Section 3. Introductions and Discussions

Transcription

1 Section 3 Introductions and Discussions

2 Introductions & Discussions Introduction General introduction Current state of the field Problem in the field Aims Specific aims

3 Introductions & Discussions Writing the Introduction Interest Beginning should demonstrate relevance/interest 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. Identified problem is directly related to the aims and scope Busch et al. BMC Cancer. 2012; 13: 211.

4 Introductions & Discussions Aims and scope BMC Cancer BMC Cancer is an open access, peer-reviewed journal that considers articles on all aspects of cancer research, including the pathophysiology, prevention, diagnosis and treatment of cancers. The journal welcomes submissions concerning molecular and cellular biology, genetics, epidemiology, and clinical trials.

5 Introductions & Discussions Writing the Introduction Problem Identify an important problem State aims that directly address this problem Therefore, it is of great interest to investigate whether reduction in obesity is associated with improvement in insulin secretion and sensitivity. However, the relationship between the changes in obesity and insulin resistance has not been well characterized. Aims Here, we investigated the associations between changes in obesity and insulin secretion and sensitivity in obese Japanese participants over a 1-year period. Modified from: Goto et al. PLoS ONE. 2013; 8: e57964.

6 Introductions & Discussions Common mistakes in the Introduction Ideas are not logically organized Introduce topics that are not discussed later (Results/Discussion) Why study needs to be done? Keep focused Not introduce important topics that are discussed later (topics introduced in the Discussion) Write last Cited studies are not up-to-date Cited studies are geographically biased <5 years International

7 Introductions & Discussions Discussion Summary of findings Relevance of findings Implications for the field Similarities/differences Unexpected results Negative results Limitations

8 Introductions & Discussions 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

9 Introductions & Discussions Writing the beginning of your Discussion State the major conclusion of the study Re-introduction GPER is an E 2 binding, G-protein coupled membrane receptor that was reported to be overexpressed in breast, endometrial, ovarian and thyroid cancers. However, it is currently unclear if different types of lung cancers including adenocarcinomas, squamous Problem cell carcinoma and large cell carcinomas express higher GPER than normal lung tissue. Here, we demonstrate for the first time that GPER is overexpressed in lung tumors and lung adenocarcinoma cell lines relative to normal lung and immortalized normal lung cell lines, although the expression of GPER transcript in HPL1D cells is higher than that of HBECs. Conclusion Modified from: Rao Jala et al. BMC Cancer 2012; 12: 624.

10 Introductions & Discussions Writing the middle of your Discussion Describe any unexpected/negative results In this study, we found that leaf N, P and N:P of the desert flora were unrelated to mean annual precipitation and only weakly related to mean annual temperature (Fig. 3). Possibly, the range in temperature ( C) and precipitation Likely ( mm) at our study site was too small to detect strong patterns with leaf N and P. Leaf N and P stoichiometry of different desert plants can temporally fluctuate because of seasonal climate variation that can obscure the spatial relationships between this stoichiometry and mean annual climate parameters. Future studies should evaluate these patterns in other areas throughout the year to address this issue. Negative results Possible reasons Suggest future directions Modified from: He et al. Sci Rep. 2014; 4: 6932.

11 Introductions & Discussions Writing the middle of your Discussion Describe any negative results Why? Reporting transparency Allows complete evaluation of your study Prevents others from repeating those experiments Allows others to modify those experiments Prevents funding agencies from wasting money

12 Introductions & Discussions Writing your limitations Identify limitations Important limitations of our study include an inadequate sample size and duration to detect differences in the incidence of diabetes complications, Address limitations such as myocardial infarction, stroke, or death. The protocol specifies further follow-up at 5 years for all patients, which should allow additional Sentence assessment structure of even longer-term efficacy and safety. Despite these limitations, we conclude that bariatric surgery represents a potentially useful strategy for the management of type 2 diabetes, allowing many patients to reach and maintain therapeutic targets of glycemic control that otherwise would not be achievable with intensive medical therapy alone. Modified from: Schauer et al. New Engl J Med. 2014; 370:

13 Introductions & Discussions Writing your limitations Identify limitations Important limitations of our study include an inadequate sample size and duration to detect differences in the incidence of diabetes complications, Address limitations such as myocardial infarction, stroke, or death. The protocol specifies further follow-up at 5 years for all patients, which should allow additional Sentence assessment structure of even longer-term efficacy and safety. Despite these limitations, we conclude that bariatric surgery represents a potentially useful strategy for the management of type 2 diabetes, allowing many patients to reach and maintain therapeutic targets of glycemic control that otherwise would not be achievable with intensive medical therapy alone. Application Modified from: Schauer et al. New Engl J Med. 2014; 370:

14 Introductions & Discussions Writing your limitations Limitation Use sentence structure to emphasize the application of your study Although the estimated quantum efficiency of the Pt-modified C 3 N 4 catalyst is rather low, this study opens new directions for the search of energy production schemes, using thermally and oxidation-stable polymeric organic semiconductor structures as the functional material that are cheap and commonly available. Limitation Modified from: Wang et al. Nat Mater. 2008; 8: Although this study used T. gondii as a model organism for evaluating terrestrial pathogen transport in coastal ecosystems, the polymer-mediated mechanisms identified here are likely relevant to disease transmission of numerous terrigenous pathogens that pose health risks to marine hosts or humans. Modified from: Shapiro et al. Proc R Soc B. 2014; 281: Application Application

15 Introductions & Discussions Writing your limitations Limitation Use sentence structure to emphasize the application of your study Although the estimated quantum efficiency of the Pt-modified C 3 N 4 catalyst is rather low, this study opens new directions for the search of energy production schemes, using thermally and oxidation-stable polymeric organic semiconductor structures as the functional material that are cheap and commonly available. Limitation Limitations related to: Data analysis Study design Modified from: Wang et al. Nat Mater. 2008; 8: Although this study used T. gondii as a model organism for evaluating terrestrial pathogen transport in coastal ecosystems, the polymer-mediated mechanisms identified here are likely relevant to disease transmission of numerous terrigenous pathogens that pose health risks to marine hosts or humans. Modified from: Shapiro et al. Proc R Soc B. 2014; 281: Application Application

16 Introductions & Discussions Writing the Discussion End should state the major conclusion of the study Re-state your major conclusion Describe the key implications Recommend future research

17 Introductions & Discussions Writing a strong conclusion paragraph Why your study is important In conclusion, we found an independent, graded association between lower levels of the estimated GFR and the risks of death, cardiovascular events, and hospitalization. These risks were evident at an estimated GFR of less than 60 ml per minute per 1.73 m 2 and substantially increased with an estimated GFR of less than 45 ml per minute per 1.73 m 2. Our findings support the validity of the National Kidney Foundation staging system for chronic kidney disease but suggest that the system could be further refined, since all persons with stage 3 chronic kidney disease (GFR, 30 to 59 ml per minute per 1.73 m 2 ) may not be at equal risk for each outcome. Our findings highlight the clinical and public health importance of chronic kidney disease that does not necessitate dialysis. Conclusion Key finding Implications Future directions Clinical importance Go et al. N Engl J Med. 2004; 351:

18 Introductions & Discussions Writing a strong conclusion paragraph Why your work is important to your readers 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 Kassin et al. Child Adolesc Psychiatry Ment Health. 2013; 7: 25.

19 Academic publishing Writing the Discussion Why your work is important to your readers 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. Conclusion Key finding Implications Future directions Importance King et al. Plant Cell. 2014; 26:

20 Introductions & Discussions Common mistakes in the Discussion Do not restate your results After policy implementation, cadmium levels at sites adjacent to the factory significantly decreased from 113.9±12.6 g m 2 to 53.4±6.3 g m 2 (p=0.034). This demonstrates that this policy is effective in reducing cadmium contamination and should be considered in other similar regions as well. Our results demonstrate that the implementation of the new policy was effective in reducing cadmium contamination at factoryadjacent sites by 53.1%. This suggests that this policy may also be effective in reducing cadmium levels in other similar regions as well.

21 Introductions & Discussions Common mistakes Do not overgeneralize your findings Policy implementation in Japan reduces cadmium contamination Our results demonstrate that the implementation of the new policy was effective in reducing cadmium contamination at factoryadjacent sites by 53.1%. This proves that this policy will be effective in reducing industrial contamination worldwide. Our results demonstrate that the implementation of the new policy was effective in reducing cadmium contamination at factoryadjacent sites by 53.1%. This suggests that this policy may also be effective in reducing cadmium levels in other similar regions as well.

22 Introductions & Discussions Linking your ideas in your manuscript Introduction Methods Results General background Current state of the field Problems in the field Objectives Methodology Results and figures Summary of findings Discussion Relevance of findings Implications for the field Logically link your ideas throughout your manuscript

23 Introductions & Discussions Linking your ideas 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 and biosynthesis of lipids and fatty acids Discussion 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 Objective Conclusion Elloumi et al. Botanical Studies. 2014; 55: 61.

24 Introductions & Discussions 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

25 Introductions & Discussions activity Please see Activity 3 in your Workbook

26 Activity 3: Introductions & Discussions 1. Based on the following problem identified in the field, chose which aims are most appropriate. Problem: However, it is not clear which membrane is most effective in reducing microbial and particulate contamination in freshwater reservoirs. A. In this study, we compared the efficacy of three currently available membranes in reducing the levels of microbes in freshwater S reservoirs. B. In this study, we evaluated if nanoporous sponges were more effective in reducing microbial and particulate contamination in freshwater reservoirs. C. In this study, we investigated how surface modifications of currently available membranes can improve their efficacy in reducing particulate contamination and the levels of microbes in freshwater reservoirs.

