20140710 Edanz Kyushu Session 6

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20140710 Edanz Kyushu Session 6

  1. 1. Andrew Jackson, PhD Senior Editor Kyushu University Department of Agriculture Session 6 – Writing Your Manuscript Kyushu University 10 July 2014
  2. 2. Seminar series June 5 Effective presentations June 12 Reviewing the literature June 19 Academic publishing June 26 Research and publication ethics July 3 Effective writing July 10 Manuscript structure July 17 Communicating with journals July 24 Peer review and revisions
  3. 3. Professional writing strategies Section 1
  4. 4. Coverage and Staffing Plan Writing strategies Use your figures to structure your manuscript Where to start?  Your findings are why you want to publish your work  Form the basis of your manuscript  First step, is to logically organize your findings Figure 1 Figure 2 Table 1 Figure 3 Logical presentation Is anything missing? ? Additional analyses?
  5. 5. Coverage and Staffing Plan Writing strategies Where to start?  Your findings are why you want to publish your work  Form the basis of your manuscript  First step, is to logically organize your findings Figure 1 Figure 2 Table 1 Figure 3 Figure 4 Logical presentation New data Use your figures to structure your manuscript
  6. 6. Coverage and Staffing Plan Writing strategies Prepare an outline I. Introduction A. General background B. Related studies C. Problems in the field D. Aims II. Methods A. Subjects/Samples/Materials B. General methods C. Specific methods D. Statistical analyses III. Results A. Key points about Figure 1 B. Key points about Table 1 C. Key points about Figure 2 D. Key points about Figure 3 E. Key points about Figure 4 IV. Discussion A. Major conclusion B. Key findings that support conclusion C. Relevance to published studies D. Unexpected/negative findings E. Limitations F. Implications G. Future directions What background information you will introduce Introduction What analyses you will describe Methods What findings you will present Results What interpretations, limitations, and implications you will discuss Discussion
  7. 7. Coverage and Staffing Plan Writing strategies Getting feedback  After completing your outline, discuss it with your colleagues  Make the necessary changes before you begin writing  Write your manuscript section-by-section, do not get overwhelmed by thinking about writing an entire manuscript  Set deadlines as to when the first draft of each section will be completed  Get feedback from you colleagues after each section and make changes before beginning the next section
  8. 8. Coverage and Staffing Plan Writing strategies The ‘write’ order Manuscript sections • Title • Abstract • Introduction • Methods • Results • Figures • Discussion Writing order • Methods • Figures • Results • Discussion • Introduction • Abstract • Title
  9. 9. Coverage and Staffing Plan Writing strategies The ‘write’ order Methods Figures Results • Write as you are doing experiments • Include any changes you’ve made • Methods sections are usually consistent • Prepare figures after choosing journal • Repeat experiments if necessary • Based on prepared figures • Subsections based on each figure
  10. 10. Coverage and Staffing Plan Writing strategies The ‘write’ order Discussion Introduction Abstract • Conclusions based on presented data • Discuss relevant studies • Narrow- or broad-focused journal • Introduce ideas necessary for understanding the Results/Discussion • Concisely summarize manuscript • According to author guidelines Title • Concisely summarize key finding • Include key words
  11. 11. Target the journal Section 2
  12. 12. Target the journal Broad vs. narrow focus Aims and scope Broad focus Narrow focus Make sure your findings will be of broad interest Make sure your findings will be of interest to specific area(s)
  13. 13. Target the journal Broad focus Aims and scope Planta publishes timely and substantial articles on all aspects of plant biology. We welcome original research papers on any plant species. Planta
  14. 14. Target the journal How did related articles target the journal? Chlorophyll is present in many plant organs, including immature fruit where it is usually degraded during ripening. Mature green kiwifruit (Actinidia deliciosa) are an exception, with high concentrations of chlorophyll remaining in the fruit flesh. In gold-fleshed kiwifruit (A. chinensis), chlorophyll is degraded to colourless catabolites upon fruit ripening, leaving yellow carotenoids visible. We have identified candidate genes for the control of chlorophyll degradation in kiwifruit… Pilkington et al. Planta. 2012; 236: 1615−1628. The control of chlorophyll levels in maturing kiwifruit Broad interest Broad interest Broad focus
  15. 15. Target the journal Aims and scope The aim of Paddy and Water Environment is to advance the science and technology of water and environment related disciplines in paddy-farming. The scope includes the paddy- farming related scientific and technological aspects in agricultural engineering such as irrigation and drainage, soil and water conservation, land and water resources management, paddy multi-functionality, agricultural policy, regional planning, bioenvironmental systems, and ecological conservation and restoration in paddy farming regions. Paddy and Water Environment Narrow focus
