.

Shuai:  I read the results first, then the methods.  It will be clear if the methods section is inadequate.

Summarize the manuscript.  This helps the editor, who may not have read the paper.  If you don t get it right, helps the author know they were not communicating effectively.  Hopefully, it establishes your credibility with the author.

Be professional:  criticize the paper, not the author.  Mention the good things and not just the bad things.  Use positive constructions:   The writing could be improved, instead of The writing is terrible.  Focus on the desired behavior (important in other kinds of relationships, including parenting).

The audience for your review is the Associate Editor AND the authors.  Some reviews address the authors ( you need to address...: )  and some are written in the third person ( the authors ).

Provide suggestions for improvement.  Put the most important topics first.  You might have a heading for General Comments and Specific Comments.  The AE shouldn t have to wade through unimportant stuff to get to your main points.

Provide page and line references for specific comments.  Authors: Please provide line numbers (continuous)

The review process (for journals)

The Associate Editor solicits reviews and makes a decision based on this feedback.  Decisions include accept, reject, revise.  (Lots more on this topic at the end of the semester.)

Author Updates

Alex is still working on results, she could have a draft by Monday.

Pu Ge:  Methods is almost done, but I still need to run a couple more results.  Next week hopefully.

Thu Ya:  I finished the Methods, I will finish probably next week the results.  I m waiting for data from the Forest Department.

Shuai: Next Monday.

Joseph: The very last day that you need it.  I m going to a conference Thursday to Sunday.

Gretchen:  data from 22 more states will be delivered next week.  We can review what she has based on 2 states.

Reviewer Assignments

Joseph reviews Shuai reviews Yang reviews Pu Ge reviews Alex reviews Gretchen reviews Thu Ya reviews Joseph.

Please ask your reviewer whether they want your paper on paper or electronically.

Email them to me, I will review them in the order received.

Feb 15:  Writing Exercise

Gretchen likes revising better than writing.  It s overwhelming to put it all down, but once it s there I can see how to organize it and what needs to be added or deleted.

Using other people review.

Yang writes an outline first.  Others agree.  Write the topic sentence for each paragraph, then you know what to put there to fill in the paragraph.  After I have an outline, I write all the sentences I have in my mind.  Then later on I come back and search the literature (relevant to Intro and Discussion).  Alternatively, you can start by reading the literature, then put the useful information into your paper and write from there.

Pu Ge:  I try to force myself to write every day, especially when the experiment is going on.  It s easier to write the methodology when you re doing it.

I just read a book that says to spend 15 minutes writing every day.  Write anything you want.  Later you organize it.

Yang:  Writing is what graduate students do.  You re not taking classes.

Thu Ya:  I prefer decoration, it s my personality. How to write in a colorful way.  I write a list of all the problems I have.  I think of all the ways I can improve, I don t write them down.  It s not perfect at first but then I fix it.

Shuai:  I don t like writing.  I hate writing.  I only write what I have to.  I gather all the information and prepare, but I don t start writing until I have to.  I have an outline for all the sections.  For each section, I put all the information, just a few sentences for each part.  Before I write, I reorganize them and try to tell a story.

Shuai wrote the methods (20 pages) in two days, because he was ready.  He would not enjoy the 15-minutes-per-day approach.

Shuai: I prefer thinking. (3 authors agree).  3 authors say they can t think about it until they write it down.  We need Joseph to break the tie.  Does this relate to introversion and extraversion?

Alex:  I don t like writing.  At all.  I write everything without having to write it.  My outline with only headings.  Then all the subheadings.  Then under each subheading.  I write the paper in pieces, but I don t have to think about it all at once.

Citation software:  Endnote (2), Mendeley (4)

Smith and Brown

Break into paragraphs to separate your main points.

Short sentences are easier to understand than long sentences.

First person, active voice constructions are more straightforward.

Subject-verb-object is the simplest and most common sentence structure in English.

Avoid redundancy.

Pay attention to the order of presentation.  Give directional signals to indicate the logic of your paragraphs.

Proofreading Marks

We also talked about adjectival nouns and hyphenating compound modifiers.


Alex: There is a little blue book on citation styles that I read in high school.

Pu Ge: A Manual for Writers of research papers, theses, and dissertations.

February 20: Introductions

Author updates

Gretchen has results to incorporate, needs to strategize about what version to get reviewed.  She s aiming for Friday.

Shuai s co-author noticed some problems with the analysis.  He will be double checking some things.  He might have something (not the final wording) Wednesday or Thursday.

Thu Ya is still waiting for forester input.  Do you want review of it without that?  Yes, Thursday.

Pu Ge: Thursday or Friday.

Alex doesn t have significant results with N and P.  Should she include Ca results in the paper?  Maybe by Friday.

Joseph is still working on the results.  Most probably by Friday.

Shuai will ask Yang when to expect his paper.

What needs to be accomplished in an Introduction?

Start broad and work down to the pinpoint of what you are trying to solve.

Set up the problem statement to lead to your objectives.

The objectives are usually at the end of the Introduction.

Why is this research important?

Background information necessary to understand the need for the research.

Identify the knowledge gap that your research will fill.

What is novel or unique about your study.

You might have to introduce your study system--why is this the best place to address this problem?

Reference relevant major studies.  Place your study in the context of previous scholarship.

Examples you brought

Pu Ge

  1. Problem of human modification to streams.
  2. Identify the need, proposed solution
  3. More specific:  Need for spatial analysis tools.
  4. GIS solution
  5. Past studies However, none of them...  The gap!
  6. Objectives.  Should we have heard earlier about about the 2007 plan and the East Credit?  Don t make people feel like they are bad readers.   Did I miss something?

Citations in the Objectives can be a sign of material out of place.


  1. Acid rain was bad.  Regulations are working.  So we don t know the problem yet.  (and we don t have clue words to tell us that sulfate is bad and ANC is good)
  2. Introduce study area, objectives.  We were confused by the reference to effects on soils and forests, if the study is about surface waters.
  3. Study site, overview of methods.

