Scientific Reading and Writing in English

1. Scientific Reading and Writing in English • Lectures on: 12/01, 12/22 “Abstract” & Practice 12/08, 12/29 “References, Acknowledgements, and Front page” & Practice 12/15, 1/05 “Cover letter” & Practice • Readings: “How to Write & Publish a Scientific Paper” by Robert A. Day, 6th Edition • Pin Ling (凌 斌), Ph.D. Department of Microbiology & Immunology, NCKU ext 5632 lingpin@mail.ncku.edu.tw

2. How to prepare the abstract? • Definition and function of the abstract • Organization of the abstract • Tips for writing the abstract • Example and practice Your involvement is the key to success in this lecture. Speak Up!

3. Read them first and decide to read the rest or not The Structure of A Paper

4. What is the abstract? • Ab, Out trahere, to Pull To pull out the “key points” from the paper • An abstract can be viewed as a mini-version of the paper. • Two common types of Abstracts - Informative abstracts: most research papers (five elements) -Indicative (Descriptive) abstracts: review articles to Pull Out

5. A Good Abstract The Whole Paper The Whole Paper A Poor Abstract X The function of the abstract • The first contact to readers Readers A good abstract delivers the paper’s key points “Concisely” and “Precisely”.

6. How to prepare the abstract? • Definition and function of the abstract • Organization of the abstract • Tips for writing the abstract • Example and practice

7. The Organization of the abstract (I) • The organization of the (informative) abstract is similar to the organization of the paper. • It includes the key information from the paper : - Introduction - Purpose (Key Question) - Materials & Methods (What was done) - Results (What was found) - Conclusions & Discussion (Answer & Implication)

8. Introduction & Purpose Materials & Methods Abstract (One paragraph) Title (One sentence) Results & Figures Conclusions & Discussion The Organization of the abstract (II) • Pull out the key information from each part to form a paragraph.

9. How to prepare the abstract? • Definition and function of the abstract • Organization of the abstract • Tips for writing the abstract • Example and practice

10. Tips for writing the abstract • Timing to write the abstract • Length • Sentence structure & word choice • Other issues

11. The Structure of A Paper

12. Introduction & Purpose Title (One sentence) Abstract (One paragraph) Materials & Methods Results & Figures Conclusions & Discussion Main text Overview sections The order to write a paper Write the main text first and then the overview sections

13. The length of the abstract • One paragraph (usually) • Most journals limit the length within 250 words. Some are even lesser. *Check the journal submission rules • Do not add unimportant details or unnecessary words to fill up the space. • Add more details => Out of => Lost the "Focus" "Big Picture"

16. Sentence Structure • Write short and simple sentences • Short sentences are easy for readers to follow up. • By contrast, long sentences tend to make readers lost.

17. Word choice & Abbreviations • Use simple words. Avoid jargon. • Avoid noun clusters (try your best) e.g. Real-time quantitative polymerase chain reaction (qPCR) • Rules of using abbreviations: Use standard (std) abbreviations => units of measurement, e.g. microgram (mg) => widely accepted, e.g. DNA & NF-kB Define a non-std abbreviation the first time you use it. e.g. Epidermal Growth Factor Receptor (EGFR), c-Jun N-terminal Kinase (JNK)

18. Other issues for writing the abstract • Verb tenses in the abstract = those in the paper. Present tense => Question & Answer Past tense => What was done & What was found • Continuity Keep clear continuity throughout the abstract • Signaling Topics Signal the parts of an abstract by starting a new sentence and by stating the topic at the beginning of the sentence.

19. How to prepare the abstract? • Definition and function of the abstract • Organization of the abstract • Tips for writing the abstract • Example and practice

20. Example of an informative abstract Regulation of IkB Kinase (IKK)g/NEMO Function by IKKb-mediated Phosphorylation* Shashi Prajapati and Richard B. Gaynor‡ J Biol Chem. 2002 Jul 5;277(27):24331-9. The IkappaB kinase (IKK) complex includes the catalytic components IKKalpha and IKKbeta in addition to the scaffold protein IKKgamma/NEMO. Increases in the activity of the IKK complex result in the phosphorylation and subsequent degradation of IkappaB and the activation of the NF-kappaB pathway. Recent data indicate that the constitutive activation of the NF-kappaB pathway by the human T-cell lymphotrophic virus, type I, Tax protein leads to enhanced phosphorylation of IKKgamma/NEMO by IKKbeta. To address further the significance of IKKbeta-mediated phosphorylation of IKKgamma/NEMO, we determined the sites in IKKgamma/NEMO that were phosphorylated by IKKbeta, and we assayed whether IKKgamma/NEMO phosphorylation was involved in modulating IKKbeta activity. IKKgamma/NEMO is rapidly phosphorylated following treatment of cells with stimuli such as tumor necrosis factor-alpha and interleukin-1 that activate the NF-kappaB pathway. By using both in vitro and in vivo assays, IKKbeta was found to phosphorylate IKKgamma/NEMO predominantly in its carboxyl terminus on serine residue 369 in addition to sites in the central region of this protein. Surprisingly, mutation of these carboxyl-terminal serine residues increased the ability of IKKgamma/NEMO to stimulate IKKbeta kinase activity. These results indicate that the differential phosphorylation of IKKgamma/NEMO by IKKbeta and perhaps other kinases may be important in regulating IKK activity. One paragraph, 201 words