  16. 16. Target the journal Aims and scope The aim of Paddy and Water Environment is to advance the science and technology of water and environment related disciplines in paddy-farming. The scope includes the paddy- farming related scientific and technological aspects in agricultural engineering such as irrigation and drainage, soil and water conservation, land and water resources management, paddy multi-functionality, agricultural policy, regional planning, bioenvironmental systems, and ecological conservation and restoration in paddy farming regions. Paddy and Water Environment Narrow focus
  17. 17. Target the journal Aims and scope The aim of Paddy and Water Environment is to advance the science and technology of water and environment related disciplines in paddy-farming. The scope includes the paddy- farming related scientific and technological aspects in agricultural engineering such as irrigation and drainage, soil and water conservation, land and water resources management, paddy multi-functionality, agricultural policy, regional planning, bioenvironmental systems, and ecological conservation and restoration in paddy farming regions. Paddy and Water Environment Make sure your manuscript specifically targets one of these areas of interest! Narrow focus
  18. 18. Target the journal How did related articles target the journal? Effects of tillage and irrigation on the occurrence and establishment of native wetland plant species in fallow paddy fields Traditional weed management, such as tillage and irrigation, has led to an enhanced maintenance of wetland plant species in fallow paddy fields. Recent herbicide usage and improvements in irrigation and drainage systems however have caused habitat loss of these species, especially in fields on open lowlands… Takanose et al. Paddy Water Environ. 2013; 11: 1−4. Keywords from the Aims and Scope Narrow focus
  19. 19. Target the journal Your references Related articles from the journal Include references to those articles in your manuscript Shows the journal editor that your study is building on research already published in their journal
  20. 20. Manuscript structure Section 3
  21. 21. Manuscript structure Introduction General introduction Specific aimsAims Current state of the field Problem in the field
  22. 22. Manuscript structure The objectives of the research were: (1) to monitor agricultural inputs and outputs of N, P, and K, to quantify and assess element balances at the field level for a two-year period; (2) to identify the main contributory factors causing element imbalances; and (3) to assess socio-economic factors that drive nutrient management. This will allow future research to explore risks for soil accumulation and potential losses to the water environment. Aims Problem However, information on major nutrient balances driven by underlying socioeconomic factors is lacking in peri-urban areas. Your aims should address a problem Wang et al. Nutr Cycl Agroecosyst. 2008; 81: 203−218.
  23. 23. Manuscript structure Ezeala et al. Ann Med Health Sci Res. 2013; 3: 376–379. Most common reason for rejection? Analyzed 42 manuscripts rejected from 8 biomedical journals Flaws found in: Introduction 66.7% Methods 85.7% Results 66.7% Discussion 71.% Experimental design
  24. 24. Manuscript structure Participants Age and gender Enrollment Inclusion/exclusion criteria Animals, cells Materials Species/cell type Age, gender, weight Living/incubation conditions Where purchased [city, state (if US), country] How much was used Methods – What/who was used
  25. 25. Manuscript structure Previously used methods • Cite previous publications • XXXX was done as previously described23. Briefly… • Give enough detail to be reproducible • Validation for new technique Order • General methods first • Specific techniques in order of appearance New methods Always state sample number and controls Methods – How it was done
  26. 26. Manuscript structure Computer programs • Where obtained • Which version • Specific parameters • Choose right test! • P-value for significance • Consult with a statistician Quantification methods • Explain how the data was quantified • Rationale Statistical analyses Methods – How it was analyzed
  27. 27. Manuscript structure 1. Initial observation 2. Characterization 3. Application Logical presentation Example: 1. New gene expressed in the heart 2. Regulation of gene expression, when it is expressed, function of the produced protein 3. Role of the gene in heart development Results
  28. 28. Manuscript structure 1. Initial observation 2. Characterization 3. Application Each subsection corresponds to one figure What you found, not what it means Logical presentation Subsections Factual description Results
  29. 29. Manuscript structure Display items Present large amount of data quickly and efficiently Keep it simple: use separate panels if necessary Must be able to stand alone: clear labels and figure legends Usually the first thing readers will look at Figures, graphs & tables
  30. 30. Manuscript structure Figures Clear figure legend Kindlin-2 knockdown and focal adhesion localization. Confocal immunofluorescent microscopy with anti-β1 integrin and anti-paxillin on C2C12 cells transfected with RNAi and then changed to differentiation media for 2 days. Control cells show linear staining consistent with localization to costameres (arrows), as well as punctate focal contact staining (arrowheads). Focal contact proteins in the kindlin-2 RNAi cells fail to form linear structures and instead are concentrated in unusual appearing puncta (*). (Scale bar = 20 μM). Dowling et al. (2008) BMC Cell Biol 9:36. Clear indicators Title of the experiment Brief methodology Key findings
