Writing Scientific Papers

1. Writing Scientific Papers A Mini-Workshop presented at the Beijing Municipal Research Institute of Environmental Protection (BIEP) Patricia J. S. Colberg, Ph.D., Professor Department of Civil and Architectural Engineering University of Wyoming, Laramie, Wyoming 82071 USA pczoo@uwyo.eduwww.uwyo.edu/colberg University of Wyoming College of Engineering and Applied Science

2. It is our responsibility as scientists to PUBLISH our work! • If you do research, you need to share your findings. • If you do other important work you need to share you discoveries. The WAY to share your findings and discoveries is to PUBLISH!

3. Preview of today’s workshop 1. Some common questions: What type of paper should I write? How do I choose a journal? Should I write my first draft in Chinese or English? Do I need an English editor? 2. Components of a typical journal article What is the purpose of each section of a paper? 3. Figures and Tables 4. Where do I begin? 5. Additional help and resources

4. What type of paper should I write? Review Article • Normally reserved for authors who are distinguished in the field • Review articles are sometimes ‘invited’ or require ‘permission’ of editors. • They are usually peer-reviewed, though not always. Research Article (page length may vary) • A journal article that focuses on original research • Manuscripts undergo “peer review” • A minimum of two reviewers (usually three) Comment/Editorial • Some journals allow comments and editorials.

5. How do I choose a journal? Does my research fit the topical theme of a journal? • Look up journals on-line: how do they describe papers they want to publish? • Read some of the recent papers the journal has published. • See where papers you read or cite are getting published.

6. How do I choose a journal? How important is ‘editorial turnaround’ and ‘time to publication’? • You want to get feedback from reviewers quickly. • Even if your paper is accepted for publication, you will need to make revisions. • Getting your work published rapidly is often more important than anything else. • Do not submit to a journal that has a rejection rate >75%.

7. How do I choose a journal? Should I consider the ‘Impact Factor’ of a journal? • A journal’s reputation is more important than published ‘impact factors’ (IF). • The IF is meaningless if it is the wrong journal for your work! • There are many excellent journals that have relatively low IFs. Very High IFs Nature = 38.597 Science = 31.077 >90% rejection rate Good journals with OK IFs Environ SciTechnol = 5.257 J Hazard Mat = 4.679 Appl Environ Microbiol= 3.678 Good journals with Low IFs Groundwater = 1.102 76% rejection rate J Hydrology = 1.675 Water SciTechnol= 1.053

8. Should I write my first draft in Chinese or English? Try to write your paper in English! Avoid writing in Chinese and then translating to English! 英语 Read “Foreign Tongues” (2012) by Kendall Powell published in Nature 487:129-131.

9. Do I need an English editor? YES, probably!

10. 2. Components of a Typical Journal Article What is the purpose of each section of a paper? Title of paper/Keywords (List of authors and affiliations) Abstract Introduction Materials and Methods Results and Discussion Summary/Conclusions (Acknowledgements) References Cited Figures and Tables (Figure Legends)

11. Title and Keywords • The TITLE of your paper is important. • It needs to accurately describe its content. • Make a list of potential titles; choose a ‘working title’. • Do not choose the final title until the paper is nearly finished. • Consult your co-authors. • KEYWORDS are important too. • This is how other scientists find your work!

12. Abstract The ABSTRACT is often the most difficult part of a paper to write. I recommend writing it last .. not first! It usually has a 250-300 word limit, so it must be carefully crafted! We read abstracts for two reasons: (1) to decide whether or not we want the read the entire paper and (2) to prepare ourselves for the details presented in the whole paper. Briefly state the context for your work and what you did. Summarize your results (the “what”) and your conclusions (the “so what”?). NEVER CITE FIGURES, TABLE OR REFERENCES IN AN ABSTRACT! Handout: NatureAbstract.pdf

13. Introduction The Introduction clarifies the rationale for the work presented, summarizes the state of knowledge, and prepares readers for the rest of the paper. A good Introduction should: 1. Provide context to orient readers to your topic and establish the importance of your study. 2. State the need for your work. 3. Indicate what you have done in an effort to address this need (=task). 4. Preview rest of paper to prepare the reader for its structure (=object of the document)

14. Introduction: context and need 1. Provide context to orient readers to your topic and establish the importance of your study. Write the context to appeal to a broad range of readers. Be selective in citing references: include only information that is needed to understand the need and importance of study. Place the context in time; use phrases like “since the early 1970s” or “over the past decade”. 2. State the need for your work. Start by stating the current situation or state of knowledge; contrast this to what the desired situation or state of knowledge should be (what we want). Emphasize the contrast between the current and desired situations by using words like “but”, “however” or “unfortunately”. Try to link context with need: EXAMPLE: This is the first study since 1980 to definitively link automobile emissions with documented changes in urban microclimates. These results should contribute to the development of meaningful changes in emissions standards for new cars.

15. Introduction: task Indicate what you have done in an effort to address this need (=task) • Be sure to separate what others have done from what you have done. • The task clarifies your contribution as a scientist. For the TASK of the paper: Use whoever did the work as the subjectof the sentence: “we” or “ “the authors”. Use a verb expressing a research action: e.g., “measured”, “calculated”, “evaluated”. Set that verb in the PAST tense. EXAMPLES: based on examples from www.nature.com/scitable To tackle this problem, wedeveloped a new software verification protocol .. During controlled laboratory experiments, weinvestigated the influence of boundary conditions on ..