21. Dissection of the abstract-1 The IkappaB kinase (IKK) complex includes the catalytic components IKKalpha and IKKbeta in addition to the scaffold protein IKKgamma/NEMO. Increases in the activity of the IKK complex result in the phosphorylation and subsequent degradation of IkappaB and the activation of the NF-kappaB pathway. Recent data indicate that the constitutive activation of the NF-kappaB pathway by the human T-cell lymphotrophic virus, type I, Tax protein leads to enhanced phosphorylation of IKKgamma/NEMO by IKKbeta. To address further the significance of IKKbeta-mediated phosphorylation of IKKgamma/NEMO, we determined the sites in IKKgamma/NEMO that were phosphorylated by IKKbeta, and we assayed whether IKKgamma/NEMO phosphorylation was involved in modulating IKKbeta activity. IKKgamma/NEMO is rapidly phosphorylated following treatment of cells with stimuli such as tumor necrosis factor-alpha and interleukin-1 that activate the NF-kappaB pathway. By using both in vitro and in vivo assays, IKKbeta was found to phosphorylate IKKgamma/NEMO predominantly in its carboxyl terminus on serine residue 369 in addition to sites in the central region of this protein. Surprisingly, mutation of these carboxyl-terminal serine residues increased the ability of IKKgamma/NEMO to stimulate IKKbeta kinase activity. These results indicate that the differential phosphorylation of IKKgamma/NEMO by IKKbeta and perhaps other kinases may be important in regulating IKK activity. Introduction (Background)

22. Dissection of the abstract-2 The IkappaB kinase (IKK) complex includes the catalytic components IKKalpha and IKKbeta in addition to the scaffold protein IKKgamma/NEMO. Increases in the activity of the IKK complex result in the phosphorylation and subsequent degradation of IkappaB and the activation of the NF-kappaB pathway. Recent data indicate that the constitutive activation of the NF-kappaB pathway by the human T-cell lymphotrophic virus, type I, Tax protein leads to enhanced phosphorylation of IKKgamma/NEMO by IKKbeta. To address further the significance of IKKbeta-mediated phosphorylation of IKKgamma/NEMO, we determined the sites in IKKgamma/NEMO that were phosphorylated by IKKbeta, and we assayed whether IKKgamma/NEMO phosphorylation was involved in modulating IKKbeta activity. IKKgamma/NEMO is rapidly phosphorylated following treatment of cells with stimuli such as tumor necrosis factor-alpha and interleukin-1 that activate the NF-kappaB pathway. By using both in vitro and in vivo assays, IKKbeta was found to phosphorylate IKKgamma/NEMO predominantly in its carboxyl terminus on serine residue 369 in addition to sites in the central region of this protein. Surprisingly, mutation of these carboxyl-terminal serine residues increased the ability of IKKgamma/NEMO to stimulate IKKbeta kinase activity. These results indicate that the differential phosphorylation of IKKgamma/NEMO by IKKbeta and perhaps other kinases may be important in regulating IKK activity. Purpose (Question)

23. Dissection of the abstract-3 The IkappaB kinase (IKK) complex includes the catalytic components IKKalpha and IKKbeta in addition to the scaffold protein IKKgamma/NEMO. Increases in the activity of the IKK complex result in the phosphorylation and subsequent degradation of IkappaB and the activation of the NF-kappaB pathway. Recent data indicate that the constitutive activation of the NF-kappaB pathway by the human T-cell lymphotrophic virus, type I, Tax protein leads to enhanced phosphorylation of IKKgamma/NEMO by IKKbeta. To address further the significance of IKKbeta-mediated phosphorylation of IKKgamma/NEMO, we determined the sites in IKKgamma/NEMO that were phosphorylated by IKKbeta, and we assayed whether IKKgamma/NEMO phosphorylation was involved in modulating IKKbeta activity. IKKgamma/NEMO is rapidly phosphorylated following treatment of cells with stimuli such as tumor necrosis factor-alpha and interleukin-1 that activate the NF-kappaB pathway. By using both in vitro and in vivo assays, IKKbeta was found to phosphorylate IKKgamma/NEMO predominantly in its carboxyl terminus on serine residue 369 in addition to sites in the central region of this protein. Surprisingly, mutation of these carboxyl-terminal serine residues increased the ability of IKKgamma/NEMO to stimulate IKKbeta kinase activity. These results indicate that the differential phosphorylation of IKKgamma/NEMO by IKKbeta and perhaps other kinases may be important in regulating IKK activity. J Biol Chem. 2002 Jul 5;277(27):24331-9. What was done