27 Activity 3: Introductions & Discussions 1. Based on the following problem identified in the field, chose which aims are most appropriate. Problem: However, it is not clear which membrane is most effective in reducing microbial and particulate contamination in freshwater reservoirs. A. In this study, we compared the efficacy of three currently available membranes in reducing the levels of microbes in freshwater S reservoirs. Not focused B. In this study, we evaluated if nanoporous sponges were more effective in reducing How microbial would and you particulate rewrite contamination the problem in fresh to water be more reservoirs. appropriate? C. In this study, we investigated how surface modifications of currently available membranes can improve their efficacy in reducing particulate contamination and the levels of microbes in freshwater reservoirs. However, it is not clear which membrane is most effective in reducing microbial contamination in freshwater reservoirs.

28 Activity 3: Introductions & Discussions 1. Based on the following problem identified in the field, chose which aims are most appropriate. Problem: However, it is not clear which membrane is most effective in reducing microbial and particulate contamination in freshwater reservoirs. How would you rewrite the problem to be more A. In this study, we compared the efficacy of three currently available membranes appropriate? in reducing the levels of microbes in freshwater S reservoirs. B. In this study, we evaluated if nanoporous sponges were more effective in reducing microbial and particulate contamination in freshwater reservoirs. Not focused C. In this study, we investigated how surface modifications of currently available membranes can improve their efficacy in reducing particulate contamination and the However, levels of microbes it is not in freshwater clear if alternative reservoirs. strategies are more effective than membranes in reducing microbial contamination in freshwater reservoirs.

29 Activity 3: Introductions & Discussions 1. Based on the following problem identified in the field, chose which aims are most appropriate. It is important to further improve available membranes to enhance their efficacy in reducing microbial and particulate Problem: However, it is not clear which membrane is most effective in reducing microbial and particulate contamination in freshwater in reservoirs. A. In this How study, would we compared you the rewrite efficacy the of three problem currently to available be more membranes in reducing the levels of microbes in freshwater S reservoirs. appropriate? B. In this study, we evaluated if nanoporous sponges were more effective in reducing microbial and particulate contamination in freshwater reservoirs. Still not focused C. In this study, we investigated how surface modifications of currently available membranes can improve their efficacy in reducing particulate contamination and the levels of microbes in freshwater reservoirs.

30 Activity 3: Introductions & Discussions 2. 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. Here, we aimed to evaluate how literacy rates affected the economic growth of various countries from 2000 to A. Our results demonstrate the need to improve education to promote literacy in developing countries. B. This study showed that increased literacy rates are positively correlated with economic growth. C. In this study, we showed that economically developed countries spend more money on education, leading to improved literacy rates.

31 Activity 3: Introductions & Discussions 2. 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. Here, we aimed to evaluate how literacy rates affected the economic growth of various countries from 2000 to A. Our results demonstrate the need to improve education to promote literacy in developing countries. Implications B. This study showed that increased literacy rates are positively correlated with economic growth. C. In this study, we showed that economically developed countries spend more money on education, leading to improved literacy rates.

32 Activity 3: Introductions & Discussions 2. 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. Here, we aimed to evaluate how literacy rates affected the economic growth of various countries from 2000 to A. Our results demonstrate the need to improve education to promote literacy in developing countries. B. This study showed that increased literacy rates are positively correlated with economic growth. Conclusion answers the problem C. In this study, we showed that economically developed countries spend more money on education, leading to improved literacy rates.

33 Activity 3: Introductions & Discussions 2. 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. Here, we aimed to evaluate how literacy rates affected the economic growth of various countries from 2000 to A. Our results demonstrate the need to improve education to promote literacy in developing countries. B. This study showed that increased literacy rates are positively correlated with economic growth. C. In this study, we showed that economically developed countries spend more money on education, leading to improved literacy rates. Key finding

34 Section 4 Titles and abstracts

35 Titles and 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

36 Titles and Abstracts Effective titles Articles with short titles describing the results are cited more often Paiva et al. Clinics 2012; 67: Analyzed 423 research articles published in Oct 2008 and analyzed the citations in Dec 2011 Higher citations Short titles Described results Lower citations Questions Geographically restricted

37 Titles and 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

38 Titles and Abstracts Abstract Relevance of your aims Importance of your results Validity of your conclusions First impression of your paper Judge your writing style Probably only part that will be read

