20140826 Edanz Kyushu Session 2

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20140826 Edanz Kyushu Session 2

  1. 1. Kyushu University Department of Agriculture Seminar Series – Session 2 Dr Jeffrey Robens 26 August 2014
  2. 2. Seminar series Session 1 Session 2 Effective writing Manuscript structure Journal selection Cover letters Methodology Peer review
  3. 3. Section 1 Figures and Results
  4. 4. Figures & Results Present large amount of data quickly and efficiently Figures, graphs Keep it simple: use separate panels if necessary Usually the first thing readers will look at Must be able to stand alone: clear labels and figure legends & tables
  5. 5. Figures & Results 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
  6. 6. Figures & Results Data aligned and formatted Table formatting Muñoz et al. New Engl J Med. 2003;348:518−527. Clear and concise table caption Abbreviations defined
  7. 7. Figures & Results Is this a good table? Alignment and formatting problems Alignment of text Alignment of parentheses Alignment of decimals Data similarity Lines Tumor size (mm3) before treatment Mean (±SD) Tumor size (mm3) after treatment Mean (±SD) % decrease Treatment time Group 1 423.2 (6.23) 232.8 (3.18) 44.99 4 months Group 2 286.43 (4.8) 157.32 (2.29) 45.08 14 weeks Group 3 342.7 (6.88) 218.4 (5.2) 36.27 3.5 months Group 4 404 (3) 302 (4.21) 25.247 90 days
  8. 8. Figures & Results Making a good table Tumor size (mm3) before treatment Mean (±SD) Tumor size (mm3) before treatment Mean (±SD) Tumor size (mm3) after treatment Mean (±SD) Tumor size (mm3) after treatment Mean (±SD) % decrease % decrease Treatment Treatment time (weeks) Group 1 423.20 (6.23) 232.80 (3.18) 44.99 16 Group 2 286.43 (4.80) 157.32 (2.29) 45.08 14 Group 3 342.70 (6.88) 218.40 (5.20) 36.27 14 Group 4 404.00 (3.00) 302.00 (4.21) 25.25 12 time Group 1 423.2 (6.23) 232.8 (3.18) 44.99 4 months Group 2 286.43 (4.8) 157.32 (2.29) 45.08 14 weeks Group 3 342.7 (6.88) 218.4 (5.2) 36.27 3.5 months Group 4 404 (3) 302 (4.21) 25.247 90 days
  9. 9. Figures & Results Graphs 35 30 25 20 15 10 5 0 0 1 h 2 h 3 h 4 h 5 h 6 h Drug A Drug B ng/ml 35 30 25 20 15 10 5 0 0 1 h 2 h 3 h 4 h 5 h 6 h  Use high contrasting colors  Clearly label axes  Clear legends
  10. 10. Figures & Results Graphs Drug B Drug A 30 25 15 10 5 0 20 0 1 h 2 h 3 h 4 h 5 h 6 h NEVER use 3-D graphs for 2-D data
  11. 11. Figures & Results Results 1. Novel 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
  12. 12. Figures & Results Results 1. Novel observation 2. Characterization 3. Application Each subsection corresponds to one figure What you found, not what it means Logical presentation Subsections Factual description
  13. 13. Figures & Results Factual description Belongs in the Discussion Drug A is more effective in treating liver cancer as we observed a 32.7% decrease in tumor size compared with only a 22.1% decrease after Drug B treatment. The efficacy of Drug A was significantly higher than that for Drug B, with decreased tumor size 32.7% or 22.1%, respectively. Exception is when the Results and Discussion sections are combined
  14. 14. Figures & Results Group repetitive results Drug A reduced tumor volume by 32.7%, increased blood pressure by 12.3%, and decreased the patient’s weight by 7.3 kg. Drug B reduced tumor volume by 22.3%, increased blood pressure by 15.6%, and decreased the patient’s weight by 2.4 kg. Drug C reduced tumor volume by 38.1%, increased blood pressure by 6.9%, and decreased the patient’s weight by 9.2 kg.
  15. 15. Figures & Results Group repetitive results Patients treated with Drug C showed the greatest reduction in tumor volume (28.1%) compared with those treated with Drug A (32.7%) or Drug B (22.3%). Drug C also had the lowest increase in blood pressure (6.9%) compared with that seen after treatment with Drug A (12.3%) or Drug B (15.65). However, patients treated with Drug C had the highest weight gain among the three groups (Drug A, 7.3 kg; Drug B, 2.4 kg; Drug C, 9.2 kg).
  16. 16. Results Activities Please see accompanying handouts
  17. 17. Results activity In the following Results section, identify any common errors you can find.
  18. 18. Results activity Results Food consumption The first behavioral abnormality we noticed was a significant increase in food consumption immediately after the main earthquake (Figure 2A). Measuring the food consumption of mice after earthquakes and other natural disasters has long been ignored in the literature. Daily food consumption per mouse was measured by subtracting the weight of the food at the end of the eating period with the weight at the beginning of the eating period. The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). This demonstrates that earthquakes can dramatically affect the food consumption in laboratory animals, likely caused by increased stress hormone levels. Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.
  19. 19. Results activity Results More descriptive heading Food consumption The first behavioral abnormality we noticed was a significant increase in food consumption immediately after the main earthquake (Figure 2A). Measuring the food consumption of mice after earthquakes and other natural disasters has long been ignored in the literature. Daily food consumption per mouse was measured by subtracting the weight of the food at the end of the eating period with the weight at the beginning of the eating period. The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). This demonstrates that earthquakes can dramatically affect the food consumption in laboratory animals, likely caused by increased stress hormone levels. Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.
