Manuscript Reviews

1. Manuscript Reviews Guidelines for Reviewers of Scientific Manuscripts Actual Reviews ———————————— On Website next week — http://WillowsEnd.net All slides, English review (problem set)

2. Manuscript Reviews Guidelines for Reviewers of Scientific Manuscripts

3. Reviewers serve two groups • The editor and the journal • Make sure only quality work of significance is published • The author – to improve the paper, not just to judge (constructive criticism) • Give helpful, honest feedback (criticize), specific technical comments • Suggest improvements,other interpretations of results,other experiments and approaches

4. Step 1 of review:Initial assessment • Scanthe manuscript, take notes • Abstract, introduction, discussion/conclusions • Summarize the problem, approach, conclusions • Ask yourself personal questions: • Am I the right person to review this ms? • Is someone else better qualified? • Do I have a conflict of interest? • Do I know the author(s)? • Do I have time to review it well within the deadline?

5. Initial assessment • Content • Is the subject suitable for the journal? • Scientific merit • Is the manuscript worth publishing? • Is the data high quality? Is it true? • Significance of results • New knowledge, understanding, technique? • Is it interesting? • Is it a significant contribution to the field? • It should NOT be a simple extension or slight modification of past research.

6. If you will not continue the review. . . • State your specific reasons (personal or scientific) • Reasons to reject for publication at this stage: • Not suitable for journal • Work is poorly executed or not significant • Poor English, writing, or organization • Personal

7. The review • Read the entire manuscript thoroughly • Take detailed notes – they will be the outline for your review

8. Make an organized list of specific comments or recommendations • Give location (page, paragraph, line) • List by importance: most important first • This sentence/paragraph/section would be stronger if. . . • This argument would be convincing if you presented data. . .

9. Look for… •Presentation • A story line or thread to tie entire paper and each section together • Clear, logical flow (movement): sentence to sentence, paragraph to paragraph, section to section • Correct amount of detail • For experts in the field • To reproduce the work

10. Presentation . . . • The research problem • Good approach to problem • Reasonable interpretation of results, without too much speculation • No technical errors • English • Appropriate language • Correct use of terminology • Need work before acceptance? Recommend help!

11. Title • Accuratedescription of main focus • Should include most important aspects (key words) • Organism(s) • Technique • Result • Can length be reduced? • Should order of words or phrasing be changed?

12. Title Cucumber mosaic virus 2b discriminates small RNAswith different modes of binding RNA complexes  • Cucumber mosaic virus 2b discriminates small RNAs with differential binding of RNA complexes  Suppressor 2b ofCucumber mosaic virus discriminates small RNAs by differentially binding RNA complexes

13. Title Comparative analysis of gene expression of the transcript profiles of tomato roots infected with cyst nematode by SAGE  Comparative serialanalysis of gene expression (SAGE) of transcript profiles of tomato roots infected with cyst nematode

14. Title Molecular cloning of genes encoding endoglucanases RCE2 and RCE3 from Rhizopus oryzae and discussion of possible evolutionary process of the rce genes  Molecular cloning of genes for endoglucanases RCE2 and RCE3 from Rhizopus oryzae and possible evolution of the rce genes

15. Abstract • Clearly outlines the main points of focus • One or two succinct sentences on the background of organisms, problem • Approach to solving the problem, including a sentence or two about technique or method • Results • One or two sentences on significance of results in relation to research question, our understanding of the problem, and/or potential use

16. Problems with abstracts • Not including the correct information (or not enough, e.g., just a few sentences when author’s English is poor) • Including too much information • Not the place for an introduction • Methods or results too detailed • Including the wrong information • Other studies or citations should be in the Introduction or Discussion

17. Problems with abstracts Abstract for paper written in Japanese: Web blight of European pear occurred in Okayama Pref., Japan, in July of 1989 and in October of 1993. The pathogen obtained from infested leaves and sclerotia was identified as Rhizoctonia solani AG1-IB in respect to hyphal anastomosis and culture’s types. The common name of Web blight is proposed for this new disease of European pear. Need to identify all symptoms (others are given in captions), plant parts Rated disease development (table), not in abstract No mention of Koch’s postulates

18. Problems with abstracts Although isolation of an endoglucanase gene from members of the subdivision Zygomycota had not been reported,in a previous study, we cloned a new endoglucanase gene, designated the rce1 gene, from Rhizopus oryzae, a member of the subdivision Zygomycota. In this study, two endoglucanases. . . .  We previously cloned a new endoglucanase gene, rce1, from Rhizopus oryzae, the first from a member of the subdivision Zygomycota. Two endoglucanases. . . .