39 Titles and 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

40 Titles and Abstracts Unstructured abstract ErbB-2 has been implicated as a target for cancer-initiating cells in breast and other cancers. ErbB-2-directed peptide vaccines have been shown to be effective in prevention of spontaneous tumorigenesis of breast in neu transgenic mouse model, and cellular immunity is proposed as a mechanism for the anti-tumor efficacy. However, there has been no explanation as to how immunity suppresses tumorigenesis from the early stage carcinogenesis, when ErbB-2 expression in breast is low. Here, we investigated a peptidebased vaccine, which consists of two MHC class II epitopes derived from murine ErbB-2, to prevent the occurrence of spontaneous tumors in breast and assess immune impact on breast cancer stem cells. Female MMTV-PyMT transgenic mice were immunized with either ErbB-2 peptide vaccine, or a peptide from tetanus toxoid, or PBS in immune adjuvant. We found that ErbB-2 peptides vaccine completely suppressed spontaneous breast tumors, and the efficacy was correlated with antigen-specific T-cell and antibody responses. In addition, immune serum from the mice of ErbB-2 vaccine group had an inhibitory effect on mammosphereforming capacity and signaling through ErbB-2 and downstream Akt pathway in ErbB-2 overexpressing mouse mammary cancer cells. In conclusion, we provide evidence that multiepitope class II peptides vaccine suppresses tumorigenesis of breast potentially by inhibiting the growth of cancer stem cells. We also suggest that a strategy of inducing strong immune responses using multi-epitope ErbB-2-directed helper vaccine might be useful in preventing breast cancer recurrence. Modified from: Gil et al. Breast Cancer Res Treat. 2014; 147:

41 Titles and Abstracts Unstructured abstract ErbB-2 has been implicated as a target for cancer-initiating cells in breast and other cancers. ErbB-2-directed peptide vaccines have been shown to be effective in prevention of spontaneous tumorigenesis of breast in neu transgenic mouse model, and cellular immunity is proposed as a mechanism for the anti-tumor efficacy. However, there has been no explanation as to how immunity suppresses tumorigenesis from the early stage carcinogenesis, when ErbB- 2 expression in breast is low. Here, we investigated a peptide-based vaccine, which consists of two MHC class II epitopes derived from murine ErbB-2, to prevent the occurrence of spontaneous tumors in breast and assess immune impact on breast cancer stem cells. Female MMTV-PyMT transgenic mice were immunized with either ErbB-2 peptide vaccine, or a peptide from tetanus toxoid, or PBS in immune adjuvant. We found that ErbB-2 peptides vaccine completely suppressed spontaneous breast tumors, and the efficacy was correlated with antigen-specific T-cell and antibody responses. In addition, immune serum from the mice of ErbB-2 vaccine group had an inhibitory effect on mammosphere-forming capacity and signaling through ErbB-2 and downstream Akt pathway in ErbB-2 overexpressing mouse mammary cancer cells. In conclusion, we provide evidence that multi-epitope class II peptides vaccine suppresses tumorigenesis of breast potentially by inhibiting the growth of cancer stem cells. We also suggest that a strategy of inducing strong immune responses using multi-epitope ErbB-2- directed helper vaccine might be useful in preventing breast cancer recurrence. Background Aims Methods Results Conclusion Modified from: Gil et al. Breast Cancer Res Treat. 2014; 147:

42 Titles and Abstracts Writing your abstract Write the results section first Key findings that directly support your aims Will be interesting to the readers We found that ErbB-2 peptides vaccine completely suppressed spontaneous breast tumors, and the efficacy was correlated with antigen-specific T-cell and antibody responses. In addition, immune serum from the mice of ErbB-2 vaccine group had an inhibitory effect on mammosphere-forming capacity and signaling through ErbB-2 and downstream Akt pathway in ErbB-2 overexpressing mouse mammary cancer cells. Modified from: Gil et al. Breast Cancer Res Treat. 2014; 147:

43 Titles and Abstracts Writing your abstract Write the background section second Explain why this study needed to be done ErbB-2 has been implicated as a target for cancer-initiating cells in breast and other cancers. ErbB-2-directed peptide vaccines have been shown to be effective in prevention of spontaneous tumorigenesis of breast in neu transgenic mouse model, and cellular immunity is proposed as a mechanism for the anti-tumor efficacy. However, there has been no explanation as to how immunity suppresses tumorigenesis from the early stage of carcinogenesis, when ErbB-2 expression in breast is low. Problem Modified from: Gil et al. Breast Cancer Res Treat. 2014; 147:

44 Titles and Abstracts Writing your abstract Write the aims section third How to address the presented problem Here, we investigated a peptide-based vaccine, which consists of two MHC class II epitopes derived from murine ErbB-2, to prevent the occurrence of spontaneous tumors in breast and assess immune impact on breast cancer stem cells. Modified from: Gil et al. Breast Cancer Res Treat. 2014; 147:

45 Titles and Abstracts Writing your abstract Write the methods section fourth General techniques used to obtain the presented results Female MMTV-PyMT transgenic mice were immunized with either ErbB-2 peptide vaccine, or a peptide from tetanus toxoid, or PBS in immune adjuvant. Modified from: Gil et al. Breast Cancer Res Treat. 2014; 147:

46 Titles and Abstracts Writing your abstract Write the conclusion section last Major conclusion that answers the problem Implications for the readers However, there has been no explanation as to how immunity suppresses tumorigenesis from the early stage of carcinogenesis... In conclusion, we provide evidence that multi-epitope class II peptides vaccine suppresses tumorigenesis of breast potentially by inhibiting the growth of cancer stem cells. We also suggest that a strategy of inducing strong immune responses using multi-epitope ErbB-2-directed helper vaccine might be useful in preventing breast cancer recurrence. Implications Modified from: Gil et al. Breast Cancer Res Treat. 2014; 147:

47 Titles and Abstracts Writing your abstract ErbB-2 has been implicated as a target for cancer-initiating cells in breast and other cancers. ErbB-2-directed peptide vaccines have been shown to be effective in prevention of spontaneous tumorigenesis of breast in neu transgenic mouse model, and cellular immunity is proposed as a mechanism Why for the needed anti-tumor to efficacy. be done However, there has been no explanation as to how immunity suppresses tumorigenesis from the early stage carcinogenesis, when ErbB-2 expression in breast is low. Here, we investigated a peptidebased vaccine, which consists of two MHC Your class aims II epitopes derived from murine ErbB-2, to prevent the occurrence of spontaneous tumors in breast and assess immune impact on breast cancer stem cells. Female MMTV-PyMT transgenic mice were immunized with either ErbB-2 peptide vaccine, or a peptide from tetanus What toxoid, you or did PBS in immune adjuvant. We found that ErbB-2 peptides vaccine completely suppressed spontaneous breast tumors, and the efficacy was correlated with antigen-specific T-cell and antibody responses. In addition, immune serum from the mice of ErbB-2 What vaccine group you had found an inhibitory effect on mammosphereforming capacity and signaling through ErbB-2 and downstream Akt pathway in ErbB-2 overexpressing mouse mammary cancer cells. In conclusion, we provide evidence that multiepitope class II peptides vaccine suppresses tumorigenesis of breast potentially by inhibiting the growth of cancer stem How cells. contributes We also suggest that to a the strategy field of inducing strong immune responses using multi-epitope ErbB-2-directed helper vaccine might be useful in preventing breast cancer recurrence. Modified from: Gil et al. Breast Cancer Res Treat. 2014; 147:

48 Titles and Abstracts References Abbreviations Don t include Jargon, equations Non-essential numbers & statistics

49 Titles and Abstracts Do not include a lot of numbers and statistics The effect of high vacuum on the mechanical properties and bioactivity of collagen fibril matrices Results The cell area histogram and mean cell areas for the HV-treated fibril matrices (2030 μm 2 ± 137 μm 2 ) are comparable to the cell areas of untreated fibril matrices measured here (2165 μm 2 ± 206 μm 2 ) and elsewhere... Cells on LVtreated fibril matrices have larger average surface areas (3450 μm 2 ± 175 μm 2 ) than the control untreated matrices, and their spread areas are more similar to that of cells plated on dehydrated fibrils (average cell area of 4348 μm 2 ± 287 μm 2 ). The modulus results for the first analysis reveal that HV treatment of the fibrils leads to a small, but statically significant (p < ), increase in mechanical your rigidity of results the fibril matrices. Untreated matrices had a modulus of 8.1 kpa ± 2.2 kpa and HV-treated matrices had a modulus of 13.1 kpa ± 3.8 kpa. However, the HV-treated matrices are approximately a factor of three more compliant than the dehydrated fibril matrices (35.4 kpa ± 4.9 kpa). The modulus results for the second analysis (Table 2) indicate that LV-treated fibril matrices (34.7 kpa ± 3.7 kpa) are nearly as mechanically stiff (p= 0.20) as the dehydrated matrices (36.4 kpa ± 4.2 kpa), and are considerably less compliant than the untreated matrices (11.2 kpa ± 3.7 kpa) in this experiment. Abstract Summarize and simplify We find that HV exposure has an unappreciable affect on the cell spreading response and mechanical properties of these collagen fibril matrices. Conversely, low vacuum environments cause fibrils to become mechanically rigid as indicated by force microscopy, resulting in greater cell spreading. Anderton et al. Biointerfaces. 2013; 8: 2.

50 Abstract activity Please see Activity 4 in your Workbook

51 Activity 4: Abstract How is this related to mice? A devastating earthquake and tsunami hit Japan on March 11, In the present study, the effects of this earthquake on laboratory mice behavior were investigated. Earthquakeexperienced 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. Modified from: Yanai et al. PLoS One. 2012; 7: e44475.

52 Activity 4: Abstract How is this related to mice? A devastating earthquake and tsunami hit Japan on March 11, In the present study, the effects of this earthquake on laboratory mice behavior were investigated. Earthquakeexperienced mice displayed a marked increase in food consumption without Unnecessary gaining body information 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. Modified from: Yanai et al. PLoS One. 2012; 7: e44475.

53 Activity 4: Abstract How is this related to mice? A devastating earthquake and tsunami hit Japan on March 11, In the present study, the effects of this earthquake on laboratory mice behavior were investigated. Earthquakeexperienced mice displayed a marked increase in food consumption without Unnecessary gaining body information 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. Modified from: Yanai et al. PLoS One. 2012; 7: e44475.

