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    20120829 edanz kanagawa 20120829 edanz kanagawa Presentation Transcript

    • How to Write and Publish Case Studies Kanagawa Children’s Medical Center Jeff Robens, PhD Senior Editor Edanz Group 29 August 2012
    • About Jeff…Researcher, Teacher, Mentor…
    • About Jeff… Author Senior Editor
    • Today’s presentation …Section One: Scientific publication The publication process General considerations Manuscript structureSection Two: Case studies Clinical case reports Gene analysis original articles Tissue pathology reports
    • Scientific Publication Why publish? Exchange ideas globally Communicate with your peers on a global stage Your research is not complete until it is published! Establish track record Career advancement
    • Scientific Publication Why in English? Good Japanese journals are available English is the international language of science Other clinicians and scientists want to hear from Japanese researchers!
    • Scientific Publication Publishing timeline Submission to publication, 3–24 months Submit Editor: Reviewer Peer Selection Review Accepted Published!manuscript Review? Return to To save time, suggest authors possible reviewers to the journal editor Reviewers Authors Resubmit revisions
    • Scientific Publication High quality research Good design Original and novel Well executed What do journal editors want? Interesting to Clear and concise journal’s readership English
    • Before you start … 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 Discuss with colleagues
    • Before you start … 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
    • Before you start … Strategies for reading Read Title and Abstract first Self-assess knowledge of topic Read last paragraph of introduction for hypothesis/objectives Read Figures and Results Read Discussion for interpretation Refer to Introduction and Methods if necessary
    • Before you start … Journal selection
    • Before you start … Factors to consider Aims and scope Target audience Publishing frequency Indexing status Open access Impact factor Which factor is most important to you?
    • Before you start … Choosing a target journal Journal selection must be based on an honest evaluation of your manuscript Novelty Aims and Scope Significance Impact
    • Before you start … 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
    • Before you start … Evaluating significance: Novelty Bartlett et al. (2011). Am J Clin Path. 136:266. Incremental advances Conceptual advances Okita et al. (2007). Nature 448:313.
    • Before you start … Evaluating significance: Relevance Regional significance?Are your findings specificto a geographical region or ethnic population? Global significance?
    • Before you start … Evaluating significance: Appeal Is my work in an area of ‘popular appeal’ Examples: Emerging diseases Higgs boson Stem cells Global warming Tissue engineering Artificial intelligence
    • Before you start … Journal Advisor– A free service from Edanz
    • Before you start … Journal Advisor– A free service from Edanz Insert your proposed abstract
    • Before you start … Journal Advisor– A free service from Edanz Recommended journals Advanced Matching
    • Before you start … Journal Advisor– A free service from Edanz Recommended journals Advanced Matching
    • Before you start … Journal Advisor– A free service from Edanz Refined recommended journals
    • Before you start … Journal Advisor– A free service from Edanz Semantic matching terms Journals IF, Aims & Scope, and Frequency Similar published articles
    • Before you start … Journal Advisor– A free service from Edanz Insert your proposed abstract
    • Before you start … Journal Advisor– A free service from Edanz Recommended journals Advanced Matching
    • Before you start … Journal Advisor– A free service from Edanz Semantic matching terms Journals IF, Aims & Scope, and Frequency Similar published articles
    • Before you start … Publication ethics Multiple submissions Improper author contribution Conflicts of interest Data fabrication and falsification Plagiarism Online resources International Committee of Medical Journal Editors http://www.icmje.org/ Committee on Publication Ethics (COPE) http://publicationethics.org/
    • Structuring your manuscript Section threeYou are telling a storyMust be easy to read and easy to understand
    • Structuring your manuscript ‘Tell them three times’ Beginning ‘tell them what you did and why’ Middle ‘tell them how you did it and what you found’ End ‘tell them again what you did and what it means’.