24. Dissection of the abstract-4 The IkappaB kinase (IKK) complex includes the catalytic components IKKalpha and IKKbeta in addition to the scaffold protein IKKgamma/NEMO. Increases in the activity of the IKK complex result in the phosphorylation and subsequent degradation of IkappaB and the activation of the NF-kappaB pathway. Recent data indicate that the constitutive activation of the NF-kappaB pathway by the human T-cell lymphotrophic virus, type I, Tax protein leads to enhanced phosphorylation of IKKgamma/NEMO by IKKbeta. To address further the significance of IKKbeta-mediated phosphorylation of IKKgamma/NEMO, we determined the sites in IKKgamma/NEMO that were phosphorylated by IKKbeta, and we assayed whether IKKgamma/NEMO phosphorylation was involved in modulating IKKbeta activity. IKKgamma/NEMO is rapidly phosphorylated following treatment of cells with stimuli such as tumor necrosis factor-alpha and interleukin-1 that activate the NF-kappaB pathway. By using both in vitro and in vivo assays, IKKbeta was found to phosphorylate IKKgamma/NEMO predominantly in its carboxyl terminus on serine residue 369 in addition to sites in the central region of this protein. Surprisingly, mutation of these carboxyl-terminal serine residues increased the ability of IKKgamma/NEMO to stimulate IKKbeta kinase activity. These results indicate that the differential phosphorylation of IKKgamma/NEMO by IKKbeta and perhaps other kinases may be important in regulating IKK activity. What was found

25. Dissection of the abstract-5 The IkappaB kinase (IKK) complex includes the catalytic components IKKalpha and IKKbeta in addition to the scaffold protein IKKgamma/NEMO. Increases in the activity of the IKK complex result in the phosphorylation and subsequent degradation of IkappaB and the activation of the NF-kappaB pathway. Recent data indicate that the constitutive activation of the NF-kappaB pathway by the human T-cell lymphotrophic virus, type I, Tax protein leads to enhanced phosphorylation of IKKgamma/NEMO by IKKbeta. To address further the significance of IKKbeta-mediated phosphorylation of IKKgamma/NEMO, we determined the sites in IKKgamma/NEMO that were phosphorylated by IKKbeta, and we assayed whether IKKgamma/NEMO phosphorylation was involved in modulating IKKbeta activity. IKKgamma/NEMO is rapidly phosphorylated following treatment of cells with stimuli such as tumor necrosis factor-alpha and interleukin-1 that activate the NF-kappaB pathway. By using both in vitro and in vivo assays, IKKbeta was found to phosphorylate IKKgamma/NEMO predominantly in its carboxyl terminus on serine residue 369 in addition to sites in the central region of this protein. Surprisingly, mutation of these carboxyl-terminal serine residues increased the ability of IKKgamma/NEMO to stimulate IKKbeta kinase activity. These results indicate that the differential phosphorylation of IKKgamma/NEMO by IKKbeta and perhaps other kinases may be important in regulating IKK activity. Answer & Implication

26. Any suggestion for the abstract? The IkappaB kinase (IKK) complex includes the catalytic components IKKalpha and IKKbeta in addition to the scaffold protein IKKgamma/NEMO. Increases in the activity of the IKK complex result in the phosphorylation and subsequent degradation of IkappaB and the activation of the NF-kappaB pathway. Recent data indicate that the constitutive activation of the NF- kappaB pathway by the human T-cell lymphotrophic virus, type I, Tax protein leads to enhanced phosphorylation of IKKgamma/NEMO by IKKbeta. To address further the significance of IKKbeta-mediated phosphorylation of IKKgamma/NEMO, we determined the sites in IKKgamma/NEMO that were phosphorylated by IKKbeta, and we assayed whether IKKgamma/NEMO phosphorylation was involved in modulating IKKbeta activity. IKKgamma/NEMO is rapidly phosphorylated following treatment of cells with stimuli such as tumor necrosis factor-alpha and interleukin-1 that activate the NF-kappaB pathway. By using both in vitro and in vivo assays, IKKbeta was found to phosphorylate IKKgamma/NEMO predominantly in its carboxyl terminus on serine residue 369 in addition to sites in the central region of this protein. Surprisingly, mutation of these carboxyl-terminal serine residues increased the ability of IKKgamma/NEMO to stimulate IKKbeta kinase activity. These results indicate that the differential phosphorylation of IKKgamma/NEMO by IKKbeta and perhaps other kinases may be important in regulating IKK activity.