We recommend paragraphs on acid rain, key indicators (and why), the model (why it s the perfect tool), then objectives.  Should the location be introduced in the Methods?  If you can give background that interests your reader in your study system, put it in the Introduction.


  1. Background, too much packed in.  Ends with problem statement.
  2. The first sentence introduces the method, which doesn t need to be here and leads us to think that the paragraph is going to be about the method.  Review of previous studies with mixed results. The gap.  Then we got lost.
  3. Objectives.  Too much methodology.  Hypotheses are presented as expectations, with citations.  Should these have been set up in earlier paragraphs?  It ends with a statement of importance.


Problem words: degradation, pervasive negative effects, concerns,

Solutions: calls have been made for  We know However.  This problem could be reduced if  ...necessitates  We are not aware of any studies examining...

Feb 22 Authorship

Author lists

Yang 80, Ruth 50, Kevin 30, Charley 20, Mario 15.  The minimum for authorship according to Galindo-Leal is 25, but he is keeping all of these.

Lasser 45, Yanai 55, Young 30, Green 20, Campbell 20.  Should Green and Campbell be in the author list or the Acknowledgments?  She tried another point system by Stephen Kosslyn at Harvard.  He distinguished time on task from accomplishments, and emphasized ideas and creativity.

Alex:  I felt like I had a bias towards myself, because I was involved in all the steps.  Rice 80, Johnston 70, Yanai 40.  It s still not clear whether there is a separate paper with Johnston in the lead.

Joseph has a curious situation.  He took a course in Belgium, where he studied a particular fish distributed across 8 regions in Africa.  But Stewart suggested the current study.  But although the original idea came from him, he hasn t been very involved.  Makaure 100, Stewart 55.

(How often do you talk to your advisor?  Wide range of answers.)

Thu Ya:  I m a kind of generous person.  80, Germain 75, Quackenbush 60, Stehman 55.  The order might not be that.  Should Steve go in front of Lindi?  The contributions have shifted over time.

Pu Ge 90, Quackenbush 40.

We talked about the need for theses and dissertations to be single author documents.

Is last place always the least important?  In Asia, the advisor is last and corresponding, and gets as much credit as the first author.  Ask Charley if he prefers to be last!

When would you use alphabetical?

Multiple papers: consider the distribution of contributions and authorship over all the papers.

Some journals request information about author contributions.  Ecosystems, Science of the Total Environment.  Environmental Science and Technology allows two corresponding authors.

Does it hurt to have more authors?

If there are only two authors, adding a third author hurts the second author.  Consult your second author before adding a third.

Adding authors who didn t contribute much devalues authorship.

Is it possible for a student to publish a single-author paper?

Is it rare to have single-author papers?  Less common now than 50 years ago.  Review papers might be written by the most expert person in the field.  Depends on the discipline!

People expect the writer to be the first author.  THink about the overall division of labor.  For example Yang wrote a paper on trends in loon mercury, but this doesn t make him the lead compared to the person who caught the loons for 18 years.


Yang: 2 people in the field, 1 person in the lab.  For writing, this class.  Funding.

Gretchen:  Green and Campbell if not on the author list.  Chuck Barnett provided the FIA data.  Jason helped explain what the field crews do.  Chris Woodall and others.

Alex has a long list, because of two years of data collection.  Green, Templer provided baseliner, Wild helped in the field, MELNHE 2015 and 2017 summer crews.  Griffin helped with the circuitry in the field.  Bridget did the 2015 collection.  Drake helped iwth ideas.  The Yanai lab.  Mention carrying car batteries into the woods (they are heavy).

Joseph: Reviewers (some from this class, some from the journal).  The guy who supplied data from the 70s from a museum in Michigan.  Should he acknowledge libraries that provided material via ILL?  Yes, if the material is rare or unique.

Thu Ya: Fulbright.  The Forest Department of Myanmar.  A professor from Myanmar at Arizona State, who suggested that I do remote sensing and not just community forestry.

Pu Ge:  Funding source.  This class.

Authors do not belong in your Acknowledgments.

Remember to send them a copy of your paper when it s published.

1.  Use the point system described by Carlos Galindo-Leal in Ecology 101 (Bulletin of the Ecological Society of America, October 1996).  Make a column for each of the possible authors of your paper, and assign points for your various contributions.  Include yourself!

Planning, Executing, Analyzing, Interpreting, Writing

2.  Do the five categories of contributions suggested by Galindo-Leal seem appropriate for your project?  If you prefer, try applying a point system with different categories, such as those suggested by Hunt or Dickson and Conner.

3.  Name your authors, in the order you propose to list them on your publication.

4.  Does your list agree with any objective point system?  If not, what were the other factors that influenced your decision?

5.  Who will you list in your Acknowledgements section?


Feb 27: Reviews, Responses to Reviews

Thoughts on the review process

Gretchen:  I have to put it down, and go back and forth between the document and my review.  How many times should I be reading it?

Yang:  Three times, for specific comments, general comments, and a final check.

Pu Ge marks the specific and general together.

Thu Ya spent most of the time on the figures and table.  It s hard to review the use of tools that we aren t familiar with.

Ruth:  The process of writing the review gives me ideas and more confidence in my evaluation.

How to write a response to reviews

Your response is directed to the Associate Editor.

Your goal is for the AE to accept your paper on the basis of this document alone.

The AE may decide to send your revised ms. and your response document back to the same reviewer or (different reviewers).

Journals may request a revised document with tracked changes.  Use compare documents if you didn t track as you went.

Things not to do

The reviewer is stupid and we don t need to change anything.

Try not to be defensive.  Don t explain why you did something wrong.  Just say, Thank you, we fixed it, as follows....

Just We fixed it is not good enough.  You must document your changes.

How big a change is too big to copy into your response doc?  You can copy a paragraph.

Things to do

Start by thanking the editor or the reviewers.  Cite the manuscript number, maybe the title and authors.  If you used colors or italics, explain what they mean (see below).  If there are major changes, they might be detailed up front, including change to the type of article or to the author list.  Changes not requested by reviewers, such as adding to your data set, also need to be described, probably at the top or the bottom.

