References, Acknowledgements, & Front Page (12-16-2008)

1. References, Acknowledgements, & Front Page(12-16-2008) Lecturer: Pin Ling, PhD Department of Microbiology & Immunology, NCKU ext 5632 lingpin@mail.ncku.edu.tw

2. References • Functions • Criteria for selecting references • Incorporating references into the text • Citation and reference software

3. Functions of References • Direct readers to sources of other information • Give credits to the findings of others

4. Criteria for selecting references • Valid: 1. Journal articles (most thru the peer-review process) 2. Books 3. Theses • Available: Journal Articles > Books > Theses & Proceedings • Few: 1. Keep references to the fewest necessary. 2. Choose the most important, the most relevant, & the most recent.

5. Incorporating references into the text (I) • Two ways to cite references: (i) One emphasizes the science: e.g. IKK phosphorylates IkB (23). (ii) One emphasizes the scientists: e.g. Karin et al. (23) found that IKK phosphorylates IkB.

6. Incorporating references into the text (II) • Two types of ref citation are used in the text: (i) Number citation: e.g. IKK phosphorylates IkB (23). (ii) Author and year citation: e.g. It is demonstrated that IKK phosphorylates IkB (Karin et al., 1997) .

7. Incorporating references into the text (III) • Style of the references: (1) Follow the journal rules (2) Format in a single style e.g. Vancouver-style reference R. Medzhitov, P. Preston-Hurlburt and C.A. Janeway, Nature388 (1997), pp. 394–7. • Accuracy: (1) Verify the citation of a article (Authors’ names, Title, Journal, Year, Vol, & Page No.) (2) Correlation of the ref list

8. Citation and reference software (1) EndNote (2) Reference Manger (Today’s lecture based on Version X, most recent version XI)

9. EndNote’s Functions (1) Search bibliographic databases on the internet (2) Organize references and images in a database (3) Construct your paper with built-in manuscript templates (4) Watch the bibliography and figure list appear as you write

10. Connect Connect PubMed Search bibliographic databases on the internet Choose “Tools”

11. EndNote Functions (1) Search bibliographic databases on the internet (2) Organize references in a database (3) Construct your paper with built-in manuscript templates (4) Watch the bibliography and figure list appear as you write

12. EndNote Functions (1) Search bibliographic databases on the internet (2) Organize references in a database (3) Construct your paper with built-in manuscript templates (4) Watch the bibliography and figure list appear as you write

13. EndNote Functions (1) Search bibliographic databases on the internet (2) Organize references in a database (3) Construct your paper with built-in manuscript templates (4) Watch the bibliography and figure list appear as you write

15. Acknowledgements Title Abstract Main Text Introduction Materials & Methods Results & Figures Discussion Acknowledgements

16. Acknowledgements (1) Acknowledge any significant technical help in your lab or elsewhere. (2) Acknowledge the source of materials. (3) Acknowledge any outside financial assistance, e.g. grants, fellowships….etc.

17. Tips for preparing Acknowledgements (1) Being courteous. (2) Being appropriate and Do not flatter. (3) No “Wish” in Acknowledgements. e.g. I wish to thank …….. => I thank……..

18. Front Page (1) Title & Running Title (2) Author and Institution Names Corresponding Author Information (e.g. email, fax,..etc) (3) Keywords

19. Introduction & Purpose Title (One sentence or one phrase) 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

20. Title • Functions: • State the main point in a sentence or a phrase • A good “Title” attracts readers

21. Tips for preparing a good “Title” What is a good title? => The fewest words that adequately describe the contents of the paper. • Concise: • A short title has more impact than a long title • does. • (2) Important word first • Subtitles (Running titles) • (3) Accurate (Unambiguous) An improperly “Titled” paper is doomed to lost its intended readers.

22. Content of Titles for Results Papers • Stating the Topic in the Title • Effect of Ribavirin on HCV Infection in Mice • (Effect of X on Y in Z) • X: the independent variable(s) that you manipulated • Y: the dependent variable(s) you measured or • observed • Z: the species or the material on which you did the • work • (2) Stating the Point in the Title • Inhibition of HCV infection by Ribavirin in Mice

23. A Word A Phrase Examples of Titles (I) • TAB3 is a new binding partner of the protein kinase TAK1 • TAB3, a new binding partner of the protein kinase TAK1 (Biochem J, 2004)

24. Examples of Titles (II) (1) Wnt-1 signal induces phosphorylation and degradation of c-Myb protein via TAK1, HIPK2, and NLK (Genes Dev, 2004) (2) Regulation of Cell Proliferation by a Morphogen Gradient(Cell, 2005)

25. Running Title (1) A “Running Title” functions to identify the article. (2) Use a “Short Phrase” and appear at the top or bottom of every page. (3) Pick key terms and put words in the same order as “Title”.

26. Examples of Running Titles Title: Three-Dimensional Reconstruction of Alveoli in the Rat Lung for Pressure-Volume Relationships Running Title: Reconstruction of Alveoli in the Rat Lung

27. Author and Institution Names • (1) Identify the authors • Contact information: • A corresponding author required for Reprints, Communication, & Materials • (3) Use asterisks or footnotes to organize the author and institution names

28. Nature Immunology6, 1087 - 1095 (2005) Essential function for the kinase TAK1 in innate and adaptive immune responses Shintaro Sato1, 7, Hideki Sanjo2, 3, 7, Kiyoshi Takeda4, Jun Ninomiya-Tsuji5, Masahiro Yamamoto2, Taro Kawai1, Kunihiro Matsumoto6, Osamu Takeuchi1, 2 & Shizuo Akira1, 2 1  Akira Innate Immunity Project, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Osaka University, Suita, Osaka, 565-0871, Japan. 2  Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan. 3  Lymphocyte Differentiation, RIKEN Research Center for Allergy and Immunology, Yokohama, Kanagawa 230-0045, Japan. 4  Department of Molecular Genetics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan. 5  Department of Environmental and Molecular Toxicology, North Carolina State University, Raleigh, North Carolina 27695-7633, USA. 6  Department of Molecular Biology, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan. 7  These authors contributed equally to this work. Correspondence should be addressed to Shizuo Akira sakira@biken.osaka-u.ac.jp Example

29. Keywords • Link your article to the related fields • Medical Subject Headings (MeSH) Keywords • (http://www.nlm.nih.gov/mesh/meshhome.html) • (3) Pick up from the “Title” or “Abstract”. • (4) Facilitate readers to identify your article from a • database

30. Homework • Practice “References, Acknowledgements, & Front page” • We will discuss them on the 1-06-2009 lecture.

31. Examples of Titles (II) (1) Wnt-1 signal induces phosphorylation and degradation of c-Myb protein via TAK1, HIPK2, and NLK (Genes Dev, 2004) (2) Regulation of Cell Proliferation by a Morphogen Gradient(Cell, 2005)