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    130327 Edanz Hiroshima 130327 Edanz Hiroshima Presentation Transcript

    • How to Write for and Publish in Academic Journals Hiroshima University 27 March 2013 Jeff Robens, PhD Senior Editor
    • Today’s presentation …Reading strategiesIncreasing readabilityCommon mistakesAbstractsCover lettersPeer review and revision
    • Section 1Reading Strategies
    • 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
    • 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
    • Reading Strategies Strategies for reading Have you read similar papers? Read Title and Abstract first Familiar with the terminology? Self-assess knowledge of topic Do you understand the relevance of the hypothesis
    • 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
    • Section 2Increasing Readability
    • Readability Readability Your reader should… Only have to read once Not have to read slowly Understand your logic immediately
    • 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.
    • Readability 1. Verb placement• Readers expect verbs to closely follow subjects Subject Sentence Verb Verb
    • Readability Verb placement• Readers become confused when subject and verb are separated by too much contentThe 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.
    • Readability Avoid reader confusionThe largest company, a Japanese corporation founded in 1916 outside of Osaka by Takahiro Tanaka,was considered to be a model in the development of modern employee conditions by economists.The largest company was considered to be a model in thedevelopment of modern employee conditions by economists. Thiscompany was a Japanese corporation founded in 1916 outside of…Economists considered the largest company to be a model in thedevelopment of modern employee conditions. This company was aJapanese corporation founded in 1916 outside of…
    • Readability 2. Active voice Subject Verb Active• Sentences written in the active voice are: simple direct clear easy to read
    • 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
    • Readability 4. Stress position• Readers focus on information at the end of a sentence. Subject Verb take-home information
    • 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.
    • Readability 5. Topic position• Readers expect a sentence/phrase to be a story about whoever shows up first Subject Topic position Verb Stress position
    • Readability Topic position sentence idea idea idea idea Topic linkThe 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.
    • Section 3Common Mistakes
    • Common mistakes Comparisons • Needed in Results and Discussion sections • Compare ‘like’ with ‘like’ • Use ‘with’, not ‘to’ The tumor excised from the pancreas was compared to the liver.The tumor excised from the pancreas was compared with thatThe tumor excised from the pancreas was compared with the liver.from the liver.
    • Common mistakes ‘Between’ or ‘among’?• Use between for comparisons of two groups… the only difference between the original moleculeand the new molecule is ...• Use among for comparisons of more than two groups … significant differences were observed in the values among bio-, fully- and semi-synthetic molecules
    • Common mistakes Respectively• ‘Respectively’ is often misused• Used to refer to two corresponding lists – The two values were 143.2 and 21.6, respectively. – The two values were 143.2 and 21.6. – The two tubes were labeled B and S, respectively. – The tubes containing blood and saline were labeled B and S, respectively.
    • Common mistakes ExampleOxygen detector flow Nitrogen detector flow Hydrogen detector flow85 mL/min 7 mL/min 4 mL/minThe oxygen detector flow was set at 85 mL/min; the nitrogendetector flow was set at 7 mL/min; and, the hydrogen detectorflow was set at 4 mL/min. 28 wordsOxygen, nitrogen and hydrogen detector flows were set at 85, 7and 4 mL/min, respectively. 15 words
    • Common mistakes Colons and semi-colons• Colons (:) are used to introduce a list• Semicolons (;) are used to separate the items in a list too long for commas• Use ‘and’ before the last item in the list There are a number of journals for surgery manuscripts: General Surgery, published by Springer; the World Journal of Emergency Surgery, published by BioMed Central; and the British Journal of Surgery, produced by Wiley & Sons.
    • Section 3Simple Language
    • Simple language Make it easy for your reader • Simple language is best • Makes your work more relevant • Maximizes understanding • Science is complex
    • Simple language Simple wordsAvoid Preferredadditional moreadequate enoughapparent clearattempt trydemonstrate showendeavor tryexceedingly very
    • Simple language More simple wordsAvoid PreferredMagnitude SizeObjective AimPerformed DoneRequested AskedRetain KeepSubsequently LaterSufficient EnoughTerminate EndUtilization Use
    • Simple language Unnecessary wordsIn order to determine the rate of the reaction, we measured… To determine the rate of the reaction, we measured…
    • Simple language Examples of unnecessary wordsAvoid PreferredFor the reason that BecauseIn the first place FirstIn the not too distant future SoonFour in number FourGreen color GreenSubsequent to AfterPrior to BeforeExcept in a very few instances Usually
    • Section 4Abstracts
    • 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
    • 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%)
    • 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.
    • 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.
    • 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.
    • 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.
    • 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 a genome-wide analysis of DNA methylation of humanpreadipocytes and mature adipocytes to examine the differences in methylationbetween them.We found hypomethylation occurring in 2,701 genes and hypermethylation in 1,070genes after differentiation. Meanwhile, Gene Ontology analysis and Ingenuity PathwayAnalysis showed many significant gene functions and pathways with altered methylationstatus after 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 mechanisms may be involved in regulating thedifferentiation process of human preadipocytes. Zhu et al. (2012) Cell Biochem Biophys 63:1‒15.
    • 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.
    • 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.
    • Abstracts References Abbreviations Don’t include… Non-essential Jargon numbers & statistics
    • 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.
    • Abstracts Graphical Abstracts Composite of RhyCr2‒yO3/(Ga1‒xZnx) (N1‒xOx) photocatalysts with hydrophobic polytetrafluoroethylene (PTFE) membranes for the fabrication of novel reaction sites for water vapor splitting under visible lightRh y Cr2−y O3/(Ga1−x Zn x )(N1−x O x ) photocatalysts immobilized in polytetrafluoroethylene(PTFE) membranes has been investigated for the design of novel reaction sites. In the caseof hydrophobic PTFE membranes, the Rh y Cr2−y O3/(Ga1−x Zn x )(N1−x O x ) photocatalystsimultaneously evolved both H2 and O2, even from an aqueous AgNO3 solution as sacrificialreagent. This indicates that water vapor was split into H2 and O2 by the Rh y Cr2−y O3/(Ga1−xZn x )(N1−x O x ) photocatalyst particles in the hydrophobic pores of PTFE. Isogai et al. (2013) Catalysis Letters 143:150‒153.
    • Abstracts Graphical AbstractsComposite of RhyCr2‒yO3/(Ga1‒xZnx) (N1‒xOx) photocatalysts with hydrophobic polytetrafluoroethylene (PTFE) membranes for the fabrication of novel reaction sites for water vapor splitting under visible light Isogai et al. (2013) Catalysis Letters 143:150‒153.
    • Section 5Cover Letters
    • Coverage andCover LettersStaffing Plan Make it easy Is there a Cover Letter? Are there reviewer recommendations? Is it easy to read? Inbox
    • 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?
    • 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
    • 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
    • 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
    • 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.”
    • 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
    • Section 6Peer Review
    • 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 Where does the peer review process fit in?
    • Peer Review The submission process Peer review Results novel? Topic relevant?Author Editor Reject Revision New experiments Improve readability Accepted— Add information publication!
    • 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
    • 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
    • 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.
    • 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.
    • 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…
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