Be nice.  Thank the reviewer for finding your errors.

You need to respond to every point made by the reviewers.

Start with the review comments (you will have these electronically) and insert your responses.

You can use color or italics to distinguish your responses from the reviewers comments.  You might use another color for quoted material or changed material.  You can also write Comment and Response.

You don t have to agree with the reviewer.  But, if you aren t going to make a change, show that you at least gave it some thought and make the case that the suggested improvement is not an improvement.  For example, a reviewer might suggest another approach to data analysis. It s better to try it and say whether it worked than to say you know it won t work.  It might work!

If the reviewer misunderstood you, change something so that future readers don t have the same problem.

When you are not agreeing with the reviewer, provide evidence from the paper.

In general, provide evidence of your changes.  It s shorter than describing them and more convincing to the AE.

For very simple edits (deletions, minor edits), you can just say, Done.

How do you end it?  You can say thank you at the end, but it s not uncommon to end with the last detailed comment.

How to handle revisions

Advice to authors, using anonymous examples

March 1:  Discussions (examples)

What needs to be accomplished in the Discussion?

Interpret results.  Don t spend too much space repeating your results.

Address problems, unusual results, or limitations.

Reference similar work.

Alternatives to this approach (unless the approach is very standard).

Implications for management.  Recommendations, if relevant.

Next steps.  Future work.

Point out the resolution of the problem posed in the Introduction.  Why is this important

Conclusions.  This might include highlights of major findings.

Examples you brought


  1. Summary of result, comparison to other studies.
  2. Interpretation.  REFERENCE YOUR FIGURES!
  3. Interpretation, different factors

4, 5, 6. Interpretation, unusual result

 7.  Conclusions, limitations


  1. Interpretation
  2. Reference to other studies.
  3. Interpretation
  4. Interpretation
  5. Reference to other studies
  6. Why this is important.


  1. Justification for the study, related works

2, 3. How our results differ from others.

4.  Why is this figure in the Discussion?  Is a one-sentence paragraph okay?

The rest of the Discussion is divided into the 5 regions they studied.  Most of the paragraphs seem like Results, some are labeled Discussion.

9.  Conclusions, reads like a summary.

Thu Ya

 Two subheadings, very helpful

  1. Interpret and compare with other studies
  2. Other studies, limitations.  With a lot of citations and background
  3. Ditto.  This author likes long paragraphs!

 The final paragraph gets to management implications.

 Conclusions includes a nice summary.


  1. Interpretation

2, 3, 4. Comparison to other work.  This author likes short paragraphs.

5, 6.  Results and interpretation

7, 8.  Implications for management

9, 10, 11, 12.  Comparison to other studies (one paragraph per study).  Don t make authors the subjects of your sentences.

15, 16.  Recommendations

17, 18.  Conclusions

 It could have been more concise, and subheadings might have helped.

Pu Ge

  1. Justification for the study (how does this differ from what they said in the Intro)
  2. Value of the results
  3. Explain an unusual result
  4. New subheading.  Implications, explanations.
  5. Interpretation, comparison to other studies.  Importance.
  6. Comparison to other studies.  Interpretation.  Recommendations.

Conclusions and Implications, with 4 more subsections


 The paper has three sections, and each section has Methods, Results, and Discussion.

March 6:  Introductions (yours)

Gretchen: In progress.  I only have 12 citations, enough to fall into reading more.  I m learning how to use Mendeley for the very first time.  I have trouble getting articles from CJFR.  (Yang says to email the library.  Thu Ya has a secret illegal web site.)  I am having fun but I m disappointed that I m not making more progress.  I m still getting more results!  Tumbleweed.

Yang:  It s done.  Please take a look at the topic sentences and transition sentences.

Pu Ge:  It s in progress and I don t have it with me today.  I have a problem with the methodology and I need to check the literature.

Thu Ya:  I m done.  Three pages.  Please look for repetition and check my transitions.

Joseph:  I have something.  I m not sure about the length.  Is it too short?  Am I missing anything?

Alex:  It s in progress.  It s a compilation of the intro from my proposal and from a class paper I wrote.  It needs editing.  Some of this material might belong in Chapter 1.  (Your thesis committee needs to know that you have a command of the literature, but your journal audience just needs to be led to your Objectives.)

Referencing software:  EndNote is not free.  Mendeley and Zotero are free.

March 8: Discussion (yours)

Alex:  I have insight on better analysis.  The discussion is what I wrote last fall for a class project.

Gretchen:  I m finishing writing my Methods and Results.  I want to make an outline for the Discussion.  Priority for spring break!

Yang:  I wrote the Discussion a week ago and didn t have time to revise it.  I was working on Chapter 1.

Thu Ya:  I have 7 pages, I wrote it quickly last night.  The whole night.  Sometimes I sleep at the library.

Shuai:  I have 2 sections, I wrote the Discussion even though I haven t finished the Results.  Some of the material might belong in the Results.

Joseph had a hectic week, he has a draft of a Discussion that shows the sections he intends to write.  More like an outline.

March 20:  Feedback for Improvement

Google Doc

1.  Below is a list of the topics and activities in the course so far.  Please indicate which you found especially useful, which least useful.  (Scale of 1 to 5 with 5 being most useful.)  Give specific suggestions for improvement if you have any.

For example: 3, 5, 2, 4, 1, 2, 4, 5,  (you each type one number)

and comments go after each heading

Jan 16  Background presentation, discuss Why Publish?

--invited experienced students to do a panel talking about this class

4, 4, 4, 3, 5, 4, 4

Maybe more time...maybe 7 mins..

Gretchen: not the regular presentation, I know what should goes into the presentation now than before. Should be more like a teaching thing...

