5. Reading Strategies Reading improves manuscript writing Read often! Learn how native Learn manuscript Article and journal English speakers write structure and style quality Learn proper Get new ideas, argument structure identify knowledge gaps Discuss with colleagues
6. Reading Strategies Make time to read Most researchers read 60–90 min per day Spend 20–30 min every day reading abstracts Spend 60 min 2 or 3 days a week reading papers Join a journal club
7. Reading Strategies Strategies for reading Read Title and Abstract first Self-assess knowledge of topic Have you read similar papers? Familiar with the terminology? Do you understand the relevance of the hypothesis
8. Reading Strategies Strategies for reading Read Title and Abstract first Self-assess knowledge of topic Read last paragraph of introduction for hypothesis/objectives Read Figures and then Results Read Discussion for interpretation Refer to Introduction and Methods if necessary
9. Section 2Abstracts
10. Abstracts Important points Relevance of Importance of Validity of your your aims your results conclusions First impression of your paper Judge your Probably only part writing style that will be read
11. Abstracts General GuideBackground Why the study was done (20%) Aims Your hypothesis (10%) Methods Techniques (10%) Results Most important findings (40%)Conclusion Conclusion & implications (20%)
12. Abstracts Structured abstractImmunotherapy using slow-cycling tumor cells prolonged overall survival of tumor-bearing miceBackgroundDespite considerable progress in the development of anticancer therapies, there is still a high mortality rate caused by cancerrelapse and metastasis. Dormant or slow-cycling residual tumor cells are thought to be a source of tumor relapse and metastasis,and are therefore an obstacle to therapy. In this study, we assessed the drug resistance of tumor cells in mice, and investigatedwhether vaccination could promote survival.MethodsThe mouse colon carcinoma cell line CT-26 was treated with 5-fluorouracil to assess its sensitivity to drug treatment. Mice withcolon tumors were immunized with inactivated slow-cycling CT-26 cells to estimate the efficacy of this vaccine.ResultsWe identified a small population of slow-cycling tumor cells in the mouse colon carcinoma CT-26 cell line, which was resistant toconventional chemotherapy. To inhibit tumor recurrence and metastasis more effectively, treatments that selectively target theslow-cycling tumor cells should be developed to complement conventional therapies. We found that drug-treated, slow-cyclingtumor cells induced a more intense immune response in vitro. Moreover, vaccination with inactivated slow-cycling tumor cellscaused a reduction in tumor volume and prolonged the overall survival of tumor-bearing mice.ConclusionsThese findings suggest that targeting of slow-cycling tumor cells application using immunotherapy is a possible treatment tocomplement traditional antitumor therapy. Sun et al. (2012). BMC Medicine 10:172.
13. Abstracts Unstructured abstract Differential DNA Methylation Status Between Human Preadipocytes and Mature Adipocytes Obesity is a multifactorial disease resulting from interactions between susceptibility genes, psychosocial, and environmental factors. However, it is becoming evident that interindividual differences in obesity susceptibility depend also on epigenetic factors, although the mechanisms have not been fully elucidated. We have undertaken a genome- wide analysis of DNA methylation of human preadipocytes and mature adipocytes to examine the differences in methylation between them. We found hypomethylation occurring in 2,701 genes and hypermethylation in 1,070 genes after differentiation. Meanwhile, Gene Ontology analysis and Ingenuity Pathway Analysis showed many significant gene functions and pathways with altered methylation status after adipocyte differentiation. In addition, Signal-Net analysis showed that tumor necrosis factor-α, mitogen-activated protein kinase, and interleukin-8 were important to the formation of this network. Our results suggest that DNA methylation mechanisms may be involved in regulating the differentiation process of human preadipocytes. Zhu et al. (2012) Cell Biochem Biophys 63:1‒15.