16. Task: important verbs to use Words that express ‘research actions’: us PAST TENSE Apply: We applied the Michaelis-Menten equation .. Assess: We assessed the effects of increasing TCE concentrations .. Calculate: We calculated the concentration of TCE downstream .. Compare: We compared the effects of .. to those of .. Design: We designed a set of experiment to test the hypothesis .. Determine: We determined the complete nucleotide sequence of .. Develop: We developed a new approach to .. Evaluate: We evaluated the efficiency of the process .. Implement: We implemented a strategy that .. Investigate: We investigated the behavior of .. Measure: We measured the concentration of cadmium in .. Based on a list at www.nature.com/scitable

17. Introduction: object 4. Preview rest of paper to prepare the reader for its structure (=object of the document) For the OBJECT of the paper: Use the document itself as the subjectof the sentence: e.g., “this paper ..” Use a verb expressing a communication action: e.g., “presents”, “summarizes”, “explains”. Set that verb in the PRESENT tense. EXAMPLES: based on examples from www.nature.com/scitable This paper describesthe flow effects induced by increasing the hepatic-artery pressure .. The paper discussesthe theory behind this new software verification protocol and demonstrates how this approach may be applied ..

18. Object of document: important verbs to use Words that express ‘communication action’: use PRESENT TENSE Clarify: This paper clarifies the role of bacteria in remediation of .. Describe: The paper describes the mechanisms whereby .. Detail: This paper details the algorithm used to .. Discuss: This paper discusses in detail the influence of influent concentration .. Explain: This paper explains how .. Offer: This papers offers three recommendations .. Propose: This paper proposes a new pathway .. Provide: This paper provides a complete framework .. Report: This paper reports on our progress in .. Summarize: This paper summarizes our results for 998 patients .. Based on a list at www.nature.com/scitable

19. Example: Handout from Nature: “An effective introduction for a paper” A good Introduction should: 1. Provide context to orient readers to topic and establish importance of study 2. State the need for the work 3. Indicate what you was done in an effort to address this need (=task) Preview rest of paper (=object of the document) Handout from Nature: NatureIntroduction.pdf

20. Materials and Methods The Materials and Methods section should provide enough detail so that other scientists could repeat your experiments. This section is often boring to read, but veryinteresting to those who want to understand how you got your results or repeat your work! There should be NO SECRETS about how you did you study!

21. Results and Discussion The Results and Discussion section presents and then discusses your research results. This is the section where your data should speak .. with only a few words from you. This section should be written only AFTER you have decided on which figures and tables to include and put them ‘in order’ of how you want to discuss them. Be concise. Be precise. The best way to learn to write this section is to READ OTHER PAPERS! Handout from Nature: NatureR&D.pdf

22. Summary/Conclusions The Summary or Conclusions section of your paper should interpret your work at a higher level of abstraction than is presented in the discussion. It is also the place where you can discuss the importance or application of the results as well as ideas for futurework. State the MOST IMPORTANT OUTCOME OF YOUR WORK. Do not simply repeat the points already made in the body of the paper! What do your findings mean? Offer some perspective: “One remaining question that needs to be answered ..” or “Future work must focus on ..” Handout from Nature: NatureConclusion.pdf

23. References Cited • Accuracy in citations is very important. • Follow citation format that your journal uses! • Avoid citing websites. NEVER cite Wikipedia! • Check spelling of names and titles of articles cited. • Used journal abbreviations! Consult a website to find correct abbreviations

24. Figures and Tables There is no substitute for good data. These is also no substitute for well designed graphs and tables that help the reader understand your data! FIGURES Accurately label figures. Keep them as simple as possible. Let the figure legend explain your figure. TABLES Tables should be used only when the data is not readily presented as a graph or when there is simply too much data to graph.

25. Figures: an example From Hou and Liu, in preparation

26. Which font to choose for graphs and tables? Look at the lowercase “g” .. g: this is a good choice (Arial) g: this is a good choice (Geneva) g: this is a good choice (Helvetica) g: this is a poor choice (Times New Roman) g: this is a poor choice (Calibri) g: this is a poor choice (Palatino)

27. Tables: an example From Chen et al., 2012

28. Some easily confused words .. Refer to last six pages of handout ..

29. Where do I begin? 1. Select one or two journals for potential submission. 2. Carefully read the “INSTRUCTIONS TO AUTHORS” for each journal. 3. Prepare a list of figures and tables: this will provide the FOUNDATION for your paper! 4. Make a ‘checklist’ for each section of the paper that lists what should be included. 5. Start organizing the list of ‘References Cited’ before you write the paper. 6. Start writing any section except the Abstract.

30. Summary of my advice .. Write your manuscript in ENGLISH! Do not translate from Chinese! Ask a native English speaker to edit your paper. Read LOTS of journal papers! Follow ALL instructions from the journal. Pay attention to your ‘references cited’ section! Be prepared to REVISE and RESUBMIT. Don’t worry so much about the Impact Factor as the journal’s quality, reputation and fit!

31. Additional Help and Resources To get help with grammar questions: http://depts.washington.edu/engl/askbetty/ To learn more about writing scientific papers and related topics: http://www.nature.com/scitable/ebooks/english-communication-for-scientists-14053993/contents Need more help? To find abbreviations of journal names: http://images.webofknowledge.com/WOK46/help/WOS/A_abrvjt.html English editing services from the Nature Publishing Group: https://languageediting.nature.com/