Jan 18  Getting Started Exercise

5, 5, 5, 5, 5, 5, 5

Jan 23  Choosing your Journal

4, 5, 4, 5, 5, 5, 5

Jan 25, 30  Figures and Tables

5, 5, 5, 5, 5,5, 5

Feb 1  Outline and Objectives

5, 5, 5, 5, 5,5, 5

Feb 6  Drafts of Results

5, 5, 5, 5, 3,4, 4

Feb 8  Drafts of Materials and Methods

4, 5, 4, 5, 5,4, 4

Feb 13  Writing exercise, in class

4, 4, 4, -, 3,4, 4

Ask students interests and change every year?

Feb 15  Preparation for peer review

5, 4, 4, 5, 3,4, 5

Sometimes the google doc is not clear...what information is accessible.

Feb 20  Introductions (examples)

4, 5, 4, 4, 5,4, 5

Feb 22  Authorship Exercise

5, 4, 4, 5, 3,5, 5

Feb 27  Responses to Reviews

5, 5, 5, 5, 3,4, 5

Mar 1  Discussions (examples)

4, 5, 4, 4, 3,5, 5

Mar 6  Drafts of Introductions

5, 5, 4, 5, 5,5, 4

Mar 8  Drafts of Discussions

5, 5, 5, 5. 5 ,5, 4

2.  What future sessions would most help you prepare your manuscript for publication?  Are there other related topics you would like to address that aren't on the list?  Here are the proposed future topics, please rate them on a scale of 1 to 5.

Mar 22  Readings on Peer Review

5, 5, 5, 5, 5,4,3

Mar 27  Ethics (Allison)

4, 4, 5, 5, 3,4,3

Maybe give a sentence or two to illustrate what the topics are about .

Mar 29  Statistical Considerations (Pu Ge and Yang)

4, 5, 4, 5, 3,4,5

Discussing how people solve their own statistical issues .

Some basic stats knowledge. Experimental design ----

Apr 3  Proposals (Bring examples of RFPs, proposals)

4, 5, 5, 5, 2,4,4

Jeff does not like it because it is not related to publications..

Alex: so far in the end. Not really interested...

Grethen: don t have the time to produce the results/methods in section due per week and the week after due...remind students before they register the class, they should have the outline, this class is fast!!!

Joseph: maybe emphasis what the class is about, what students can get out from the class.

Yang: people nervous if they plan to graduate but they get an incomplete for this class...maybe give us how grade this course or not taking the final draft into account.

Thuya: Provide the policy about grading..

Apr 5  Readings on Publication Productivity

3, 4, 3, 5, 5,4,2

Apr 10  Reviewer feedback and help session

4, 5, 5, 5, 5,4,5

Apr 12  Help with revisions

4, 5, 5, 5, 5,4,5

Apr 17  Abstracts (examples)

4, 4, 4, 5, 5,5

 Apr 19  Work session

4, 5, 5, -, 6,4,5

Apr 24  Drafts of Abstracts

5, 5, 5, 5, 5,5,

Apr 26  Steps to Publication

5, 5, 5, 5, 3,5,

May 1  Last Class (Final Steps)

4, 5, 5, 5, 6,4,?

---talk about what you learn from this course

Grethen: call this class publication bootcamp

3.  There are many ways we can work together.  Do you have comments or suggestions on the value of these alternatives

Pairs or triples, trading feedback in class

Triples! Getting feedback from two people at once was helpful. It usually led to discussions of what was important to consider and what was not.

Triples! I don t find feedback from someone who has little experience writing/publishing to be helpful

Cannot read her handwriting---it is a lot and you don t have time to figure it out...maybe have to ask her

Shuai: read them many times--

Peer review (one so far, one to go)

This is a great exercise. Although one reviews a study divorced from their area of specialization, the process makes you to become more conscious of common errors authors make and this provides a great learning my opinion.

Informal peer assistance outside of class

I think this would be a great way to keep my writing in check if this is done on a regular basis.

Group discussion

This would be helpful if every can read the same draft before the class.

This is helpful for remembering that we re all on the same path, warriors fighting a similar battle!

Going around the table to equalize participation

I like this approach. The learning environment was more participative and learner oriented. This allowed us to share more diverse opinions and approaches on issues under discussion.

Yes. I like to hear what everyone has to say.

Depends..generally it was good. If there are too many students, maybe it is not good. It is informal, have more perspective..

Class notes

Having the class notes accessible has been helpful when trying to remember specific discussions we had in class. I also really like that you have the topics lined out on the first page of the notes so that we can easily reference them to prepare for upcoming assignment due dates.

I like this because its easy to retrieve later to remind myself of what we talked about. It important and more helpful to be specific (ex, if we re talking about methods and Ruth writes  remember tense ...writing remember past tense is more helpful to follow at a later date)

Ruth sometimes write not clear or unnecessary information in the google doc. Sometimes she wants to make the class more fun but maybe it is hard for students to go back and find the important points..

Electronic midterm evaluation

I am taking the class again because I really enjoy the material, but some of my evaluations are a bit biased because I took the class before.

Sure, why not? Feedback is arguably always helpful or neutral. It can t hurt.

4.  We have a very diverse group of papers, and we don't all know each other's fields.  Do you have any suggestions for improving our effectiveness in spite of this diversity?  How much diversity is desirable?

I think diversity is great and this open my eyes to a variety of fields. Unless there is a very very different publication style/process from another field (ex. Law) in this class, I would not mind reading papers from other fields.

I think bringing in different examples of writing from journals of similar topics helps shed some light on this (for instance, with methods, intro, discussion sections)

5.  Other comments or suggestions

  1. This may not be true for previous years but I feel like our class is behind schedule. I was wondering if requiring a rough draft by the start of class might make this less likely to happen in the future. This way each student has something already on paper and has been forced to think about each section.
  2. I concur with the comment above. Setting a rough draft prerequisite might help to avoid delays as students start the course at the same level.

I'm not sure if the following topics are covered in some of the broad topics above,

cause i thought they might be a useful addition to the course syllabus:

  1. Referencing and plagiarism, 2. Animal care considerations and permits

Turn it in is a self check tool..---it might be too specific...