54 Activity 4: Abstract How is this related to mice? A devastating earthquake and tsunami hit Japan on March 11, In the present study, the effects of this earthquake on laboratory mice behavior were investigated. Earthquakeexperienced mice displayed a marked increase in food consumption without Unnecessary gaining body information weight. The food was purchased from a company based in New Zealand. The mice also displayed enhanced anxiety. How Maze was performance this measured? 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. No conclusions Modified from: Yanai et al. PLoS One. 2012; 7: e44475.

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56 Section 5 Cover letters

57 Coverage and Cover Staffing letters Plan Significance Relevance Why your work is important! Cover letter: First impression for journal editors Interesting to their readers? Writing style

58 Coverage and Cover Staffing letters Plan Building your cover letter Marc Lippman, MD Editor-in-Chief Breast Cancer Research and Treatment 3 September 2013 Dear Dr Lippman, Please find enclosed our manuscript entitled Evaluation of the Glasgow prognostic score in patients undergoing curative resection for breast cancer liver metastases, which we would like to submit for publication as a Original Article in Breast Cancer Research and Treatment. Journal editor s name Article type Did you read the aims and scope? Did you read the author guidelines? Manuscript title

59 Coverage and Cover Staffing letters Plan Building your cover letter Second paragraph: Current state of the field Problem researchers are facing The Glasgow prognostic score (GPS) is of value for a variety of tumours. Several studies have Introduction investigated the prognostic value of the GPS in patients with metastatic breast cancer, but few studies have performed such an investigation for patients undergoing liver resection for liver metastases. Furthermore, there are currently no Problem studies that have examined the prognostic value of the modified GPS (mgps) in these patients. The present study evaluated the mgps in terms of its prognostic value for postoperative death in patients Objectives undergoing liver resection for breast cancer liver metastases.

60 Coverage and Cover Staffing letters Plan Building your cover letter Third paragraph: Briefly describe your methodology Summarize your key findings A total of 318 patients with breast cancer liver metastases who underwent hepatectomy over a 15-year period were included in this study. The mgps was calculated Methods based on the levels of C-reactive protein and albumin, and the disease-free survival and cancerspecific survival rates were evaluated in relation to the mgps. Overall, the results showed a significant association between cancerspecific survival and the mgps and carcinoembryonic antigen level. A Key results higher mgps was associated with increased aggressiveness of liver recurrence and poorer survival in these patients.

61 Coverage and Cover Staffing letters Plan Building your cover letter Fourth paragraph: Why interesting to the journal s readership This study is the first to demonstrate that the preoperative mgps, a simple clinical tool, is a useful Conclusion prognostic factor for postoperative survival in breast cancer patients undergoing curative resection for liver metastases. This information is immediately clinically applicable for surgeons and medical oncologists treating such patients. As a premier journal Relevance covering breast cancer treatment, we believe that Breast Cancer Research and Treatment is the perfect platform from which to share our results with all those concerned with breast cancer.

62 Coverage and Cover Staffing letters Plan Building your cover letter Fourth paragraph: Why interesting to the journal s readership This study is the first to demonstrate that the preoperative mgps, a simple clinical tool, is a useful prognostic factor for postoperative survival in breast cancer patients undergoing curative resection for liver metastases. This information is immediately clinically applicable for surgeons and medical oncologists treating such patients. As a premier journal covering breast cancer treatment, we believe that Breast Cancer Research and Treatment is the perfect platform from which to share our results with all those concerned with breast cancer. From the aims and scope

63 Coverage and Cover Staffing letters Plan Building your cover letter Last paragraph: Disclaimers related to publication ethics Source of funding Conflicts of interest We confirm that this manuscript has not been published elsewhere and is not under consideration Ethics by another journal. All authors have approved the manuscript and agree with submission to the Breast Cancer Research and Treatment. This study was funded by the Funding Japanese Ministry of Health, Labour and Welfare. The authors have no conflicts of interest to Conflicts declare. of interest

64 Coverage and Cover Staffing letters Plan 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: Reviewers 1. Reviewer 1 and contact information 2. Reviewer 2 and contact information 3. Reviewer 3 and contact information 4. Reviewer 4 and contact information Contact information Please address all correspondence to: Can also exclude reviewers