19. Introduction • Concise: only what is necessary • Explain problem in relation to past work by other researchers and authors. • Compare and contrast past work. • New, relevant references

20. Problems with Introduction • Too much detail (perhaps more suitable for Discussion), every paper cited (should not be a review of the literature) • Includes areas not directly related to research question • Relevant papers not included

21. Materials and methods • Was the work done well? Described well? • Are there flaws in methods, artifacts in measurements? • Are techniques appropriate to answer the questions, address the problem? • Manufacturers included?

22. Methods . . . • Appropriate sample size, controls, and statistical tests? • Statistics included, explained well? Citations, programs included?

23. Problems with methods • Too much detail of routine methods (e.g., size of flask) • Do not need to include every experiment: if poorly designed or unexpected results required a change in plans • Equations and statistics – examine closely for accuracy, correct use

24. Results • Findings and observations • Logical order • Tables and figures • Point out important features, relationships • Must be suitable for the type of data

25. Problems with results • Poor presentation • Not complete • Not logical order • Not specific — too general • Irrelevant findings • Are not related to research problem • Data in tables, figures repeated in text • Unnecessary tables, figures • Can a sentence or two explain the illustrations?

26. Problems with results • Not specific — too general Other isolates such as Alternaria alternata and Cladosporium species including C. clado-sporioides, C. oxysporum, C. tenuissimum and C. sphaerospermum were detected frequently from both cultivars and all lots. Other isolates such as R. stolonifer, Fusarium spp. and M. verrucaria were also detected at low frequencies. The percentages of infected or infested seeds were very high on new lots (Table 3), but the fungal flora of new lots was simpler than that of old ones.

27. Problems with results • Not specific — too general The percentages of infected or infested seeds were very high on new lots (Table 3), but the fungal flora of new lots was simpler than that of old ones. • Give percentages • What does simpler mean? • Suggest: In new lots, ___% of the seeds were infected or infested, but fewer species were isolated.

28. Problems with results • Not specific — too general In 2003, submerged application of simeconazole in paddy water on 15, 22, or 29 July showed potent efficacy against kernel smut (Table 3) The highest efficacy was obtained by submerged application on 29 July. In 2004, the fungicide gave excellent control against kernel smut in every test (Table 4). • What does potent efficacy mean? • What is excellent control? “Excellent” may differ in percentage depending on the particular disease. Give specific percentage, result with no fungicide.

29. Tables and Figures • Are all tables and figures present? Are all mentioned in the text? • Note the first mention of every illustration. • Evaluate presentation of data • Is it clear and logical? • Necessary? Or better described in text only? • Is data organized well in table? • Are headings appropriate, placed correctly? • Does each column (including the first on left) have a heading?

30. Tables and Figures • Clearly labeled? • Key for symbols in figures? • Consistent with text, other tables and figures?

31. Problems with Tables and Figures • Unnecessary • Fewer than 8 data points or many zeroes, etc. • Incomplete captions • Unexplained abbreviations • Tables • No heading above 1st column on left • Headings with too many words • Figures • Caption not worded properly • Not explained clearly

32. Problems with Tables and Figures • Incomplete captions Fig. 1. Natural symptoms on leaf of Europeanpear. (identify specific symptom, use arrow) Fig. 1. Leaf blight on European pear after natural infection by Rhizoctonia solaniin an orchard. Fig. 5. Lesion of European pear leaf by artificial inoculation with R. solani. Fig. 5. Lesion on European pear leaf __ daysafter inoculation with Rhizoctonia solani. (Better to replace “inoculation” with type ofinoculation, inoculum, etc.)