  1. Thank goodness I am not taking more than 1 other class along with do students keep up with this class if they are enrolled it other classes? The amount of work is overwhelming if you find yourself needed to restart a step from square one
  2. Can we post good examples on our google doc? Of abstracts or graphs/figures/tables? Not of whole papers or long section.


 Assign reviewers

 Expert reviewers:

Feedback with Anonymous Examples

Sentences about statistics can be rearranged to be about your study system.

"Time did not affect the change in mass loss with leaf litter type."

Statistics:  There was no interaction of time and litter type on mass loss.

Mass loss was consistent across litter types over time.

Don t say There was a significant effect of litter type.

Mass loss differed by litter type.   Litter types differed  Elaborate

Direction is most important, magnitude is important, statistical significance is least important (as long as you don t describe insignificant effects).

Oak leaf litter decayed 23% slower than elm leaves (P = 0.03).

Reporting P values is more informative than using an alpha.

There was a significant relationship between the observed and predicted percent lipid values via this method of estimation.

Describe the dependent variable as a function of the independent variable.

Predicted and observed percent lipid values were significantly related via this method of estimation.

Lipid values predicted by this method were significantly related to measured lipids.

Lipid concentrations were predictable from volumetric reactance in series (r2 = 0.88).

March 22:  Peer Review (Readings)

Review assignments:

Alex: Next week, like Tuesday.  I don t have all the information for one of my tables.

Yang: I was working on the literature review.  I need your reviews, then I can get it done by Tuesday.

Shuai will pull out the Results from the Discussion and send it to Joseph.

Joseph is done!

Thu Ya and Gretchen still need to write the Discussion.

Pu Ge is at the DEC.

Publication rejection among ecologists

Who gets rejected?  Everyone.  They sent a survey to authors who had at least 10 papers; 40% (60) responded; having published 2907 papers, 15% of which were rejected at least once, 8% were rejected at least twice.  72% of the authors had at least one paper that they were not able to publish anywhere.  People with more publications were more likely to agree with a rejection on a scientific basis; people with fewer publications blame the peer review process.  Mixed opinions on whether it s getting harder (35%) or easier (15%), 2002 compared to 1990

How well does a journal s peer-review process function

Survey of authors published in a particular medical journal: 95 of 209 surveys were returned.  4 categories:  Accepted, 67% Accept with revisions, 43% Reject with invitation to resubmit, 30% Reject.  Authors with rejected manuscripts were less likely to judge the review process helpful.

Papers on blinding

It s common for the author not to know the identity of the reviewer.  It s less common for the reviewers not to know the identity of the author.

The conclusions differ.  Some say that it makes no difference.  The reviewers can tell who the authors are anyway!  One study used citation to evaluate the quality of papers--double blinding resulted in papers that were more often cited.

More transparency in reviewing is called for

Nations are differently represented in publication.  40 countries, positive correlation between submission and publication.  Science, Nature, and PNAS.

Paranoid about peer review?

It would be hard to test whether authors from emerging countries are more critically scrutinized, without fabricating submissions.

A troubled tradition: It is time to rebuild trust among authors, editors, and peer reviewers

Published in a journal called Ethics:  An anecdote about a paper held up in review by a reviewer who wanted to publish a competing paper.  Is this a fault of the blind reviewing process?  Open review: anyone can comment and all the reviews remain visible.  This could be done during particular time (a one-month window).  There is no perfect solution.

The evolution of editorial peer review

After WWII, there was a tradition of one strong editor per journal, with no other reviewers.  They are not based on evidence, more like opinion pieces.  A minority of journals used a model where the editor is a professor, but there was still no peer review.  Peer review began when an editor at Yale didn t want to publish a paper by a rival and used the opinions of others to justify the rejection.

Peer review in 18th century scientific journalism

Some journals established a peer-review system, with policies for the process, making it available to everyone.  They had a committee and a pool of professional reviewers.

Peer review is an effective screen process to evaluate medical manuscripts

Reviewer assignments

Alex reviews Joseph reviews Gretchen reviews Shuai reviews Alex.

Yang reviews Thu Ya  reviews Pu Ge reviews Yang.

March 27: Ethics

Retraction Watch

Outlier: 139

If you see results that don t look right, do it again.  If you get the same result, you believe it.

A statistical outlier can be defined (e.g. 1.5 times the interquartile range, 3 times the standard deviation)

In this case, they might be able to explain the outliers.

The model fit is not very convincing and we don t know what range would be an acceptable

If you have to question something because it gives you a grimy feeling inside, you probably shouldn t do it.

Conflicts of interest: 142 industrial, 144  competition

A student s work is funded by a company that will need to approve her work.  The professor was not forthcoming about the sources of the funding or the conditions of the work.

Who can you talk to if you have a problem with your major professor?

Friends who have nothing to do with your work may be more objective than you are.

Another professor whom you are close to.

Official channels:  Dean of Graduate Studies, Scott Shannon.  Chair of the department.  Your committee.  Grad Coordinator.

What about talking to the professor?

Ed s work would be advanced if he could use materials developed by a collaborating lab, but the other lab is not cooperating.  A post-doc believes that they just don t want to share.

Ed could offer authorship if warranted.

Ed should start in his own lab, starting at the bottom of the hierarchy.  The two directors should work it out.

Allocation of credit: 145

Ben talked to a researcher at a conference who used his ideas without giving him credit.

Ben should talk to his advisor.  Is failing to credit Ben worthy of

Authorship (credit): (146,) 147,

Hewish got a Nobel Prize for the discovery of pulsars and Bell, the grad student who first noticed the anomaly, was overlooked.

Two grad students and an assistant professor are in conflict over how many papers to prepare.  The professor benefits more from one important paper.  The grad students benefit more from each leading one paper as long as they are each publishable.

The professor could research the criteria and standards for promotion and tenure to see if it s true that it matters.

It s the responsibility of the person with more power to identify the conflicts of interest.