  20. 20. Results activity Results Increased food consumption The first behavioral abnormality we noticed was a significant increase in food consumption immediately after the main earthquake (Figure 2A). Measuring the food consumption of mice after earthquakes and other natural disasters has long been ignored in the literature. Daily food consumption per mouse was measured by subtracting the weight of the food at the end of the eating period with the weight at the beginning of the eating period. The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). This demonstrates that earthquakes can dramatically affect the food consumption in laboratory animals, likely caused by increased stress hormone levels. Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.
  21. 21. Results activity Results Increased food consumption “significant increase” The first behavioral abnormality we noticed was a significant increase in food consumption immediately after the main earthquake (Figure 2A). Measuring the food consumption of mice after earthquakes and other natural disasters has long been ignored in the literature. Daily food consumption per mouse was measured by subtracting the weight of the food at the end of the eating period with the weight at the beginning of the eating period. The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). This demonstrates that earthquakes can dramatically affect the food consumption in laboratory animals, likely caused by increased stress hormone levels. Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.
  22. 22. Results activity Results Increased food consumption The first behavioral abnormality we noticed was a marked increase in food consumption immediately after the main earthquake (Figure 2A). Measuring the food consumption of mice after earthquakes and other natural disasters has long been ignored in the literature. Daily food consumption per mouse was measured by subtracting the weight of the food at the end of the eating period with the weight at the beginning of the eating period. The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). This demonstrates that earthquakes can dramatically affect the food consumption in laboratory animals, likely caused by increased stress hormone levels. Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.
  23. 23. Results activity Results Increased food consumption The first behavioral abnormality we noticed was a marked increase in food consumption immediately after the main Belongs earthquake in Introduction (Figure 2A). Measuring the food consumption of mice after earthquakes and other natural disasters has long been ignored in the literature. Daily food consumption per mouse was measured by subtracting the weight of the food at the end of the eating period with the weight at the beginning of the eating period. The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). This demonstrates that earthquakes can dramatically affect the food consumption in laboratory animals, likely caused by increased stress hormone levels. Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.
  24. 24. Results activity Results Increased food consumption The first behavioral abnormality we noticed was a marked increase in food consumption immediately after the main earthquake (Figure 2A). Daily food consumption per mouse was measured by subtracting the weight of the food at the end of the eating period with the weight at the beginning of the eating period. The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). This demonstrates that earthquakes can dramatically affect the food consumption in laboratory animals, likely caused by increased stress hormone levels. Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.
  25. 25. Results activity Results Increased food consumption The first behavioral abnormality we noticed was a marked increase in food consumption immediately after the main Belongs earthquake in Methods (Figure 2A). Daily food consumption per mouse was measured by subtracting the weight of the food at the end of the eating period with the weight at the beginning of the eating period. The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). This demonstrates that earthquakes can dramatically affect the food consumption in laboratory animals, likely caused by increased stress hormone levels. Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.
  26. 26. Results activity Results Increased food consumption The first behavioral abnormality we noticed was a marked increase in food consumption immediately after the main earthquake (Figure 2A). The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). This demonstrates that earthquakes can dramatically affect the food consumption in laboratory animals, likely caused by increased stress hormone levels. Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.
  27. 27. Results activity Results Increased food consumption The first behavioral abnormality we noticed was a marked increase in food No problems consumption immediately after the main earthquake (Figure 2A). The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). This demonstrates that earthquakes can dramatically affect the food consumption in laboratory animals, likely caused by increased stress hormone levels. Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.
  28. 28. Results activity Results Increased food consumption The first behavioral abnormality we noticed was a marked increase in food consumption immediately after the main earthquake (Figure 2A). The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). This demonstrates that earthquakes can dramatically affect the food consumption in laboratory animals, likely caused by increased stress hormone levels. Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.
  29. 29. Results activity Results Increased food consumption The first behavioral abnormality we noticed was a marked increase in food consumption immediately after the main earthquake (Figure 2A). The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption Belongs in Discussion was significant after the earthquake (t (5) = 18.5, p<0.001). This demonstrates that earthquakes can dramatically affect the food consumption in laboratory animals, likely caused by increased stress hormone levels. Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.
  30. 30. Results activity Results Increased food consumption The first behavioral abnormality we noticed was a marked increase in food consumption immediately after the main earthquake (Figure 2A). The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.
  31. 31. Results activity Results Increased food consumption The first behavioral abnormality we noticed was a marked increase in food consumption immediately after the main earthquake (Figure 2A). The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake Should (t (5) show = 18.5, the p<data 0.001). Even though food consumption continued for over one month, the body weight of earthquake-experienced mice increased only slightly during that period.
  32. 32. Results activity Results Increased food consumption The first behavioral abnormality we noticed was a marked increase in food consumption immediately after the main earthquake (Figure 2A). The day before the earthquake, food consumption was 1.7±0.13 (mean±SD) g. Three days after the main seismic event, mean food consumption increased to 2.5±0.16 g (Figure 2A). Analysis using a paired t-test revealed that the increase in food consumption was significant after the earthquake (t (5) = 18.5, p<0.001). Even though food consumption continued for over one month with an average daily consumption of 2.3±0.12 g, the body weight of earthquake-experienced mice increased only slightly during that period (186.3±1.2 g on day 1 and 188.2±1.6 g on day 30).