65 Coverage and Cover Staffing letters Plan A good cover letter Marc Lippman, MD Editor-in-Chief Breast Cancer Research and Treatment 3 September 2013 Dear Dr Lippman, Manuscript information Please find enclosed our manuscript entitled Evaluation of the Glasgow prognostic score in patients undergoing curative resection for breast cancer liver metastases, which we would like to submit for publication as an Original Article in Breast Cancer Research and Treatment.. The Glasgow prognostic score (GPS) is of value for a variety of tumours. Several studies have investigated the prognostic value of the GPS in patients with metastatic breast cancer, but few studies have performed such an investigation for patients undergoing liver resection for liver metastases. Furthermore, there are currently no studies that have examined the prognostic value of the modified GPS (mgps) in these patients. The present study evaluated the mgps in terms of its prognostic value for postoperative death in patients undergoing liver resection for breast cancer liver metastases. A total of 318 patients with breast cancer liver metastases who underwent hepatectomy over a 15-year period were included in this study. The mgps was calculated based on the levels of C-reactive protein and albumin, and the disease-free survival and cancer-specific survival rates were evaluated in relation to the mgps. Prognostic significance was retrospectively analyzed by univariate and multivariate analyses. Overall, the results showed a significant association between cancer-specific survival and the Key mgps and findings carcinoembryonic antigen level. Furthermore, we demonstrated that a higher mgps was associated with increased aggressiveness of liver recurrence and poorer survival in these patients. This study is the first to demonstrate that the preoperative mgps, a simple clinical tool, is a useful prognostic factor for postoperative survival in breast cancer patients undergoing curative resection for liver metastases. This information is immediately clinically applicable for surgeons and medical oncologists treating such patients. As a premier journal covering breast cancer treatment, we believe that Breast Cancer Research and Treatment is the perfect platform from which to share our results with all those concerned with breast cancer. We confirm that this manuscript has not been published elsewhere and is not under consideration by another journal. All authors have approved the manuscript and agree with submission to Breast Cancer Research and Treatment. This study was funded by the Japanese 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, Background Relevance Disclaimers Recommended reviewers

66 Coverage and Cover Staffing letters Plan Specific cover letter styles

67 Coverage and Cover Staffing letters Plan Additional points Highlight recent issues in the media Given the considerable attention climate change has received worldwide, it will be important to Highlight recently published articles in their journal It has recently been shown that PMS2 mutations cause Lynch Syndrome (ten Broeke et al. J Clin Oncol. 2015;33:319). However, it still remains unclear Highlight recent policy changes Recently, the Japanese government has implemented new incentives to promote entrepreneurship Highlight current controversies Currently, there is disagreement on the effect of substrate rigidity on stem cell differentiation. Our study aims to address this controversy with a novel

68 Coverage and Cover Staffing letters Plan Do you need to recommend reviewers? Desalination Authors are required to provide the names and e- mail addresses of at least 3 international reviewers in their cover letter. Experimental Brain Research When submitting your paper, you must provide the names, affiliations, and valid addresses of five (5) reviewers. If you do not do so, your paper will be returned, unreviewed.

69 Coverage and Cover Staffing letters Plan Recommending reviewers PNAS 11 people!

70 Coverage and Cover Staffing letters Plan Why recommend reviewers? Reviewers recommended by authors are usually more favorable 1. Scharschimidt et al. J Clin Invest. 1994; 93: Earnshaw & Farndon. Ann R Coll Surg Engl. 2000; 82: Grimm. Science 2005; 309: Wager et al. BMC Med. 2006; 4: Schroter et al. JAMA 2006; 295: Rivara et al. J Pediatr. 2007; 151: Bornmann & Daniel. Res Eval. 2009; 18: Bornmann & Daniel. PLoS One 2010; 5: e13345.

71 Coverage and Cover Staffing letters Plan Recommending reviewers Where to find them? How senior? Who to avoid? From your reading/references, networking at conferences Aim for mid-level researchers Collaborators (past 5 years), researchers from your university International list: 1 or 2 from Asia, 1 or 2 from Europe, and 1 or 2 from North America Have they published in your target journal?

72 Section 6 Peer review & revisions

73 Peer review What reviewers are looking for The science Relevant hypothesis Good experimental design Appropriate methodology Good data analysis Valid conclusions The manuscript Logical flow of information Manuscript structure and formatting Appropriate references High readability

74 Peer review Unclear decision letter 30 August 2014 Dear Dr. Robens, Manuscript ID NRL : Gene regulatory networks in living cells Decision Your manuscript has been reviewed, and we regret to inform you that based on our Expert reviewers comments, it is not possible to further consider your manuscript in its current form for publication in Neurogenetics. Reason Although the reviews are not entirely negative, it is evident from the extensive comments and concerns that the manuscript, in its current form, does not meet the criteria expected of papers in Neurogenetics. The results appear to be too preliminary and incomplete for publication at the present time. Comments The reviewer comments are included at the bottom of this letter. I hope the information provided by the reviewers will be helpful in future. Thank you for your interest in the journal and I regret that the outcome has not been favorable at this time.

75 Peer review Editor may be interested in your work The Reviewer comments are not entirely negative. It is not possible to consider your manuscript in its current form. I hope the information provided by the reviewers will be helpful in the future. I regret that the outcome has not been favorable at this time.

76 Peer review Editor is not interested in your work We cannot publish your manuscript Your study does not contain novel results that merit publication in our journal. We appreciate your interest in our journal. However, we will not further consider your manuscript for publication. We wish you luck in publishing your results elsewhere.