14. Abstracts Unstructured abstractObesity is a multifactorial disease resulting from interactions between susceptibility genes,psychosocial, and environmental factors. However, it is becoming evident thatinterindividual differences in obesity susceptibility depend also on epigenetic factors, Backgroundalthough the mechanisms have not been fully elucidated.We have undertaken a genome-wide analysis of DNA methylation of human preadipocytesand mature adipocytes to examine the differences in methylation between them. MethodsWe found hypomethylation occurring in 2,701 genes and hypermethylation in 1,070 genesafter differentiation. Meanwhile, Gene Ontology analysis and Ingenuity Pathway Analysisshowed many significant gene functions and pathways with altered methylation status afteradipocyte differentiation. In addition, Signal-Net analysis showed that tumor necrosis Resultsfactor-α, mitogen-activated protein kinase, and interleukin-8 were important to theformation of this network.Our results suggest that DNA methylation mechanisms may be involved in regulating thedifferentiation process of human preadipocytes. Conclusion Zhu et al. (2012) Cell Biochem Biophys 63:1‒15.
15. Abstracts Writing your abstractObesity is a multifactorial disease resulting from interactions between susceptibilitygenes, psychosocial, and environmental factors. However, it is becoming evident thatinterindividual differences in obesity susceptibility depend also on epigenetic factors,although the mechanisms have not been fully elucidated. We have undertaken agenome-wide analysis of DNA methylation of human preadipocytes and matureadipocytes to examine the differences in methylation between them. We foundhypomethylation occurring in 2,701 genes and hypermethylation in 1,070 genes afterdifferentiation. Meanwhile, Gene Ontology analysis and Ingenuity Pathway Analysisshowed many significant gene functions and pathways with altered methylation statusafter adipocyte differentiation. In addition, Signal-Net analysis showed that tumornecrosis factor-α, mitogen-activated protein kinase, and interleukin-8 were important tothe formation of this network. Our results suggest that DNA methylation mechanismsmay be involved in regulating the differentiation process of human preadipocytes. Zhu et al. (2012) Cell Biochem Biophys 63:1‒15.
17. Abstracts Do not include a lot of numbers and statistics The effect of high vacuum on the mechanical properties and bioactivity of collagen fibril matricesResults The cell area histogram and mean cell areas for the HV-treated fibril matrices (2030 μm2 ± 137 μm2) are comparable to the cell areas of untreated fibril matrices measured here (2165 μm2 ± 206 μm2) and elsewhere... Cells on LV- treated fibril matrices have larger average surface areas (3450 μm2 ± 175 μm2) 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 μm2 ± 287 μm2). Summarize and simplify your results The modulus results for the first analysis reveal that HV treatment of the fibrils leads to a small, but statically significant (p < 0.0001), increase in mechanical rigidity of 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 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. (2013) Biointerfaces 8:2.
18. Abstracts Effective titles Important points AvoidCatch reader’s interest QuestionsSummarize key finding Abbreviations Contains keywords “New” or “novel” Less than 20 words
19. Section 3Manuscript Structure
20. Coverage and ManuscriptStaffing Plan structure IMRaD Abstract Introduction The beginning Methods The middle Results and Discussion The end
21. Coverage and ManuscriptStaffing Plan structure The ‘write’ order Methods Results During your research FiguresIntroduction Discussion After selecting target journal References Title Abstract Write last
22. Coverage and ManuscriptStaffing Plan structure Introduction Sufficient background information Current state of the field Identify knowledge gaps/problems Puts your work into context General Aims Specific
23. Coverage and Manuscript New biocompatibleStaffing Plan structure material for osteoporosis Osteoporosis Diagnosis Drug treatments Bioengineering Design Technique Material
24. Coverage and Manuscript Staffing Plan structure Methods Multiple methods = New methods Models andseparate subheadings described in detail equations What you did Materials General techniques Method order Specific techniques Statistics
25. Coverage and ManuscriptStaffing Plan structure Results Each subsection Order of results is corresponds to one logical, tells a story figure What you found Avoid data duplication Factually describe among figures, tables, your results and text
26. Coverage and ManuscriptStaffing Plan structure Display items Present large amount Usually the first thing of data quickly and readers will look at efficiently Figures, graphs & tables Keep it simple: use Must be able to stand separate panels if alone: clear labels necessary and figure legends
27. Coverage and ManuscriptStaffing Plan structure Figures/schematics Clear figure legend Kindlin-2 knockdown and focal adhesion localization. A. Confocal immunofluorescent microscopy with anti- β1 integrin (green) and anti-paxillin (red) on C2C12 cells transfected with RNAi and then changed to differentiation media for 2 days. Control cells (scr RNAi) show linear staining consistent with localization to costameres (arrows), as well as punctate focal contact staining (arrowheads). Conversely, 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). Clear indicators Scale bars Dowling et al. (2008) BMC Cell Biol 9:36.