33. Discussion • Should not repeat Results! • Don’t need to repeat exact data; can summarize trend, relevance, relationships • Should not repeat Introduction! • Logical order: usually by importance • Places results in context of past work, compares/contrasts • Significance of results are explained well and are justified by the data (that is, the results support the conclusions)

34. Problems with Discussion • Repeats the Results! • Repeats the Introduction! Exact words! • Plagiarism??!! • Look for unusual wording, perfect English • Too much speculation, not enough evidence • Too much hedging (not willing to commit to a conclusion): It may possibly be… that it could perhaps…

35. Literature Cited • Be concerned if most are the author’s own publications or none are recent (within 2-3 yrs) • Is journal style used?

36. Summary of review… • Note: • Other interpretations of data • Errors in reasoning • Point out problems with clarity • Where more explanation is needed • Suggest different wording

37. Summary of review. . . • Be helpful • Do not say only: Publish without change… too specialized…do not publish • Explain problems • Make specific suggestions for improvement or revision, additional experiments or data, treatment of data, statistical tests

38. Summary of review. . . • Confirm (or not): • Excellent coverage of literature and interpretation of results and available data • Identify related studies • Suggest methods, further experiments • Suggest methods for better approaches • Identify missed opportunities

39. Time for questions

40. Tables • Use to present specific data, relationships; to make exact comparisons, to illustrate/make a point or points (idea or ideas), easier than describing it in the text. • If there are <8 data points presented in a table, then the data can probably be described more efficiently in the text rather than in a table. • Text of article refers to main points of table, does not repeat all contents.

41. Table organization • Title briefly describes the experiment, data given, organisms and location if appropriate, and gives enough detail for the table to be understood without referring to rest of the article. • The table should contain like items or compare like items. • Comparisons should be down columns, not across lines (across rows) — it is easier to read and compare down, rather than across.

42. Table organization • Use headings and subheadings to organize the data, clearly and identify the data in each column. • Horizontal headings of columns should identify the dependent variables (measured variable). Items below the leftmost heading (stub head) identify the independent variables for the horizontal rows. • Every column must have a heading. Include the unit of measure in the heading (not after the data within the table): Width (mm)

43. Table organization • Group items logically, include necessary controls and statistics. • Define all nonstandard abbreviations and symbols (in caption or footnotes). • Label footnotes with superscript letters (not numbers, which can be mistaken for exponents in the table), from left to right, top to bottom.

44. Tables: Critical points • Verify all data! Check accuracy, consistency with text and other tables and figures (including labels, units of measure, abbreviations, and fonts). • Can a readerunderstand the table without reading the article? The table must be able to “stand alone.” • Simplify as much as possible. • Proofread, proofread, proofread.

45. Figure checklist Figure text and axis labels __ Between 6 and 10 pt __ Lightface type recommended (i.e., plain, not boldface) __ Consistent size in all figures at printed size of figure __ First letter of labels capped (or consistent capitalization style)

46. Figure checklist __ Units in parentheses at end of axis labels: Length (mm) __ Units written the same way as in text __ Multiplier dots (not bullet ) used between multiple units in numerator and in denominator: (mmol·m–2·s–1) __ Axis label c. 0.2 cm from units on axis, no more than 0.5 cm; x- and y-axis labels equidistant from axes

47. Figure Checklist __ All appropriate words and letters in italics (e.g., genus, species, section, 1-letter constants and variables) __ Space before and after all operation signs (e.g., =, +) with equations and definitions, use en dash (width of two hyphens) for minus sign. __ Make sure all abbreviations are consistent from figure to figure.

48. Figure checklist Figure Panels __ Named with capital letters, preferably inside each panel __ Less than 0.5 cm between vertically aligned panels Multipanel Figures __ All panels for one figure placed in one file as they should appear in print __ Each panel labeled with letter (capital preferred), consistently labeled

49. Figure checklist Micrographs and Photographs __ Scale bar on each image, defined in caption __ Type of micrograph, optical system, stains, etc. defined in caption Rules (= lines) __ Not less than 1 pt, not more than 2 pt __ Scale bar present in each micrograph

50. Figure checklist Remember to Check File Resolution(required resolution may vary with journal) __ Line art: 1200 dpi __ Grayscale, halftones: 300 dpi __ Color: 300 dpi __ Combination line art and halftone (or color)*: 600 dpi *e.g., micrographs with text or bars