Misconduct:  148, 149, 150

A student makes up a title and author list for a paper and claims that it s submitted when it s not.  The student is dismissed from the PhD program and denied a masters degree even though he met the requirements except for this ethical breach.

Francine realizes that Sylvia is fabricating data.  She and their professor both rely on her data.

I d like to see what you re doing, because it s important that I understand your results.  Yours look better than mine

April 19: Statistical Considerations

Pu Ge has some notes.  Handouts will be on the web site soon..

Alex: ANOVA, regression, factorial (SAS, excel)

Gretchen: ANOVA, binomial, 2-directional T test ( R )

Yang: ANOVA, piece-wise regression  (SAS)

Joseph: multi-variate, DCA, cluster analysis ( PAST )

Thuya: Random point sampling, map accuracy (SAS)

Pu Ge: Spatial Autocorrelation (ArcMap)

Topics Covered:

Sample population

Target population

Total population

Flow of design

Sampling strategy

Presenting results



Could have this class earlier.

April 3: Publication Productivity (readings)

Alex Rice redoing analyses

Gretchen shooting for Friday

Yang:  It s part of the dissertation, which is due on Tuesday.

Pu Ge:  Friday (for the first draft).  Trying to revise the methodology because the results don t make sense.  Now I m seeing the light at the end of the tunnel.

Thu Ya finished a second draft, it s similar to the thesis but might omit the final section.

Shuai completed the first draft.

Alex reviews Joseph reviews Gretchen reviews Shuai reviews Alex.

Yang reviews Thu Ya  reviews Pu Ge reviews Yang.

Alex:  I need time to work on it.  I need most help with my Introduction.

Gretchen:  Bringing in a section would help.  I don t know what section.

Yang:  Bring a section.  Ruth: or the GSE for your merged papers?

Pu Ge:  Bring a section with the GSE.

Thu Ya:  Bring a section to improve it.  Maybe methods.

Shuai:  Bring a section.

Joseph:  Time, cancel class.

Childcare, research collaborations and gender differences in scientific productivity

The two variables that have the most effect are the age of the children: women with children under 6 published 2.8 papers/year, whereas men published 6.6 papers/year.  They studied 1277 men, 252 women, at least assistant professors. 1989-1991, 3 years.

The other variable is research collaborations:  women without collaborators published 2.3/year, men 5.2/year.  With collaborators 6.4 for women, 7.2 for men.  Does it matter whether the other collaborators are women or men?

After the age of 40, there was no difference between men and women.

Motherhood and scientific productivity

Single women are less likely to collaborate with males than married women are.

Women under 53 are less productive than men.  Women with 2 children are more productive than women with more than 2 children; women with no children are the least productive.

From 1979 to 1981, survey of 1370 men, 199 women.  Europeans.

Several different studies:

Women reach a peak in their 50s, later than men.

After the children are 11 years old, there is no difference.

Women are more productive after that point.

Delayed in careers by raising children.

Publish or perish: A limited author analysis

In communications field, women graduate students were more productive, assistant professors were equal, women were less productive in associate and full professors (but there were fewer to survey).

If you are in a highly research oriented university, you will be productive because you will have constant pressure to publish.

Is publishing the result of cumulative advantage (where you came from) or institutional isomorphism (where you are is what determines your expectations and resources).  Both are important.  This was done in the 60s and 70s, where there were more communication barriers.

Gender, life course, and publication decisions  (epidemiology)

60 US professors were interviewed.  42 men, 19 women.  Young women took fewer risks, but when older they take more risks and are more interested in collaboration.  Men are taking risks and collaborating in early career but less in later career.

Women are more cautious about submitting papers before they are perfect.

Publish or perish, some reasons to perish

Everyone should read this.  Five reasons for perishing: if you didn t do your homework and don t know what s publishable and what s already been done.  If they are too busy, too critical of their own work, afraid to be criticized, or miscellaneous (getting organized, telling a story, identify what s important).

Apr 5: Abstracts (examples)

What do we expect to find in the abstract?

Problem statement - background


Methods, if necessary

Main results, interpretation or discussion

Management or other implications: What does it contribute?

Conclusion that relates back to the problem statement


  1. Objective (no problem statement)
  2. Methods
  3. Hypotheses
  4. Results (field)
  5. Results (model)
  6. Methods (model description)
  7. Results (model)
  8. Conclusion

The problem statement should have been:  Models assume uniform water loss, and we need to know whether we can correct for this.  Missing why this is important.


  1. Objective (no problem statement)
  2. Methods (2 sentences)
  3. Results (4 sentences, with interpretation and  implications)
  4. Conclusions

The problem statement could have been about the source of Hg to wood and its suitability for biomonitoring.


  1. We present a new map.  Is this objectives?  Or a result.
  2. Methods
  3. Management implications
  4. Result and implications

If your result is a map, how would you present it in an abstract?


  1. Objectives
  2. Objectives
  3. The existence of a result (not the result)
  4. The last 3 sentences do the same thing.  They tell us that a result is presented in the paper but they don t report the result in the abstract.


  1. Problem statement
  2. Statement of need
  3. Methods (3 sentences)
  4. Results (3 sentences)  The last sentence of the methods and results are almost the same.  If you need to save words, see if you can indicate methods in the sentences about results.
  5. Conclusions, relates back to problem


  1. Background
  2. Method or Result (the paper presents an approach)
  3. Results (or Method)
  4. Results (or interpretation).  Implications
  5. Result
  6. Results and implications

Because it s a sensitivity analysis, all the results are implications.  Or if it s a methods paper, are the results methods?

Pu Ge

  1. Problem statement
  2. Statement of need
  3. Methods, Objectives
  4. Methods (5 sentences)
  5. Results (3 sentences)
  6. Management implications

How do you choose what results to present in your abstract?

As many as you can fit in the word limit?

Shuai has too many scenarios and solutes to describe them all.

Yang: Focus on the ones the most people care about.  Or group them.

Ruth:  It s important to indicate that you have information people might be looking for.  Your other solutes will show up in a keyword search if they are in your abstract, title, or keywords.