28. Coverage and Manuscript Staffing Plan structure TablesClear and concise table captionData aligned and Abbreviations formatted defined Muñoz et al. New Engl J Med. 2003;348:518−527.
29. Coverage and ManuscriptStaffing Plan structure Discussion Summarize key findingsBeginning State major conclusion Interpret results in context Middle of other studies Describe limitations Restate major conclusion End Applications/implications Suggest future work
30. Coverage and ManuscriptStaffing Plan structure References Cite all statements from previously published works Cite broadly from different groups in your field Use reference management software EndNote, Papers, RefWorks, Mendeley
31. Coverage and ManuscriptStaffing Plan structure Papers
32. Section 4Increasing Readability
33. Readability Readability Your reader should… Only have to read once Not have to read slowly Understand your logic immediately
34. Readability Too long Subject-verb placement Passive voiceThe largest company, a Japanese corporation founded in1916 outside of Osaka by Takahiro Tanaka, wasconsidered to be a model in the development of modernemployee conditions by economists.
36. Readability Verb placement• Readers become confused when subject and verb are separated by too much contentThe smallest ORF, a 105-nucleotide reading frame foundin the third intron of the nicotinic acetylcholine receptorβ2 subunit gene, was found to be expressed in responseto long-term treatment with 1 µM cytochalasin D.
37. Readability Avoid reader confusionThe smallest ORF, a 105-nucleotide reading frame found in the third intron of the nicotinicacetylcholine receptor β2 subunit gene, was found to be expressed in response to long-termtreatment with 1 µM cytochalasin D.The smallest ORF was found to be expressed in response to long-term treatment with 1 μM cytochalasin D. This ORF is a 105-nucleotide reading frame found in the third intron of the nicotinicacetylcholine receptor β2 subunit gene.We found the smallest ORF was expressed in response to long-termtreatment with 1 μM cytochalasin D. This ORF…
38. Readability 2. Active voice Subject Verb Active• Sentences written in the active voice are: simple direct clear easy to read
39. Readability Increasing readability: 3. Short sentences Reading once…4% of readers can understand a 27-word sentence75% of readers can understand a 17-word sentence Pinner and Pinner (1998) Communication Skills Goals to aim for: One idea per sentence 15–20 words per sentence
40. ReadabilitySubject-verb placement Passive voice Too long (30 words)The largest company, a Japanese corporation founded in1916 outside of Osaka by Takahiro Tanaka, wasconsidered to be a model in the development of modernemployee conditions by economists.Economists considered the largest company to be amodel in the development of modern employeeconditions. This company was a Japanese corporationfounded in 1916 outside of Osaka by Takahiro Tanaka.
41. Readability 4. Stress position• Readers focus on information at the end of a sentence. Subject Verb take-home information
42. Readability Stress position• Property prices increased after a 2% rise in taxes.• Property prices increased after taxes rose 2%.• A 2% rise in taxes increased property prices.• Readers, without thinking, concentrate on the end of a sentence.
43. Readability Stress position• Property prices increased after a 2% rise in taxes.• Property prices increased after taxes rose 2%.• A 2% rise in taxes increased property prices.• Readers, without thinking, concentrate on the end of a sentence.
44. Readability 5. Topic position• Readers expect a sentence/phrase to be a story about whoever shows up first Subject Topic position Verb Stress position
45. Readability Topic position sentence idea idea idea idea Topic link• Linkage and contextThe patient went to the hospital to see agastroenterologist. The doctor then performed a seriesof diagnostic tests. The results showed the patientsuffered from a bacterial infection. The patient recoveredafter a 2-week course of antibiotics.
46. Author Academy:Steps to Publication Success II University of Malaya 5 March 2013 Jeff Robens, PhD Senior Editor
49. Why publish? Exchange ideas globallyCommunicate on a global stage One publication per yearYour research is not complete until it is published
50. People want to hearInternational language from Malaysian of academics researchers Why English?International Career Funding reputation advancement Which journal to choose?
51. Section 1Journal selection
52. Journal Selection Factors to consider Aims and scope Readership Open access Publishing frequency Impact factor IF varies by fieldWhich factor is most important to you?