  33. 33. Section 2 Introduction and Discussion
  34. 34. Introduction & Discussion Introduction General introduction Current state of the field Problem in the field Aims Specific aims
  35. 35. Introduction & Discussion Target your journal Major nutrient balances in small-scale vegetable farming systems in peri-urban areas in China Nutrient Cycling in Agroecosystems Aims and Scope Nutrient Cycling in Agroecosystems (formerly Fertilizer Research) considers manuscripts dealing with aspects of carbon and nutrient cycling as well as management, their effect in ecological, agronomic, environmental and economic Key terms. point Contributions may deal with subjects in agronomic, agro-forestry and fallow systems or system components such as plants and the fertility, chemistry or microbiology of soils, as well as with system inputs and losses.
  36. 36. Introduction & Discussion Beginning should demonstrate relevance/interest Cities in China and other developing countries continue to expand as people migrate from rural to urban areas, and agricultural land in peri-urban areas decreases rapidly as a result. Farmers are challenged to intensify production per unit area with decreasing amounts of land to satisfy food production demands and increase revenue. This intensive production will inevitably cause serious nutrient imbalances, exacerbated by the limited nutrient-retention capacity of soils in peri-urban areas. Moreover, inefficient nutrient management and concomitant nutrient enrichment of agro-ecosystems have contributed to agriculture’s impact on aquatic systems. Specifically, soils in vegetable lands are often characterized by continuous and large quantities of organic and inorganic fertilizer application, which inevitably lead to a serious pollution threat to the water environment. Wang et al. Nutr Cycl Agroecosyst. 2008; 81: 203−218. Interest Writing the Introduction
  37. 37. Introduction & Discussion Writing the Introduction Beginning should demonstrate relevance/interest Cities in China and other developing countries continue to expand as people migrate from rural to urban areas, and agricultural land in peri-urban areas decreases rapidly as a result. Farmers are challenged to intensify production per unit area with decreasing amounts of land to satisfy food production demands and increase revenue. This intensive production will inevitably cause serious nutrient imbalances, exacerbated by the limited nutrient-retention capacity of soils in peri-urban areas. Moreover, inefficient nutrient management and concomitant nutrient enrichment of agro-ecosystems have contributed to agriculture’s impact on aquatic systems. Specifically, soils in vegetable lands are often characterized by continuous and large quantities of organic and inorganic fertilizer application, which inevitably lead to a serious pollution threat to the water environment. Wang et al. Nutr Cycl Agroecosyst. 2008; 81: 203−218. Interest Keywords from the Aims and Scope
  38. 38. Introduction & Discussion Writing the Introduction Clearly state an interesting problem in the field Therefore, the large net balances [of N, P, and K] indicate a substantial risk of long-term effects on soil fertility, because of soil accumulation and losses to ground and surface waters. However, information on major nutrient balances driven by underlying socioeconomic factors is lacking in peri-urban areas. Wang et al. Nutr Cycl Agroecosyst. 2008; 81: 203−218.
  39. 39. Introduction & Discussion Writing the Introduction Clearly state an interesting problem in the field Therefore, the large net balances [of N, P, and K] indicate a substantial risk of long-term effects on soil fertility, because of soil accumulation and losses to ground and surface waters. However, information on major nutrient balances driven by underlying socioeconomic factors is lacking in peri-urban areas. Keywords from the Aims and Scope Wang et al. Nutr Cycl Agroecosyst. 2008; 81: 203−218.
  40. 40. Introduction & Discussion Writing the Introduction Your aims should directly address this problem However, information on major nutrient balances driven by underlying socioeconomic factors is lacking in peri-urban areas. 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. Wang et al. Nutr Cycl Agroecosyst. 2008; 81: 203−218.
  41. 41. Introduction & Discussion Flow of information Lung cancer is the leading cause of cancer mortality for men and women. Despite smoking prevention and cessation programs and advances in early detection, the 5-year survival rate for lung cancer is only 16% with current therapies. Although lung cancer incidence rates have recently declined in the United States, more lung cancer is now diagnosed when considered together in former- and never-smokers than in current smokers. Thus, even if all of the national anti-smoking campaign goals are met, lung cancer will remain a major public health problem for decades. New ways to treat or prevent lung cancer are therefore needed. One potential therapeutic target for lung cancer is the Wnt signaling pathway. The canonical Wnt signaling pathway in mammals consists of a family of secreted lipid-modified Wnt protein ligands that bind to a family of 7-pass transmembrane Frizzled (Fzd) receptors, as reviewed… Busch et al. BMC Cancer. 2012; 13: 211. Topic sentence Stress sentence Topic sentence Support
  42. 42. Introduction & Discussion Discussion Summary of findings Relevance of findings Similarities/differences Unexpected results Limitations Implications for the field
  43. 43. Introduction & Discussion Discussion 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
  44. 44. Introduction & Discussion Writing the Discussion Beginning should re-state problem and your conclusion that answers that problem 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… Wang et al. Nutr Cycl Agroecosyst. 2008; 81: 203−218. Problem Answer Keywords from the Aims and Scope
  45. 45. Introduction & Discussion Writing the Discussion End should state the major conclusion of the study Re-state your major conclusion Describe the key implications Recommend future research
  46. 46. Introduction & Discussion Writing the Discussion End should summarize your conclusion and clearly state implications In summary, we identified a P. infestans RXLR-WY–type effector, PexRD2, which interacts with MAPKKKε and perturbs plant immunity associated signaling pathways dependent on this kinase. Either overexpression of PexRD2 or knockdown of MAPKKKε supports enhanced pathogen growth and suppression of MAPKKKε-triggered or - dependent cell death readouts in N. benthamiana. This study represents a step toward understanding how oomycete RXLR-type effectors directly interact with MAPK cascades, which are well established as key regulators of plant immunity. The next challenge is to better understand the role of PexRD2 and PexRD2-like effectors, and their targets, in the progression of disease in important host crop plants, such as tomato and potato. The ultimate aim of this would be to manipulate these interactions to tip the balance in the coevolutionary arms race between pathogen and host in favor of the plant. King et al. Plant Cell. 2014; 26: 1345−1359.