    • Structuring your manuscript IMRaD Abstract Introduction The beginning Methods The middle Results and Discussion The end
    • Structuring your manuscript The ‘write’ order Methods Results During your research Introduction Discussion After selecting target journal Title Abstract Write last
    • Structuring your manuscript Manuscript title World Class Manuscript IntroduceGrab reader attention manuscript to editor Index label Convey main topics Be specific and concise Avoid jargon, abbreviations and acronyms
    • Structuring your manuscript Abstract Brief (100–250 words) Describe problem(s) addressed Objectives/hypotheses Techniques; avoid details Most important results Concluding statement
    • Structuring your manuscript Introduction Sufficient background information Puts your work into context General Specific Comprehensive literature review Cite reviews
    • Structuring your manuscript Methods Subheadings with multiple methodsNew methods must be described in sufficientdetail that they can be reproduced Established methods can be referenced
    • Structuring your manuscript Results Do not explain the results Avoid duplicating data among figures, tables and text Past tense to describe your results
    • Structuring your manuscript Figures - Display items Present a large amount of data quickly andefficiently Keep it simple — use separate panels ifnecessary Label all parts of your figures Legends must be able to ‘stand alone’
    • Structuring your manuscript Tables Clear concise legend/caption ) Dataformattedfor clarity Abbreviations defined
    • Structuring your manuscript Figures Scale bars Clear, ‘standalone’ legend Axes labeled
    • Structuring your manuscript Discussion Beginning Avoid repeating the results section Answer the research question(s) posed Last paragraph of your introduction Emphasize the major finding(s) first What is your major conclusion, based on the results you have presented?
    • Structuring your manuscript Discussion Middle Interpret your results Compare with other studies Same or different? Unexpected results Briefly describe limitations How could experiments be improved?
    • Structuring your manuscript Discussion End Restate major conclusion(s) In summary … or In conclusion … Possible applications and implications Suggest future work“In conclusion, pancreatic metastasis of ovarian papillary serousadenocarcinoma has to be kept in mind when a patient with pancreaticmass has a history of ovarian malignancy. Surgical approach may offer thechance of longer survival in pancreas metastasis. Since pancreas resectiondue to pancreatic metastasis of ovarian cancer rarely reported, weconsider it worthwhile to report this case.” – Gunay, Demiralay, & Demirag. Case Reports Med. 2012
    • Structuring your manuscript ReferencesAlways format your references! Check journal guidelines Both in text and reference sectionUse reference management software EndNote, RefWorks, Mendeley, Zotero
    • First section today…Section One: Scientific publication The publication process General considerations Manuscript structureAny Questions?
    • Section Two – Case Reports 1. Clinical case reports 2. Genetic analysis studies 3. Tissue pathology reports
    • Case Reports Unusual New or emerging presentation of disease disease What is publishable? New or unusual New treatment or adverse effect of diagnosis treatment
    • Case Reports Extensive database General online search for published Medical forums searches articles Is my finding novel? Be careful with your terminology during your searches Try to also use ICD codes from WHO for consistency Cases may be unpublished, but their treatments may be already clinically acceptedSo even if yours is the first case to be published, it now lacks educational/clinical value
    • Case Reports Why historically difficult to publish? Most case studies are not highly cited…lowerthe impact factor of a journalBut case studies are significant!A series of case studies can often show newdisease patterns
    • Case Reports General considerationsTell a story! Timeline of events…Short, 500-1500 wordsWrite simple and concisely Be careful with using “he” and “she”, be specific when referring to patient’s family members or other patients Needs to have educational value in additionto novelty Kukreja et al. BMJ Case Reports 2011.