  31. 31. Manuscript structure Discussion Summary of findings Relevance of findings Implications for the field Similarities/differences Unexpected results Limitations
  32. 32. Manuscript structure Beginning should state the major conclusion of the study Re-introduce the topic Re-introduce the problem State major conclusion to answer the problem Summarize key data to support conclusion Writing the beginning of your Discussion
  33. 33. Manuscript structure Current management practices caused a large quantity of nutrient inputs on both sites. Two recent one-year studies, one in the same study area and the other in Hanoi, Vietnam, showed similar nutrient balances for N, P, and K. However, it is hard to show main control factors on element balances based on one-year study because of short-term observation. This paper shows that positive net N and P balances in conjunction with negative net K balances on these plots are most likely because of the irregularity of organic manure application… Beginning should re-state problem and your conclusion that answers that problem Wang et al. Nutr Cycl Agroecosyst. 2008; 81: 203−218. Problem Answer Writing the beginning of your Discussion
  34. 34. Manuscript structure End should state the major conclusion of the study Re-state your major conclusion Describe the key implications Recommend future research Writing the end of your Discussion
  35. 35. Manuscript structure The Spanish version of AIDA showed good psychometric properties in Mexico and can be used to assess the construct “pathology-related identity integration vs. diffusion” with reliability, validity, and content equivalence in comparison with the original AIDA questionnaire. This finding supports the cross-cultural generalizability of the underlying concept and confirms the importance of culture-specific test adaption in addition to literal translation of the questionnaire. Nevertheless, some items should be improved. Therefore, the test version of “AIDA Spanish – Mexico” should be further adapted and should be tested in a more heterogeneous population. Conclusion Implications Future directions Why your work is important to your readers Kassin et al. Child Adolesc Psychiatry Ment Health. 2013; 7: 25. Writing the end of your Discussion
  36. 36. Manuscript structure Linking your ideas in your manuscript General background Objectives Methodology Results and figures Summary of findings Implications for the field Relevance of findings Problems in the field Logically link your ideas throughout your manuscript Current state of the field Introduction Methods Results Discussion
  37. 37. Manuscript structure New ways to treat or prevent lung cancer are therefore needed. This study explored the hypothesis that inhibition of TNKS…would inhibit lung cancer growth… Pharmacological or genetic inhibition of TNKS1 and TNKS2…reduces lung cancer proliferation... Problem Objectives Conclusion Discussion Introduction Busch et al. BMC Cancer. 2012;13:211. Linking your ideas in your manuscript
  38. 38. Manuscript structure Writing effective conclusions Your conclusion is a summary of your findings Your conclusion should be the answer to your research problem that is supported by your findings Emphasizes how your study will help advance the field
  39. 39. Titles and abstracts Section 4
  40. 40. Titles & abstracts Important points  Summarize key finding  Contains keywords  Less than 20 words Avoid Effective titles Your title should be a concise summary of your most important finding Questions Describing methods Abbreviations “New” or “novel”
  41. 41. Titles & abstracts Abstract First impression of your paper Importance of your results Validity of your conclusions Relevance of your aims Judge your writing style Probably only part that will be read
  42. 42. Titles & abstracts Sections of an abstract Aims Background Methods Results Conclusion Why the study was done Your hypothesis Techniques Most important findings Conclusion/implications Concise summary of your research
  43. 43. Titles & abstracts Abstract Induced penetration resistance is triggered by failed penetration attempts of nonpathogenic fungi. The resistance mechanism is an important nonhost reaction in plants that can block the invasion of filamentous pathogens such as fungi and oomycetes. However, it remains unclear whether the mechanical stimuli accompanying fungal penetration play a role in induced penetration resistance, whereas the perforation of the cell wall may provide significant stimuli to plant cells. Here, we used microneedles or biolistic bombardment to mimic fungal penetration pegs and a micromanipulation transfer technique of the bio-probe, a germling of Blumeria graminis hordei, to the wounded cells to demonstrate that microwounds derived from fungal penetration attempts may trigger induced penetration resistance in plant cells. When preinoculated with the nonpathogenic fungi Erysiphe pisi and Colletotrichum orbiculare, which were unable to penetrate a barley cell, the penetration of a bio-probe that was transferred by micromanipulation onto the same cell was completely blocked…Treatment with the actin polymerization inhibitor cytochalasin A or expression of the actin depolymerizing protein HvPro1 caused complete ablation of the induced penetration resistance triggered by either failed fungal penetration or artificial microwounds. These results strongly suggest that microwounding may trigger actin-dependent induced penetration resistance. Manipulation of induced penetration resistance may be a promising target to improve basic disease resistance in plants. Kobayashi and Kobayashi. Planta 2013; 237: 1187−1198.