  47. 47. Introduction & Discussion Writing the Discussion End should summarize your conclusion and clearly state implications In summary, we identified a P. infestans RXLR-WY–type effector, PexRD2, which interacts with MAPKKKε and perturbs plant immunity associated signaling pathways dependent on this kinase. Either overexpression of PexRD2 or knockdown of MAPKKKε supports enhanced pathogen growth and suppression of MAPKKKε-triggered or - dependent cell death readouts in N. benthamiana. This study represents a step toward understanding how oomycete RXLR-type effectors directly interact with MAPK cascades, which are well established as key regulators of plant immunity. The next challenge is to better understand the role of PexRD2 and PexRD2-like effectors, and their targets, in the progression of disease in important host crop plants, such as tomato and potato. The ultimate aim of this would be to manipulate these interactions to tip the balance in the coevolutionary arms race between pathogen and host in favor of the plant. King et al. Plant Cell. 2014; 26: 1345−1359. Conclusions Key findings Implications Future directions Field advancement
  48. 48. Introduction & Discussion Linking your ideas in your manuscript General background Current state of the field Problems in the field Objectives Methodology Results and figures Summary of findings Relevance of findings Implications for the field Introduction Methods Results Discussion Logically link your ideas throughout your manuscript
  49. 49. Introduction & Discussion Linking your ideas in your manuscript Introduction Contamination of the soil by heavy metals is a serious environmental problem... Little is known how heavy metals affect membrane lipid metabolism… Our aim was to assess how Cd stress affects the composition Our results showing changes in total fatty acids, profiles of individual polar lipids, and unsaturation levels suggest that Cd stress might alter membrane structure and function. Background Problem Conclusion Discussion Elloumi et al. Botanical Studies. 2014; 55: 61. and biosynthesis of lipids and fatty acids…… Objective
  50. 50. Introduction & Discussion 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
  51. 51. Introduction activity 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. 1. In this study, we evaluated the effect of working hours on the efficacy of three popular weight management programs S for the prevention of weight gain in men after smoking cessation. 2. 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. 3. In this study, we evaluated the efficacy of three popular weight management programs for the prevention of weight gain in men after smoking cessation.
  52. 52. Introduction activity Based on the following problem identified in the field, chose which aims are most appropriate. Problem: Current climate change is mainly driven by historic emissions. The countries responsible for the majority of historic emissions are not necessarily the same as those responsible for the dominant share of current emissions. 1. We report on historical trends in climate change to better understand future S changes. 2. This paper provides an original quantitative analysis of historic emissions by tracing sources of industrial CO2 and methane, to compare with current emissions. 3. In this paper, we identify those countries responsible for the dominant share of current emissions.
  53. 53. Discussion activity 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 different tissue pressures on tumor growth. In this study, we aimed to evaluate how varying the pressure within brain, liver, and lung tissues affected the growth of transplanted tumors. A) Our results demonstrate the need to monitor pressures within different tissues when determining effective treatments. Implications
  54. 54. Discussion activity 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 different tissue pressures on tumor growth. In this study, we aimed to evaluate how varying the pressure within brain, liver, and lung tissues affected the growth of transplanted tumors. B) This study has shown that the increasing the pressure within tissues significantly reduces tumor growth. Conclusion answers the problem
  55. 55. Discussion activity 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 different tissue pressures on tumor growth. In this study, we aimed to evaluate how varying the pressure within brain, liver, and lung tissues affected the growth of transplanted tumors. C) In this study, we have shown that high pressure environments reduce the vascularization of growing tumors. Key finding
  56. 56. Discussion activity Presentation of ideas in the Discussion This study has shown that the increasing the pressure within tissues significantly reduces tumor growth. Conclusion In this study, we have shown that high pressure environments reduce the vascularization of growing tumors. Key findings Our results demonstrate the need to monitor pressures within different tissues when determining effective treatments. Implications
  57. 57. Section 2 Titles and abstracts
  58. 58. Titles & Abstracts Effective titles Important points  Summarize key finding  Contains keywords  Less than 20 words Avoid Questions Describing methods Abbreviations “New” or “novel” Your title should be a concise summary of your most important finding
  59. 59. Titles & Abstracts Abstracts Importance of your results First impression of your paper Validity of your conclusions Relevance of your aims Judge your writing style Probably only part that will be read
  60. 60. Titles & Abstracts Sections of an abstract Concise summary of your research Background Aims Methods Results Conclusion Why the study was done Your hypothesis Techniques Most important findings Conclusion & implications
  61. 61. Titles & Abstracts Writing your 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. Fungal penetration was essential to the triggering of induced penetration resistance because a penetration-peg-defective mutant of C. orbiculare completely lacked the ability to trigger resistance. The artificial microwounds significantly, but not completely, blocked the penetration of the bio-probe. 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.