27. Tips for the abstract • Use simple words and define abbreviations • Write short and simple sentences • Verb tenses • Continuity • Signal Topics

28. Define the Abbreviations

29. Tips for the abstract

30. The Revised Abstract The IkappaB kinase (IKK) complex includes the catalytic components IKKalpha (IKKa) and IKKbeta (IKKb) in addition to the scaffold protein IKKgamma (IKKg)/NEMO. Activation of the IKK complex results in the phosphorylation and subsequent degradation of IkappaB and the activation of the NF-kappaB (NF-kB) pathway. Recent data indicate that the constitutive activation of the NF-kB pathway by the human T-cell lymphotrophic virus, type I, Tax protein leads to enhanced phosphorylation of IKKg/NEMO by IKKb. To address the significance of IKKb-mediated phosphorylation of IKKg/NEMO, we determined the sites in IKKg/NEMO that were phosphorylated by IKKb. We also assayed whether IKKg/NEMO phosphorylation was involved in modulating IKKb activity. Our result showed that IKKg/NEMO was rapidly phosphorylated following stimulation by tumor necrosis factor-alpha and interleukin-1 that activate the NF-kB pathway. IKKb was found to phosphorylate IKKg/NEMO predominantly in its carboxyl terminus on serine residue 369 in addition to sites in the central region of this protein. Surprisingly, mutation of these carboxyl-terminal serine residues increased the ability of IKKg/NEMO to stimulate IKKb kinase activity. These results indicate that the differential phosphorylation of IKKg/NEMO by IKKb and perhaps other kinases may be important in regulating IKK activity. One paragraph, 201=>191 words • Use simple words & abbreviations • Write short and simple sentences • Verb tenses • Signal Topics

31. Common Problems in Abstracts • Excessive details (length) => make the abstract unreadable (the trees overshadow the forest) • Omitting the question or Stating the question vaguely => No goal for this work • Answer not stated => No ending

33. The Divided Abstract

34. Abstracts for conferences (I) • Abstracts for conferences • show a valuable contribution • lure audiences to your talk • Follow the most of guidelines as abstracts of research papers. • To encourage speculation, alternative theories, and suggestion for further research, the conference abstract is not as strict as the abstract for research papers.

35. Abstracts for conferences (II) • Several differences as below: => include more details for methods => display data in a table or a graph sometimes => include more implications (to indicate the importance of the work) • Abstracts for conferences self-destruct after a year. • If the paper is not published eventually, the details and data in the conference abstract can not be used because of no validation.

36. A Example of the Conference Abstract

37. Indicative (Descriptive) Abstracts • Usually for the review articles • Tell readers what information the article contains • Include the purpose, methods, and scope of the article • DO NOT provide results, conclusions, or recommendations

38. A Example of an indicative abstract

39. The IkappaB kinase (IKK) complex includes the catalytic components IKKalpha and IKKbeta in addition to the scaffold protein IKKgamma/NEMO. Increases in the activity of the IKK complex result in the phosphorylation and subsequent degradation of IkappaB and the activation of the NF-kappaB pathway. Recent data indicate that the constitutive activation of the NF- kappaB pathway by the human T-cell lymphotrophic virus, type I, Tax protein leads to enhanced phosphorylation of IKKgamma/NEMO by IKKbeta. To address further the significance of IKKbeta-mediated phosphorylation of IKKgamma/NEMO, we determined the sites in IKKgamma/NEMO that were phosphorylated by IKKbeta, and we assayed whether IKKgamma/NEMO phosphorylation was involved in modulating IKKbeta activity. IKKgamma/NEMO is rapidly phosphorylated following treatment of cells with stimuli such as tumor necrosis factor-alpha and interleukin-1 that activate the NF-kappaB pathway. By using both in vitro and in vivo assays, IKKbeta was found to phosphorylate IKKgamma/NEMO predominantly in its carboxyl terminus on serine residue 369 in addition to sites in the central region of this protein. Surprisingly, mutation of these carboxyl-terminal serine residues increased the ability of IKKgamma/NEMO to stimulate IKKbeta kinase activity. These results indicate that the differential phosphorylation of IKKgamma/NEMO by IKKbeta and perhaps other kinases may be important in regulating IKK activity.