53. Journal Selection Choosing a target journal Journal selection must be based on an honest evaluation of your manuscript Significance Aims and Scope Impact
54. Journal Selection Evaluating significance: Novelty How new are my results compared with those already published? New findings Incremental Conceptual advances advances Low to medium Medium to high impact impact
55. Journal Selection Evaluating significance: Relevance How broadly relevant is my work? Population specific? Restricted to geographical Medical location? How common is the disease? Relevant to business or marketing?Psychology Have impact on government policy? Is my design applicable to other fields?Engineering Is it cost-effective?
56. Journal Selection Evaluating significance: Appeal Area of popular Stem cells, tissue engineering, appeal global warming, artificial intelligence Important real Rice resistant to high salt conditions, world applications shrimp resistant to infection
57. Journal Selection Journal Selector Input your abstract or selected keywords Filter your results
58. Journal Selection Visit journal websites
59. Section 2Cover Letters
60. Coverage andCover LettersStaffing Plan Make it easy Is there a Cover Letter? Are there reviewer recommendations? Is it easy to read? Inbox
61. Coverage andCover LettersStaffing Plan Significance Why your work Relevance is important! Cover letter: Abstract: First impression for journal editors First impression for readers Interesting to Level of English their readers?
62. Coverage and Cover Letters Staffing Plan Bad example Not personal No information about Dear Editor-in-Chief, the manuscript I am sending you our manuscript entitled “Techniques to detect entanglement in cats” by Schrodinger et al. We would like to have the manuscript considered for publication in Quantum Theory Frontiers. Please let me know of your decision at your earliest convenience.Too short Sincerely yours, Albert Einstein, PhD
63. Coverage and Manuscript Staffing Plan structure A good cover letterDear Dr Graeber, Editor’s name Manuscript titlePlease find enclosed our manuscript entitled “Amyloid-like inclusions in the brains of Huntington’s disease patients”, byMcGowan et al., which we would like to submit for publication as a Research Paper in Neurogenetics. Publication typeRecent immunohistochemical studies have revealed the presence of neuronal inclusions containing an N-terminal portion ofthe mutant huntingtin protein and ubiquitin in the brain tissues of Huntington’s disease (HD) patients; however, the role of Give thethese inclusions in the disease process has remained unclear. One suspected disease-causing mechanism in Huntington’s background todisease and other polyglutamine disorders is the potential for the mutant protein to undergo a conformational change to a the researchmore stable anti-parallel β-sheet structure…To confirm if the immunohistochemically observed huntingtin- and ubiquitin-containing inclusions display amyloid features, weperformed Congo red staining and both polarizing and confocal microscopy on post-mortem human brain tissues obtained What wasfrom five HD patients, two AD patients, and two normal controls. Congo red staining revealed a small number of amyloid-likeinclusions showing green birefringence by polarized microscopy, in a variety of cortical regions.... ….detected inclusions done and whatobserved in parallel sections, suggesting that only a relatively small proportion of inclusions in HD adopt an amyloid-like was foundstructure.We believe our findings will be of particular interest to the readership of Neurogenetics, which includes researchers and Interest toclinicians studying the genetic and molecular mechanisms underlying neurodegenerative diseases. Therefore, we feel that your journal’s readersjournal provides the most suitable platform for the dissemination of our work to the research community.We would also like to suggest the following reviewers for our manuscript… Recommend reviewers
64. Coverage andCover LettersStaffing PlanOriginal and Not submitted Authors agree onunpublished to other journals paper/journal “Must-have” statementsNo conflicts of Source of Authorship interest funding contributions
65. Coverage andCover Letters RecommendingStaffing Plan reviewers “Authors are requested to provide the names and full addresses (including e-mail address) of up to four potential referees…”“When submitting your paper, you must provide thenames, affiliations, and valid e-mail addresses of five (5)reviewers. If you do not do so, your paper will bereturned, unreviewed.”
66. Coverage and Cover Letters Recommending Staffing Plan reviewersWhere to find From your reading/references, them? networking at conferences How senior? Aim for mid-level researchers Collaborators (past 5 years),Who to avoid? researchers from same institution
67. Section 3Peer Review
68. Peer Review Improves your manuscript Peer review is a positive process Improves science Get involved in the peer review processhttp://www.springer.com/authors/journal+authors/peer-review-academy
69. Peer Review The submission process Peer review Results novel? Topic relevant?Author Editor Reject Revision New experiments Improve readability Accepted— Add information publication!