  62. 62. Titles & Abstracts Writing your 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. Implications
  63. 63. Titles & Abstracts Writing your 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. Fungal penetration was essential to the triggering of induced penetration resistance because a penetration-peg-defective mutant of C. orbiculare completely lacked the ability to trigger resistance. The artificial microwounds significantly, but not completely, blocked the penetration of the bio-probe. 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.
  64. 64. Titles & Abstracts Writing your 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 Why oomycetes. this study However, needed it remains to unclear be done 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 What cells to you demonstrate did 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. Fungal penetration was essential to the triggering of induced penetration resistance because a penetration-peg-defective mutant of C. orbiculare What you completely found lacked the ability to trigger resistance. The artificial microwounds significantly, but not completely, blocked the penetration of the bio-probe. 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 How can of induced advance penetration the field resistance may be a promising target to improve basic disease resistance in plants. Kobayashi and Kobayashi. Planta 2013; 237: 1187−1198.
  65. 65. Titles & Abstracts SEO Search Engine Optimization  Identify 7–8 keywords (include synonyms)  Use 2 in your title, 5–6 in the keyword list  Use 3 keywords 3–4 times in your abstract  Use keywords in headings when appropriate  Be consistent throughout your paper  Cite your previous publications when relevant • Google Scholar ranks results by citations
  66. 66. Title and Abstract Activities Please see accompanying handouts
  67. 67. Title activity Which is the best title, and why? A) Characterizing the fungal infection of wheat in high altitude environments Describes methodology B) High altitude reduces fungal infection of wheat Summary of key finding C) Does high altitude affect the fungal infection of wheat? Don’t use questions 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 Too long (25 words)
  68. 68. Abstract activity Activity : Your colleague has written an abstract and has asked you to review it for them. How would you recommend improving this abstract?
  69. 69. Abstract activity How is this related to mice? A devastating earthquake and tsunami hit Japan on March 11, 2011. In the present study, the effects of this earthquake on laboratory mice behavior were investigated. “Earthquake-experienced” mice displayed a marked increase in food consumption without gaining body weight. The food was purchased from a company based in New Zealand. The mice also displayed enhanced anxiety. Maze performance of earthquake-experienced mice showed quicker acquisition of the task compared with that of earthquake-naive mice. Stress hormone levels, which were measured three times, were elevated compared with the naive mice. This indicated that the earthquake and aftershocks were stressful for the mice.
  70. 70. Abstract activity How is this related to mice? A devastating earthquake and tsunami hit Japan on March 11, 2011. In the present study, the effects of this earthquake on laboratory mice behavior were investigated. “Earthquake-experienced” mice displayed a marked increase in food Unnecessary information consumption without gaining body weight. The food was purchased from a company based in New Zealand. The mice also displayed enhanced anxiety. Maze performance of earthquake-experienced mice showed quicker acquisition of the task compared with that of earthquake-naive mice. Stress hormone levels, which were measured three times, were elevated compared with the naive mice. This indicated that the earthquake and aftershocks were stressful for the mice.
  71. 71. Abstract activity How is this related to mice? A devastating earthquake and tsunami hit Japan on March 11, 2011. In the present study, the effects of this earthquake on laboratory mice behavior were investigated. “Earthquake-experienced” mice displayed a marked increase in food Unnecessary information consumption without gaining body weight. The food was purchased from a company based in New Zealand. The mice also displayed enhanced anxiety. Maze performance of earthquake-experienced mice showed quicker acquisition of the task compared with that of earthquake-naive mice. Stress hormone levels, which were measured three times, were elevated compared with the naive mice. This indicated that the earthquake and aftershocks were stressful for the mice. How was this measured? No conclusions
  72. 72. Section 8 Cover letters
  73. 73. Coverage and Cover letters Staffing Plan Cover letter: Significance Relevance First impression for journal editors Writing style Interesting to their readers? Why your work is important!
  74. 74. Coverage and Cover letters Staffing Plan Read the aims and scope Plant Molecular Biology Plant Molecular Biology is an international journal dedicated to rapid publication of original research articles Broad in all interest areas of plant biology. The Editorial Board welcomes full-length manuscripts that address important biological problems of broad interest, including research in comparative genomics, functional genomics, proteomics, bioinformatics, computational biology, biochemical and regulatory networks, and biotechnology. Because space in the journal is limited, however, preference is given to publication of results that provide significant new insights into biological problems and that advance the understanding of structure, function, mechanisms, or regulation. Biological problems
  75. 75. Coverage and Staffing Plan Cover letters Building your cover letter Dr Wilhelm Gruissem Editor-in-Chief Plant Molecular Biology 2 September 2013 Dear Dr Gruissem, Journal editor’s name • Have you read the aims and scope? • Have you read the author guidelines? Manuscript title Please find enclosed our manuscript entitled “Identification of the histone acetyltransferase HAF2 as a factor involved in natural variation for seed dormancy in Arabidopsis thaliana”, which we would like to submit for publication as a Research Article in Plant Molecular Biology. Article type
  76. 76. Coverage and Staffing Plan Cover letters Building your cover letter Second paragraph:  Current state of the field  Problem researchers are facing Seed dormancy is an important life-history strategy that allows plants to select favorable conditions for germination, thereby affecting long-term survival. Dormancy can be released by specific environmental factors, such as cold or dry-storage (after-ripening). However, the genetic factors that regulate this process have not been clearly elucidated. The model plant Arabidopsis has substantial natural variation in seed dormancy, and identifying genes associated with this trait is of broad interest to geneticists, ecologists, and agricultural researchers. Introduction Problem Relevance
  77. 77. Coverage and Cover letters Staffing Plan Building your cover letter Third paragraph:  Briefly describe your methodology  Summarize your key findings We combined genome-wide association (GWA) mapping with transcriptome analyses to screen candidate single nucleotide polymorphisms correlated with variation in seed dormancy in 108 accessions of Arabidopsis. The most likely candidate was a plant-specific histone acetyltransferase gene, HAF2. HAF2 expression was down-regulated by cold and after-ripening, which break seed dormancy, and was up-regulated in accessions with high levels of dormancy. When the HAF2 gene from a non-dormant accession was inserted into a dormant accession… Methods Key results