77 Peer review Why send an unclear decision letter? Publication time Long revisions = long publication times Editors hope you fully revise and then resubmit as a new submission

78 Peer review Clear decision letter 10 November 2015 Dear Dr. Robens, Manuscript ID number Manuscript ID /s : Prediction of nonlinear seismic responses of asymmetric structures under stress Decision Your manuscript has been reviewed, and we believe that after revision your manuscript may become suitable for publication in Journal of Seismology. The reviewer concerns are included at the bottom of this letter. You can submit a revised manuscript that takes into consideration these comments. You will also need to include a detailed commentary of the changes made. Please note that resubmitting your manuscript does not guarantee eventual acceptance, and that your resubmission may be subject to re-review by the reviewers before a decision is made. To revise your manuscript, log into and enter your Author Center, where you will find your manuscript title listed under "Manuscripts with Decisions." Under "Actions," click on "Create a Revision." Your manuscript number has been appended to denote a revision. How to re-submit

79 Peer review Clear decision letter You will be unable to make your revisions on the originally submitted version of the manuscript. Instead, revise your manuscript using a word processing program and save it on your computer. Please also highlight the changes to your manuscript within the document by using bold or colored text. Once the revised manuscript is prepared, you can upload it and submit it through your Author Center. How to respond When submitting your revised manuscript, you will be able to respond to the comments made by the reviewer(s) in the space provided. You can use this space to document any changes you make to the original manuscript. In order to expedite the processing of the revised manuscript, please be as specific as possible in your response to the reviewer(s). IMPORTANT: Your original files are available to you when you upload your revised manuscript. Please delete any redundant files before completing the submission. Because we are trying to facilitate timely publication of manuscripts submitted to BBE, your revised manuscript should be uploaded by 10 December. If it is not possible for you to submit your revision in a reasonable amount of time, we may have to consider your paper as a new submission. Due date for resubmission Once again, thank you for submitting your manuscript to Journal of Seismology and I look forward to receiving your revised manuscript.

80 Peer review 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 Strikethrough font for deletions

81 Peer review Writing response letters Marc Lippman, MD Editor-in-Chief Breast Cancer Research and Treatment Address editor personally 3 September 2013 Dear Dr Lippman, Re: Resubmission of manuscript reference No. WJS Manuscript ID number Thank reviewers Please find attached a revised version of our manuscript originally entitled Evaluation of the Glasgow prognostic score in patients undergoing curative resection for breast cancer liver metastases, which we would like to resubmit for consideration for publication in the Breast Cancer Research and Treatment. 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 underlined 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 the Breast Cancer Research and Treatment. Highlight major changes

82 Peer review 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.

83 Peer review 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 Why you agree 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

84 Peer review 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: It is clear that this reviewer is not familiar with the current analytical methods in the field. I recommend that you identify a more suitable reviewer for my manuscript.

85 Peer review 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 Evidence 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

86 Peer review Unfair reviewer comments Reviewer comment: Currently, the authors conclusion that this gene is involved in heart development is not completely validated by their in vitro analyses. They should do additional in vivo experiments using a genetic mouse model to show that heart development is regulated by this gene. 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

87 Peer review Unfair reviewer 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

88 Peer review 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

89 Peer review activity Please see Activity 5 in your Workbook

90 Activity 5: Peer review The journal editor has returned your manuscript along with a question from the Reviewer. Choose the most appropriate response and explain why. Reviewer 2: The concept of using conformity to explain effective policy implementation is not new. The authors should discuss what has been published previously regarding this issue, such as Stow et al. Int Policy Rev. 2008; 12: and Yajima et al. J Res Policy. 2005; 62:

91 Activity 5: Peer review Response A: We thank the reviewer for their opinion. However, we have decided to not include these references as they are not relevant to our study. If you decide not to include Reviewer recommended studies, you need to explain why.

92 Activity 5: Peer review Response B: We thank the reviewer for their comment. We have reviewed the suggested papers; however, we do not feel that these papers should be cited in our manuscript. Although these papers address conformity, they do so in a socialist context that is not appropriate for our paper. The studies by Jackson et al. (J Policy Studies. 2007; 43: ) and Pack et al. (Int Econ Rev 2011; 6: 67-71) are more relevant as they discuss the concept of conformity in a similar context as our paper. Therefore, we have included these references and added text to the Discussion of our revised manuscript. Explains why not appropriate Suggests other relevant studies Addresses problem with literature review

93 Activity 5: Peer review Response C: We thank the reviewer for their valuable suggestions. We have conducted a thorough literature search and have added the two suggested references to our revised manuscript. Where? If you decide to include Reviewer recommended studies, you should explain why you feel they are relevant. You should also state where they are discussed.

94 Activity 5: Peer review Response D: We thank the reviewer for their valuable suggestions. We have conducted a thorough literature search and have added the two suggested references to our revised manuscript. We have also expanded our Discussion section to clarify how our findings differ from those reported previously. Briefly, although the studies from Stow et al. and Yajima et al. discuss the role of conformity to effectively implement new policies, they do so only in a socialist context. Therefore, we have discussed the novelty of our findings with regard to different government systems. Discusses where added Briefly explains discussion of new ideas Addresses issue related to novelty

95 Be an effective communicator Your goal is not only to be published, but also to be widely read/cited Choose the most appropriate journal Logically organize your ideas in your manuscript Write impressive cover letters to the journal editor Successfully navigate peer review S