    • Case Reports General considerations Why is this patient interesting? Disease-Related Treatment-Related Unusual/new disease New treatment Unusual presentation Unusual adverse effect New method of diagnosis
    • Case Reports Manuscript structureResearch Paper Case ReportTitle/abstract Title/abstractIntroduction IntroductionMethods Case presentationResults Treatment/Follow-upDiscussion Discussion ConsentReferences References
    • Case Reports Title: A case report Should be short and specific to patient Informs the reader of the condition, unique presentation, and case report
    • Case Reports Title exercise Background: Lithium used for bipolar disorder Lithium therapy can cause thyroid disorders But thyromegaly/thyrotoxicosis is very rare Thyromegaly rarely causes airway obstruction
    • Case Reports Title exerciseCase presentation: 1995-2001: lithium treatment for bipolar disorder 2001: thyrotoxic goiter, prescribed Methimazole 2002: thyroid resection, only removed right lobe Remained on lithium and Methimazole until 2007 2007: (42) admitted with seizures and respiratory distress Massive thyromegaly obstructing the upper airway Thyroidectomy and withdrawal of lithium
    • Case Reports Title exerciseConclusion: Lithium-induced thyromegaly is rare Thyromegaly-induced airway obstruction is rare But this is a potentially lethal side effect of lithium treatment, so should be monitored (long-term) Surgery is an effective and the preferred treatment
    • Case Reports Title exercise Lithium has been used to treat biopolardisorder for 60 years 42-year old patient treated with lithium hadrespiratory distress and asphyxiation Lithium can cause thyroid disorders Thyromegaly can cause airway obstruction Thyroidectomy is effective treatment
    • Case Reports Title exercise A case of 42-year old man presenting withairway obstruction caused by lithium Lithium associated thyromegaly: An unusualcause of airway obstruction Bipolar disorder presenting with unusualairway obstruction
    • Case Reports AbstractShort, but can vary with journalStructured or unstructured (story) Introduction Why does this case need to be reported? Patient Age, gender, ethnicity information Case Symptoms, diagnosis, management, follow-up presentation Conclusion Clinical impact, learning points
    • Case Reports AbstractReports of epithelial ovarian carcinomas metastatic to the pancreasare very rare. We herein present a metastasis of high grade papillary Introductionserous ovarian cancer to mid portion of pancreasA 42-year old patient was admitted with a non-specified malignant Patientcystic lesion in midportion of pancreas. She had a history of surgicaltreatment for papillary serous ovarian adenocarcinoma. InformationA cystic lesion was revealed by an abdominal CT performed in herfollow up. It was considered as primary mid portion of pancreatic Casecancer and a distal pancreatectomy was performed. The finalpathology showed high grade papillary serious adenocarcinoma Presentationmorphologically similar to the previously…Pancreatic metastasis of ovarian papillary serous adenocarcinomahas to be kept in mind when a patient with pancreatic mass has a Conclusionhistory of ovarian malignancy. Gunay et al. (2012). Case Reports Med.
    • Case Reports Introduction: Why is this important? Short Background why case is worth reporting Disease-related: explain usual presentation and progression Treatment-related: explain previously reported side effects or complications Describe relevant cases in the literature Explain why this is important
    • Case Reports Introduction: Why is this important?We describe a case of a patient with Anton’s syndromeand it’s (sic) associated features. Not clear… Evaluate the Maddula et al. (2009). J Med Case Reports. significance ofTo our best knowledge, pancreatic metastasis of your findingsovarian cancer is uncommon and only a few caseshave been reported in the literature. We here report a Clearrare metastasis of papillary serous ovarianadenocarcinoma mimicking primary pancreatic cancer. Gunay et al. (2012). Case Reports Med.
    • Case Reports Case presentation: The patient’s story Age, gender, ethnicity Why did they come to see you? Introduce the patient Previous diagnoses Family history Types of tests performed Diagnostic tests Factual description of results Maintain confidentiality
    • Case Reports Treatment & follow-upWhat treatments were givenPatient’s response (even if negative)Duration of treatmentDid the patient improve? Recover?Subsequent medical health/death of patient,even if unrelated
    • Case Reports Discussion Explain and interpret your findings Summary of report Express your opinions and hypotheses Other cases about the same disease Presentation seen in other diseasesContext of relevant cases Other side effects for same treatment Side effects seen in other treatments
    • Case Reports Discussion Incomplete background/family history Diagnostic/technical Limitations Specificity of results/narrow focus Geographical/demographical Direction of future treatmentsValue case adds to the literature or investigationAlthough the incidence of kidney injury among patients receiving VEGFinhibitors is not known, our data suggests that it may be prudent to monitorpatients receiving VEGF inhibitors closely for possible kidney injury. The optimalway to monitor such patients is not known… Eremina et al. (2008). New England Journal of Medicine.