  78. 78. Coverage and Staffing Plan Cover letters Building your cover letter Fourth paragraph:  Why interesting to the journal’s readership These findings are significant in elucidating the genetic mechanisms underlying a fundamental life-history trait of plants and will be of interest to Plant Molecular Biology readers, especially those focused on Arabidopsis seed dormancy. Furthermore, our integrated approach combining GWA mapping and transcriptomics offers a promising strategy to identify candidate loci in future studies. Relevance Implications
  79. 79. Coverage and Staffing Plan Cover letters Building your cover letter Last paragraph:  Disclaimers related to publication ethics  Funding  Conflicts of interest We confirm that this manuscript has not been published elsewhere and is not under consideration by another journal. All authors have approved the manuscript, including authorship and order of authorship, and agree with submission to Plant Molecular Biology. This study was funded by the Ministry of Health, Labour and Welfare. The authors have no conflicts of interest to declare. Ethics Funding Conflicts of interest
  80. 80. Coverage and Staffing Plan Cover letters Building your cover letter Other important information:  Recommended reviewers  Author’s contact information We would like to recommend the following reviewers to evaluate our manuscript: 1. Reviewer 1 and contact information 2. Reviewer 2 and contact information 3. Reviewer 3 and contact information 4. Reviewer 4 and contact information Please address all correspondence to: Reviewers Contact information
  81. 81. Coverage and Cover letters Staffing Plan Dr Wilhelm Gruissem Editor-in-Chief Plant Molecular Biology 2 September 2013 Dear Dr Gruissem, Please find enclosed our manuscript entitled “Identification of the histone acetyltransferase HAF2 as a factor involved in natural variation for seed dormancy in Arabidopsis thaliana”, which we would like to submit for publication as a Research Article in Plant Molecular Biology. Seed dormancy is an important life-history strategy that allows plants to select favorable conditions for germination, thereby affecting long-term survival. Dormancy can be released by specific environmental factors, such as cold or dry-storage (after-ripening). The model plant Arabidopsis has substantial natural variation in seed dormancy, and identifying genes associated with this trait is of interest to geneticists, ecologists, and agricultural researchers. We combined genome-wide association (GWA) mapping with transcriptome analyses to screen candidate single nucleotide polymorphisms correlated with variation in seed dormancy in 108 accessions of Arabidopsis. The most likely candidate was a plant-specific histone acetyltransferase gene, HAF2. HAF2 expression was down-regulated by cold and after-ripening, which break seed dormancy, and was up-regulated in accessions with high levels of dormancy. When the HAF2 gene from a non-dormant accession was inserted into a dormant accession, seed dormancy was increased and HAF2 expression levels reduced. Finally, we sequenced HAF2 from 78 accessions and found that mutations were enriched in the promoter region. These findings are significant in elucidating the genetic mechanisms underlying a fundamental life-history trait of plants and will be of interest to Plant Molecular Biology readers, especially those focused on Arabidopsis seed dormancy. Furthermore, our integrated approach combining GWA mapping and transcriptomics offers a promising strategy to identify candidate loci in future studies. We confirm that this manuscript has not been published elsewhere and is not under consideration by another journal. All authors have approved the manuscript, including authorship and order of authorship, and agree with submission to Plant Molecular Biology. This study was funded by the Ministry of Health, Labour and Welfare. The authors have no conflicts of interest to declare. We would like to recommend the following reviewers to evaluate our manuscript: Reviewer 1 and contact information Reviewer 2 and contact information Reviewer 3 and contact information Reviewer 4 and contact information Please address all correspondence to: We look forward to hearing from you at your earliest convenience. Yours sincerely, A good cover letter
  82. 82. Coverage and Cover letters Staffing Plan Dr Wilhelm Gruissem Editor-in-Chief Plant Molecular Biology 2 September 2013 Dear Dr Gruissem, Please find enclosed our manuscript entitled “Identification of the histone acetyltransferase HAF2 as a factor involved in natural variation for seed dormancy in Arabidopsis thaliana”, which we would like to submit for publication as a Research Article in Plant Molecular Biology. Seed dormancy is an important life-history strategy that allows plants to select favorable conditions for germination, thereby affecting long-term survival. Dormancy can be released by specific environmental factors, such as cold or dry-storage (after-ripening). The model plant Arabidopsis has substantial natural variation in seed dormancy, and identifying genes associated with this trait is of interest to geneticists, ecologists, and agricultural researchers. We combined genome-wide association (GWA) mapping with transcriptome analyses to screen candidate single nucleotide polymorphisms correlated with variation in seed dormancy in 108 accessions of Arabidopsis. The most likely candidate was a plant-specific histone acetyltransferase gene, HAF2. HAF2 expression was down-regulated by cold and after-ripening, which break seed dormancy, and was up-regulated in accessions with high levels of dormancy. When the HAF2 gene from a non-dormant accession was inserted into a dormant accession, seed dormancy was increased and HAF2 expression levels reduced. Finally, we sequenced HAF2 from 78 accessions and found that mutations were enriched in the promoter region. These findings are significant in elucidating the genetic mechanisms underlying a fundamental life-history trait of plants and will be of interest to Plant Molecular Biology readers, especially those focused on Arabidopsis seed dormancy. Furthermore, our integrated approach combining GWA mapping and transcriptomics offers a promising strategy to identify candidate loci in future studies. We confirm that this manuscript has not been published elsewhere and is not under consideration by another journal. All authors have approved the manuscript, including authorship and order of authorship, and agree with submission to Plant Molecular Biology. This study was funded by the Ministry of Health, Labour and Welfare. The authors have no conflicts of interest to declare. We would like to recommend the following reviewers to evaluate our manuscript: Reviewer 1 and contact information Reviewer 2 and contact information Reviewer 3 and contact information Reviewer 4 and contact information Please address all correspondence to: We look forward to hearing from you at your earliest convenience. Yours sincerely, A good cover letter Manuscript information Background Key findings Relevance Disclaimers Recommended reviewers
  83. 83. Cover letters Specific cover Coverage and Staffing Plan letter styles http://www.nature.com/nature/authors/submissions/subs/#a6
  84. 84. Cover letters Recommending Coverage and Staffing Plan reviewers “The system requires authors to supply the names, e-mail addresses, and affiliations of at least four recommended reviewers. “Authors will be asked to submit, with their manuscript…ii) the names and contact details (including e-mail address) of three potential qualified reviewers...