Key words:  Your journal will tell you how many you can have.  They can be more than one word each.  Don t repeat words that are in your title or abstract, they are already included in searches.  We saw one example where most of the keywords were already in the title, and another that gave terms someone might search for that weren t included elsewhere.

We looked at authors and affiliations.


Joseph got all his second reviews.  He is still working on the map, it s not easy to get the basin delineations.  He doesn t have the DEM.  In the USA, this is easy!

Shuai sent us his first draft.  He has the Intro and is working on the Discussion.  He has data on fish populations, which he can reference in the Discussion.

Pu Ge redid everything.  I still need to interpret the results.  By the end of this week I will send the first draft to Thu Yan and Ruth.

Yang s dissertation will be distributed on Tuesday, which includes draft 2 of his tree ring Hg paper. He has Chapter 1.  Bring it Tuesday if we don t finish editing it today.

Alex is reanalyzing results and will get input at her lab meeting today.

Analysis of Abstracts

What s in an abstract?  Pick one, analyze it.  Color code it, then upload it to the google folder for background presentations.

Problem statement:  Yellow

(Background): Brown

Objectives: Red

Methods if novel:  Light blue

Results:  Dark Blue

Interpretation, Applications, Conclusions (Discussion):  Orange

The ASA has a Publications Handbook and Style Manual on line with instructions about abstracts and a good example.



What's in a proposal

Cover Page, Cover Letter


Project Summary

Written in future tense instead of past tense.


Motivation for the study.  Why should we care?

Different agencies require different sections.   Introduction and Rationale, Situation and Need, Long-Term Goals.


These may come at the end of an introductory section but may be before background.  Get them in early!

This may be a place to match tasks to your research questions.

There may be headings with narrative under them.

They may be numbered or bulleted (rarely just a paragraph as in a manuscript)


Context, previous research

Rationale and Significance


Research Approach, Experimental Plan, Technical Plan, Experimental Approach.

Site Description, Study Area (or this could be in the Introduction)

Field Methods, Experimental Methods, Experimental Design

If possible, link your activities to your Objectives or Hypotheses

You may be required to include Education or Outreach, depending on the competition you are applying for (USDA-CSREES had these categories).

Stakeholder involvement

Statistical Analysis

Pitfalls and Limitations (don t do this unless it s required)

Figures and Tables

Before modern word-processors, figures and tables were at the end of the text.  Now, most of them are embedded in the text.

Expected Products and Outcomes

Project Deliverables

Relevance to the Organization s Mission


Bulleted schedule, arrows, table with X to mark activities, tables, outlines

Collaborative Arrangements

Response to Previous Reviews

History of this Proposal.  This may or may not be required, but it s a good idea to prevent one review panel from telling you to do the opposite of what the last one sai


Literature Cited


There may be a required format or an electronic form.  It looks like a spreadsheet.

There may be a separate Budget Justification.

Investigator Qualifications

CVs: These may be limited to 1 or 2 pages, or there may be

Results of Prior Support (required by NSF), Progress Report

Statement of Success with Similar Projects

Investigator Qualifications, with publications

Conflicts of Interest

People on this list are not allowed to review your proposal.  People from the same institution, co-authors, collaborators (last 4 years or 5 years depending on the agency), those with consulting affiliations, advisor, advisees.

Current and Pending Support

Assurance Statements

Other differences from papers


Page Limits

Read the Directions!

Talk to a Program Manager.

April 5:

Resumes were assigned male or female namesChanging patterns of publication productivity: accumulative advantage or institutional isomorphism?

Rates of publication of papers and books depend on the type of institution: Faculty at research university, doctoral universities, comprehensive (professional, masters, and undergraduate), liberal arts colleges, 2-year colleges.  Recognition accrues to those at the higher institutions.  Surveys in 1972, 1989, and 1992.  Publication rates were coming up at the lower institutions.  (like the tail of a snake?)

Publish or Perish?  A limited author analysis of ICA and NCA journals (communication field)

Productivity:  publications, grad students = f (academic rank (assist, assoc, full), gender, institutional affiliation, journals published in).

Full professors are the most productive.

Among graduate students, women publish more than men.  Fewer women at higher ranks (in 2005).

Publish or perish?  Some reasons for perishing.

They think it s not worthy (they didn t do an adequate literature review).  They are too busy.  Scientists are too critical of their own work.  If you wait for it to be perfect, you ll never publish it.  Some scientists are afraid of the criticism of the reviewers.  Other excuses.  If you don t publish, what was the point of doing the work.

Equity and equality in measuring productivity between men and women (1998)

Women s productivity peaks later.  More co-authored papers.  More teaching and service.  They choose non-mainstream topics.  More likely to write books.  Women cite women, men cite men, and men get more citations.

They argue that productivity needs to be defined more broadly than publication impact.  Mentoring and teaching should be rewarded.  Co-authorship should be valued.  Quantity vs. quality.

Cumulative disadvantages in the careers of women ecologists (1993)

Survey. Productivity = papers, books, presentations, grants (these are all correlated), so they just used papers. Senior (average 44 years old) women 10.5, men 12.  Junior women (average 34 years old) 7.5, men 12.

Women are less satisfied with their PhD advisor.  They have a harder time finding a mentor.  Lower salaries, career advancement, productivity.

Motherhood and scientific productivity (1990)

Effect of having children, a previous study showed that faculty (social work field in the USA) with small children were most productive.  But in this study in Norway, women with small children were less productive, less so for men.  Better than women without children.  Having a partner is good.

Gender, household labor, and scholarly productivity among university professors (2000s)

Women spend more time on housework, and they spend more time on teaching.  No relationship between productivity and the amount of time spent on research!

Time fragmentation hurts productivity.

Maybe women compensate by reducing their leisure time.

Gender differences in India.  The cultural differences affecting women seem more severe than here (2002)  Women have a dual burden, work and family.