  44. 44. Titles & abstracts Abstract Induced penetration resistance is triggered by failed penetration attempts of nonpathogenic fungi. The resistance mechanism is an important nonhost reaction in plants that can block the invasion of filamentous pathogens such as fungi and oomycetes. However, it remains unclear whether the mechanical stimuli accompanying fungal penetration play a role in induced penetration resistance, whereas the perforation of the cell wall may provide significant stimuli to plant cells. Here, we used microneedles or biolistic bombardment to mimic fungal penetration pegs and a micromanipulation transfer technique of the bio-probe, a germling of Blumeria graminis hordei, to the wounded cells to demonstrate that microwounds derived from fungal penetration attempts may trigger induced penetration resistance in plant cells. When preinoculated with the nonpathogenic fungi Erysiphe pisi and Colletotrichum orbiculare, which were unable to penetrate a barley cell, the penetration of a bio-probe that was transferred by micromanipulation onto the same cell was completely blocked…Treatment with the actin polymerization inhibitor cytochalasin A or expression of the actin depolymerizing protein HvPro1 caused complete ablation of the induced penetration resistance triggered by either failed fungal penetration or artificial microwounds. These results strongly suggest that microwounding may trigger actin-dependent induced penetration resistance. Manipulation of induced penetration resistance may be a promising target to improve basic disease resistance in plants. Kobayashi and Kobayashi. Planta 2013; 237: 1187−1198.
  45. 45. Titles & abstracts Abstract Induced penetration resistance is triggered by failed penetration attempts of nonpathogenic fungi. The resistance mechanism is an important nonhost reaction in plants that can block the invasion of filamentous pathogens such as fungi and oomycetes. However, it remains unclear whether the mechanical stimuli accompanying fungal penetration play a role in induced penetration resistance, whereas the perforation of the cell wall may provide significant stimuli to plant cells. Here, we used microneedles or biolistic bombardment to mimic fungal penetration pegs and a micromanipulation transfer technique of the bio-probe, a germling of Blumeria graminis hordei, to the wounded cells to demonstrate that microwounds derived from fungal penetration attempts may trigger induced penetration resistance in plant cells. When preinoculated with the nonpathogenic fungi Erysiphe pisi and Colletotrichum orbiculare, which were unable to penetrate a barley cell, the penetration of a bio-probe that was transferred by micromanipulation onto the same cell was completely blocked…Treatment with the actin polymerization inhibitor cytochalasin A or expression of the actin depolymerizing protein HvPro1 caused complete ablation of the induced penetration resistance triggered by either failed fungal penetration or artificial microwounds. These results strongly suggest that microwounding may trigger actin-dependent induced penetration resistance. Manipulation of induced penetration resistance may be a promising target to improve basic disease resistance in plants. Kobayashi and Kobayashi. Planta 2013; 237: 1187−1198.