  85. 85. Coverage and Staffing Plan Cover letters PNAS http://www.pnas.org/site/authors/editorialpolicies.xhtml
  86. 86. Cover letters Why recommend Coverage and Staffing Plan reviewers? Reviewers recommended by authors are usually more favorable 1. Scharschimidt et al. J Clin Invest. 1994; 93: 1877–1880. 2. Earnshaw & Farndon. Ann R Coll Surg Engl. 2000; 82: 133–135. 3. Grimm. Science 2005; 309: 1974. 4. Wager et al. BMC Med. 2006; 4: 13. 5. Schroter et al. JAMA 2006; 295: 314–317. 6. Rivara et al. J Pediatr. 2007; 151: 202–205. 7. Bornmann & Daniel. Res Eval. 2009; 18: 262–272. 8. Bornmann & Daniel. PLoS One 2010; 5: e13345.
  87. 87. Cover letters Recommending Coverage and Staffing Plan reviewers Where to find them? From your reading/references, networking at conferences How senior? Aim for mid-level researchers Who to avoid? Collaborators (past 5 years), researchers from Kyushu University International list: 1 or 2 from Asia, 1 or 2 from Europe, and 1 or 2 from North America Choose reviewers who have published in your target journal
  88. 88. Section 5 Peer review & revisions
  89. 89. CusPteoemr erer vSieerwv ice What reviewers are looking for The science The manuscript  Relevant hypothesis  Good experimental design  Appropriate methodology  Good data analysis  Valid conclusions  Logical flow of information  Manuscript structure and formatting  Appropriate references  High readability
  90. 90. CusPteoemr erer vSieerwv ice Organize the reviewers’ comments Group similar comments together Experimental References Writing Reviewer 1: “Re-analyze the data in Figure 3 using a Mann–Whitney U test.” Reviewer 3: “Repeat the experiments in Figure 3 with additional controls.” Note: the comments of one reviewer may affect the comments of another • Mann–Whitney U test: 2 groups • Kruskal–Wallis test: >2 groups
  91. 91. CusPteoemr erer vSieerwv ice Writing response letters Read by the journal editor, not the reviewers Respond to every reviewer comment Easy to see changes Refer to line and page numbers Use a different color font Highlight the text
  92. 92. CusPteoemr erer vSieerwv ice Fernando L. Cônsoli Editor-in-Chief Neotropical Entomology 2 September 2013 Dear Dr Cônsoli, Writing response letters Address editor personally Re: Resubmission of manuscript reference No. WJS-07-5739 Manuscript ID number Thank reviewers Please find attached a revised version of our manuscript originally entitled “Population dynamics of Drosophilids in response to humidity and temperature,” which we would like to resubmit for consideration for publication in Neotropical Entomology. The reviewer’s comments were highly insightful and enabled us to greatly improve the quality of our manuscript. In the following pages are our point-by-point responses to each of the comments. Revisions in the manuscript are shown as highlighted text. In accordance with the first comment, the title has been revised and the entire manuscript has undergone substantial English editing. We hope that the revisions in the manuscript and our accompanying responses will be sufficient to make our manuscript suitable for publication in Neotropical Entomology. Highlight major changes
  93. 93. CusPteoemr erer vSieerwv ice Agreeing with reviewers Reviewer Comment: In your analysis of the data you have chosen to use a somewhat obscure fitting function (regression). In my opinion, a simple Gaussian function would have sufficed. Moreover, the results would be more instructive and easier to compare to previous results. Agreement Response: We agree with the Reviewer’s assessment of the analysis. Our tailored function, in its current form, makes it difficult to tell that this measurement constitutes a significant improvement over previously reported values. We describe our new analysis using a Gaussian fitting function in our revised Results section (Page 6, Lines 12–18). Revisions Location Why agree
  94. 94. CusPteoemr erer vSieerwv ice Disagreeing with reviewers Reviewer Comment: In your analysis of the data you have chosen to use a somewhat obscure fitting function (regression). In my opinion, a simple Gaussian function would have sufficed. Moreover, the results would be more instructive and easier to compare to previous results. Response: Although a simple Gaussian fit would facilitate comparison with the results of other studies, our tailored function allows for the analysis of the data in terms of the Smith model [Smith et al., 1998]. We have now explained the use of this function and the Smith model in Revisions our revised Discussion section (Page 12, Lines 2–6). Location Evidence
  95. 95. CusPteoemr erer vSieerwv ice “Hidden” questions Reviewer comment: The authors looked for polymorphisms in the promoter region of the gene; however, they didn't evaluate the untranslated regions. That is one of my concerns about this methodology. Rephrased question: Why didn’t the authors evaluate polymorphisms in the untranslated regions of the gene?