High ego strength.  Personal dominance.  Preference for precision and exactness.  Strong impulse control.  Preoccupation with ideas and things rather than people.  Autonomy, self-sufficiency.  Chemists, physicists, biologists.

Apr 10, 12:  Author Help Sessions

Progress reports

Joseph is trying to work on the map, Jeff gave him some web sites to look at.  How to export into software?

Yang brought Chapter 1

Pu Ge is bringing Methods

April 12

Alex brought her Introduction.  She wants help on how to focus it better, and she s concerned that it might read more like a thesis than a journal article.  1.5 pp.

Gretchen brought her Intro.  It s 4 pp. now, how much of this information is not necessary for the journal audience.  And some of it might belong in the Discussion.

Yang didn t bring anything but is offering help.

Pu Ge could bring Methods and Results.

Thu Ya is concerned about redundancy in describing his models in the Methods.  There must be a more concise way.

Shuai didn t bring anything, he was working on the Discussion, and then he got input from a co-author on the Results.  We can help with his Results.

Joseph didn t bring anything.  The map challenge:  He can t get the data to delineate the sub-basins on a map.  There is software that could do it for $5000--TNT maps.  He has the data from an ILL source, it s in an old format that TNT maps could read.

Apr 17: Abstracts

Shuai is concerned about the word limit.  He wants to say more about the results, so what can he cut.

Joseph has 242 of 250 and he thinks he has all the necessary parts!

Gretchen has 236 and all the parts, she s happy with it.

Yang brought the abstract from a different paper.  He thinks he has all the parts and could use help with the problem statement.

Pu Ge has 209 of 250, with some results still coming in and some discussion.  Missing parts are noted with x s.

Thu Ya 246.  He might change the journal, which could have different requirements.

Alex has 162, and she is allowed 400.  Her results may change on Friday.

Help on Thursday

Joseph needs software to read old map files.  Thu Ya knows someone who has it.

For Thursday, he might bring his Discussion.

Shuai might bring his Introduction.

Thu Ya might bring Methods.

Pu Ge went to go check on his car

Yang Introduction to a sap mercury paper.

Gretchen thinks maybe Methods.

Alex will bring Results if she has them and Intro if she doesn t.

Apr 17:  Help with Revisions

Status: How's it going?

Alex brought some graphs of results, with multiple ways of displaying the data.

Pu Ge is here to help. General organization of his Methods and Results?

Gretchen s Methods section is 4 pages.  She restructured it.  Readers, can you understand what s happening?

Joseph has his Discussion, 4 pages.  Does it make sense?  Please look at the flow of ideas.

Yang has an Introduction, 1.5 pages.

Shuai has an electronic copy of his paper.  He has comments already from his co-authors.

Thu Ya brought the section of the Methods that describes the model builder.  1 page.

People who want another review

Alex is working on her second draft.

Yang is already working on his next paper.

Thu Ya is working on his second draft, this weekend!

Shuai, second draft next week, maybe Tuesday.

Joseph has gotten comments, will be working on those.

Gretchen has a month to go, still generating results.

April 24: Abstracts

Maddy: I did a lot of editing and I went to the Writing Center and they helped with the flow.  There is a sentence I highlighted that may not belong--I m over the word limit if I leave it in.

Yang:  I don t have a good problem statement.

Alex:  I don t know how to analyze my data.  I need to block by tree.  It s hard because the sampling design is not balanced.  My P values will change.

Pu Ge:  My main concern is the length.  It s 400 words.  My journal doesn t have a word limit, but I think it s too long.

Autumn:  I wrote 338 words and brought it down to 231 (250 is the limit).  For my thesis, it had to be 150, but that one is not as good.

Dan will finish his paper tonight.  The abstract is short.  The results are likely to change.  Word limit is 250, does he need to add anything?

Zainab:  I have reduce my abstract from 360 to 256, but it needs to be 250 at most.  I m working on my problem statement.

April 26:  Steps to Publication

Joseph is on track, and his map problem was solved by someone in the Forest Department in Myanmar. (May 7)

Shuai will send his second draft to Ruth and Gretchen.  Today!

Alex is redoing her results, she is planning on having her second draft this weekend. (Make that Friday May 4.)

Thu Ya will finish his second draft this weekend.  It goes to Ruth and Yang. (May 2)

Yang got lots of comments on Chapter 3 from his committee on Tuesday.  He will work with his coauthors.

Gretchen is still getting results.  She will aim to have something to Joseph in time for him to have reviewed it before grades are due on May 16. (May 10 or 11)

Pu Ge (May 4) to Yang.

Electronic submission of manuscripts

Make a one-page summary and upload it to our google folder:

May 4: Final Drafts

Cover letter

Forest Ecology and Management requires a cover letter:  Author to whom to address correspondence, contact information, any previous or concurrent submissions (see copyright information), information that will support your submission original or confirmatory data, relevance, topicality.

Ecological Applications requires a cover letter: fit with scope of journal, how it advances the field.  Is it related to any other paper published in this society s journals.

Cover art



FE&M requires that these be editable, not images.  So they can typeset them, I guess.

Wishes for your fellow authors

Ruth: sleep well and write good papers.  (Gretchen changed her schedule!)

Gretchen:  Pay attention to what s working.  Work when you are effective.  Are you inspired by people reviewing your drafts?

Pu Ge:  You will struggle with time management, but you will eventually figure it out.  Respect the deadlines (ha ha).  Recidivism, recidivist.

Alex:  It s better to bring in something than nothing at all.  Even if it s just an outline.  I got help from doing that.

Joseph:  Avoid perfectionism.  We would still have suggestions for improvement if we reviewed published articles.

Alex:  A paper can always be better, but you have to get it submitted at some time.

Shuai:  When you have something in your mind, write it down before you forget it.

Ruth:  Sometimes saying it out loud helps me compose a sentence.

Yang:  You need to have your results ready before you take this class.

Shuai:  Sometimes the writing and reviewing process means that you need to generate more results.

Thu Ya:  Enjoy the struggle.  Know yourself.  Make choices.