70. Peer Review Point-by-point Respond to Be polite every comment Revision Refer to line and page numbers Easy to see Use a different color font changes Highlight the text
71. Peer Review Writing a response letterJohn G. HunterEditor-in-ChiefWorld Journal of Surgery Address editor personally16 August 2012 Manuscript ID numberDear Dr. Hunter, Thank reviewersRe: Resubmission of manuscript reference No. WJS-07-5739Please find attached a revised version of our manuscript originally entitled “Long-term outcomes following right-lobe living donor liver transplantation,” which we would like to resubmit for consideration for publication in WorldJournal of Surgery.The reviewer’s comments were highly insightful and enabled us to greatly improve the quality of our manuscript. Inthe 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 beenrevised 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 ourmanuscript suitable for publication in World Journal of Surgery. Highlight major changes
72. Peer Review AgreementReviewer Comment: In your analysis of the data you have chosento use a somewhat obscure fitting function (regression). In myopinion, a simple Gaussian function would have sufficed.Moreover, the results would be more instructive and easier tocompare to previous results.Response: We agree with the reviewer’s assessment of theanalysis. Our tailored function makes it impossible to fully interpretthe data in terms of the prevailing theories. In addition, in itscurrent form it would be difficult to tell that this measurementconstitutes a significant improvement over previously reportedvalues. We have redone the analysis using a Gaussian fittingfunction.
73. Peer Review DisagreementReviewer Comment: In your analysis of the data you have chosento use a somewhat obscure fitting function (regression). In myopinion, a simple Gaussian function would have sufficed.Moreover, the results would be more instructive and easier tocompare to previous results.Response: We agree with the reviewer that a simple Gaussian fitwould facilitate comparison with the results of other studies.However, our tailored function allows for the analysis of the datain terms of the Smith model [Smith et al, 1998]. We have addedtwo sentences to the paper (page 3 paragraph 2) to explain theuse of this function and Smith’s model.
74. Peer Review “Hidden” questionsReviewer comment: The authors hypothesized to look for thepharmacokinetics of the insulin using this 4 mm needle; howeverthey didnt do bioequivalence analyses for glucosepharmacodynamics. That is one of my concerns about thismethodology.Response: Although we wanted to do the bioequivalenceanalyses for glucose pharmacodynamics in our study, we areunable to because…
75. Section 4Avoiding Rejection
76. Avoiding Rejection The research Current state of the field Relevant hypothesis Identified knowledge gap Appropriate Up-to-date and valid methods methodology New methods validated Appropriate statistical analysis Good data analysis Consult a statistician Complete data All data are included or discussed Valid conclusions Based on your data
77. Avoiding Rejection The manuscriptJournal requirements Citations Rationale and aims Grammar Appropriate data and style presentation
78. Avoiding Rejection The manuscript Clearly state your aims Why did you do it? Why is it important? What are the implications?
79. Avoiding Rejection The manuscript Meet journal requirements Research is appropriate for the aims/scope of the journal Follow the author guidelines for formatting
80. Avoiding Rejection Reasons for rejection: the manuscript Appropriate journal selected Journal currently publishing similar papers
81. Avoiding Rejection Reasons for rejection: the manuscript Citations Cite properly • Broadly from different research groups • A couple of older seminal papers • A couple of review articles • Mostly recent original articles • Use reference management software
82. Avoiding Rejection Reasons for rejection: the manuscript Write clearly Check spelling and grammar Microsoft Word “spell check” Customize Microsoft’s dictionary High readability
83. Avoiding Rejection Reasons for rejection: the manuscript Appropriate data presentation Logical representation Do not duplicate results Only relevant data
84. Avoiding Rejection Rejection letter from NeuroRehabilitation…judged to be unsuitable for publication in NeuroRehabilitation... The following factors contributed to the final decision: The literature review was incomplete The hypothesis is not mentioned or unclear The subjects’ details are not included The manuscript does not follow journal format The authors draw conclusions that are inappropriate or unsubstantiated The statistical methodology is inappropriate, incorrect, or incomplete The manuscript is poorly written…
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