  96. 96. CusPteoemr erer vSieerwv ice “Hidden” questions Reviewer comment: The authors looked for polymorphisms in the promoter region of the gene; however, they didn't evaluate the untranslated regions. That is one of my concerns about this methodology. Response: In this study, we decided to focus on the promoter region of Evidence this gene because previous studies [Yajima et al., 2010; Jackson et al., 2011] have shown that its transcription was particularly affected. This has now been clarified in the Discussion section of our manuscript (Page 16, Line 24–28). Location Revisions
  97. 97. CusPteoemr erer vSieerwv ice “Unfair” comments Reviewer comment: Currently, the authors’ conclusion that this model is appropriate for the predicting deforestation rates worldwide is not valid because they only addressed deforestation in Asia. The authors need to include deforestation data from Africa and South America as well. Reasons why reviewers might make these comments  Current results are not appropriate for the scope or impact factor of the journal  Reviewer is being “unfair”
  98. 98. CusPteoemr erer vSieerwv ice “Unfair” comments What you should do First, contact the journal editor if you feel reviewer is being unfair  Do the experiments, revise, and resubmit  Withdraw submission and resubmit current manuscript to a journal with a different scope or lower impact factor
  99. 99. Cover letters and peer review Activities Please see accompanying handouts
  100. 100. Peer Review Exercises The Journal Editor has returned your manuscript along with questions from the reviewers. Write an appropriate response for each one, and then share with your group. One member of each group will then read their best response for one of the comments.
  101. 101. Peer Review Exercises Reviewer #1: Although the author provided controls for the first two sets of experiments, it appears that control subjects were not included in the third set. Repeat the experiments with the proper controls and update your manuscript accordingly. Agreement We would like to thank Reviewer #1 for their comment. We agree that it is important to include the controls. Therefore, we have repeated the third set of experiments with the proper controls. We have now updated Figure 3 and revised the Results section (page XX, lines YY–ZZ) of our revised manuscript. What was done Revisions Location
  102. 102. Peer Review Exercises Reviewer #2: In the Introduction, the authors failed to discuss the studies published by Robertson and colleagues regarding non-parametric analyses. These should be added to the revised manuscript. We would like to thank Reviewer #2 for identifying this oversight. We have now discussed the work from Robertson and colleagues (Robertson et al. Biophys Comm; 2005, 13: 18–29 and Robertson et al. Anal Biochem; 2008, 24: 243–252) in our revised Introduction (page XX, lines YY–ZZ). Revisions Location
  103. 103. Peer Review Exercises Reviewer #3: The authors have proposed a very interesting model to explain consumer behavior in foreign countries. I wonder how this might impact the tourism industry. We would like to thank Reviewer #3 for their comment regarding our model. We also agree it would be of interest to the tourism industry. We have added a discussion about the impact our model might have for tourism-based marketing in our revised Conclusion (page XX, lines YY–ZZ). Revisions Location Agreement
  104. 104. Section 6 Next steps
  105. 105. Next steps If rejected, what should you do? Option 1: New submission to the same journal  Fully revise manuscript  Prepare point-by-point responses  Include the original manuscript ID number Option 2: New submission to a different journal  Revise manuscript  Reformat according to the author guidelines
  106. 106. Next steps Promote your work Promote your work on social networks NEJM BMJ Nature Facebook ○ ○ ○ LinkedIn ○ ○ ○ Twitter ○ ○ ○ YouTube ○ ○ ○ Blogs ○ ○ ○ Podcasts ○ ○ ○
  107. 107. Next steps Promote your work Promote your work on social networks Cell (IF, 32) posting on Facebook
  108. 108. Next steps Promote your work Promote your work on social networks Sharing published papers on LinkedIn
  109. 109. Next steps Promote your work Promote your work on social networks Allen et al. PLoS ONE 2013; 8: e68914. • 16 PLOS ONE articles were promoted on social networks on one randomly chosen date • 16 PLOS ONE articles were not Views* Downloads* Promoted 18±18 4±4 Not promoted 6±3 1±1 *per day
  110. 110. Next steps Promote your work Respond to post-publication comments
  111. 111. Next steps Promote your work Present your work at conferences Allows you to discuss your work personally with your peers Get feedback about your work and future directions Networking and collaborations
  112. 112. Be an effective communicator Your goal is not only to be published, but also to be widely read/cited  Write effectively  Increase the readability of your manuscript  How to choose the most appropriate journal  How to logically present your research  How to write effective cover letters  Successfully navigate peer review  How to actively promote your work
  113. 113. Any questions? Thank you! Jeffrey Robens: jrobens@edanzgroup.com www.edanzediting.co.jp/kyushu_agri Download and further reading @JournalAdvisor Follow us on Twitter facebook.com/EdanzEditing Like us on Facebook

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