  46. 46. Titles & abstracts Abstract Induced penetration resistance is triggered by failed penetration attempts of nonpathogenic fungi. The resistance mechanism is an important nonhost reaction in plants that can block the invasion of filamentous pathogens such as fungi and oomycetes. However, it remains unclear whether the mechanical stimuli accompanying fungal penetration play a role in induced penetration resistance, whereas the perforation of the cell wall may provide significant stimuli to plant cells. Here, we used microneedles or biolistic bombardment to mimic fungal penetration pegs and a micromanipulation transfer technique of the bio-probe, a germling of Blumeria graminis hordei, to the wounded cells to demonstrate that microwounds derived from fungal penetration attempts may trigger induced penetration resistance in plant cells. When preinoculated with the nonpathogenic fungi Erysiphe pisi and Colletotrichum orbiculare, which were unable to penetrate a barley cell, the penetration of a bio-probe that was transferred by micromanipulation onto the same cell was completely blocked…Treatment with the actin polymerization inhibitor cytochalasin A or expression of the actin depolymerizing protein HvPro1 caused complete ablation of the induced penetration resistance triggered by either failed fungal penetration or artificial microwounds. These results strongly suggest that microwounding may trigger actin-dependent induced penetration resistance. Manipulation of induced penetration resistance may be a promising target to improve basic disease resistance in plants. Kobayashi and Kobayashi. Planta 2013; 237: 1187−1198. Methods Background Results Conclusions
  47. 47. Activities
  48. 48. Manuscript structure exercise Based on the following problem identified in the field, chose which aims are most appropriate. Problem: Currently it is not clear which weight management program is most efficient to prevent weight gain after smoking cessation in men. A) In this study, we evaluated the effect of working hours on the efficacy of three popular weight management programs for the prevention of weight gain in men after smoking cessation. Unrelated variable
  49. 49. Manuscript structure exercise Based on the following problem identified in the field, chose which aims are most appropriate. Problem: Currently it is not clear which weight management program is most efficient to prevent weight gain after smoking cessation in men. B) In this study, we evaluated the efficacy of three popular weight management programs implemented in a working environment for the prevention of weight gain in men after smoking cessation. Unrelated variable
  50. 50. Manuscript structure exercise Based on the following problem identified in the field, chose which aims are most appropriate. Problem: Currently it is not clear which weight management program is most efficient to prevent weight gain after smoking cessation in men. C) In this study, we evaluated the efficacy of three popular weight management programs for the prevention of weight gain in men after smoking cessation. Directly addresses the identified problem
  51. 51. Manuscript structure exercise Match the aims from an Introduction with the most appropriate major conclusion (to be used in a Discussion). Aims: To date, few studies have investigated the influence of literacy on economic growth. In this study, we aimed to evaluate how literacy rates affected the economic growth of various countries from 2000 to 2010. A) Our results demonstrate the need to improve education to promote literacy in developing countries. Implications
  52. 52. Manuscript structure exercise Match the aims from an Introduction with the most appropriate major conclusion (to be used in a Discussion). Aims: To date, few studies have investigated the influence of literacy on economic growth. In this study, we aimed to evaluate how literacy rates affected the economic growth of various countries from 2000 to 2010. B) This study showed that increased literacy rates are positively correlated with economic growth. Conclusion answers the problem
  53. 53. Manuscript structure exercise Match the aims from an Introduction with the most appropriate major conclusion (to be used in a Discussion). Aims: To date, few studies have investigated the influence of literacy on economic growth. In this study, we aimed to evaluate how literacy rates affected the economic growth of various countries from 2000 to 2010. C) In this study, we showed that economically developed countries spend more money on education, leading to improved literacy rates. Key finding
  54. 54. Manuscript structure exercise This study showed that increased literacy rates are positively correlated with economic growth. In this study, we showed that economically developed countries spend more money on education, leading to improved literacy rates. Our results demonstrate the need to improve education to promote literacy in developing countries. Key findings Conclusion Implications Presentation of ideas in the Discussion
  55. 55. Manuscript structure exercise Which is the best title, and why? A) Characterizing the fungal infection of wheat in high altitude environments B) High altitude reduces fungal infection of wheat C) Does high altitude affect the fungal infection of wheat? D) Low oxygen and cold temperature in high altitude environments affects the growth rate of a variety of fungi and reduces the fungal infection of wheat Summary of key finding Don’t use questions Describes methodology Too long (25 words)
  56. 56. Manuscript structure exercise A) The Introduction of your manuscript does not depend on the type of journal. B) Because most readers do not read the Methods section, it is not a very important part of the manuscript. C) Figure legends should provide enough information for the reader to understand the figure without having to refer to the main text. F True or false? F T
  57. 57. Manuscript structure exercise D) You should not emphasize the limitations of your study in you manuscript because it makes your findings look less important. E) You should write you conclusion to be an answer to the problem you identified. F) Because you want people to download and read your article, you should not give too much information (e.g., implications) in the abstract. F True or false? T F
  58. 58. Thank you! Any questions? Follow us on Twitter @JournalAdvisor Like us on Facebook facebook.com/EdanzEditing Download and further reading edanzediting.co.jp/kyushu_140710 Jeffrey Robens: jrobens@edanzgroup.com Andrew Jackson: ajackson@edanzgroup.com

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