    • Case Reports Other important items Consent: Always obtain informed consent from patient and/or family members References: Much less than research article (~15) Up-do-date research and treatments Relevant cases
    • Genetic Analysis Genetic analysis studies Similar to case reports Usually based on a unique presentation IMRaD manuscript structure Understand genetic mutations Different genetics = different presentation
    • Genetic Analysis General considerations Why did you focus on this gene/mutation? Is this gene associate with the disease? Extensive search on target sequence (e.g. polymorphisms) Found in healthy controls or in others with the disease? Is it hereditary? Do family members have the disease? How does this mutation affect the disease? To strengthen argument, may need in vitro (cell culture) or in vivo (animal models) evidence
    • Genetic Analysis Material and methods Brief case report/patient background Explanation of techniques used Statistical methods Shorter than research paper, so be brief Citations help you save space
    • Genetic Analysis Results Clearly explain genetic analyses used Identify mutations at both DNA and protein levels Use proper nomenclature when describing your results HUGO Gene Nomenclature Committee (HGNC) www.genenames.org Morphological features of human patients: “Elements of Morphology: Standard Terminology” http://onlinelibrary.wiley.com/doi/10.1002/ajmg.a.v149a:1/issuetoc
    • Genetic Analysis Tips – Gene nomenclature Italicize gene names (PPARG) Species-specific capitalization Human/primates (all capitalized): PPARG Rodent (only first letter capitalized): Pparg Never use Greek letters, or Roman numerals in gene names TGFB1 ABCG1 not not TGFβ ABCGI
    • Genetic Analysis Figures – Genetic display items Family Tree – Phenotypic Loci location presentation Genetic history Genomic structure Mutation in protein
    • Genetic Analysis Conclusions Implications for disease progression Common or rare? Affect treatment? What do these mutations mean? Geographically or What do they teach ethnically specific? us about the disease?
    • Coverage andTissue Pathology Staffing Plan General considerations Unique presentation of tissue pathology Wide variety of tissue pathological reports Genetic mutations Cancers Disease interaction Adverse effects of therapeutic treaments
    • Coverage andTissue Pathology Staffing Plan Manuscript structure Introduction Case Presentation Patient(s) and Methods (Histological methods ) Discussion
    • Coverage andTissue Pathology Staffing Plan Methods Short, but should include… Tissue preparation Staining procedure Microscopy Formalin-fixed H&E staining Microscope Paraffin-embedded Immunohistochemistry Magnification
    • Coverage andTissue Pathology Staffing Plan Figures In imaging, clear figures are crucial! …shows silver staining of two representative glomeruli in biopsy specimens from patients. In Patient 4 (left), mesangiolysis (single arrow), prominent demonstrating distorted brachial artery and “AHLE endothelial swelling (arrowhead), red-cell fragments (double arrows), classical small vessel proliferation” and thrombi are visible in some capillary loops… Eremina Kukreja et al. The New England Journal of Medicine. et al. (2008). (2010). BMJ Case Reports.
    • Coverage andTissue Pathology Staffing Plan Figures - Tips In imaging, clear figures are crucial! Compressed vs. Uncompressed 8-bit vs. 16-bit 72 ppi vs. 300 ppi RGB vs. CMYK
    • Coverage andTissue Pathology Staffing Plan Figures – Tips Uncompressed vs. Compressed Uncompressed images are your raw images Compressed images: lossless or lossy Lossless: all image information is preserved – larger files Lossy: selectively discards information – smaller files Cannot distinguish differences by eye But you will lose information if you compress Can always keep a compressed copy available
    • Coverage andTissue Pathology Figures – Tips Staffing Plan TIFF vs. JPG TIFF JPG 3.3 MB 1.8 MB
    • Coverage andTissue Pathology Figures – Tips Staffing Plan 8-bit vs. 16-bit Human eye can see about 10 million colors “Bit” is about how many colors there are What is 8-bit? 28 shades of grey/color (256) 8-bit RGB: 256 red x 256 green x 256 blue =16.7 million colors 16-bit? 216 = 65,536 shades/color 16-bit RGB: 281 trillion colors!
    • Coverage andTissue Pathology Staffing Plan Figures - Tips So why use 16-bit? Just because you cannot see it, does notmean it is not there Important in quantitative image analysis Flexibility in image adjustments Only uncompressed images can be saved in16-bit
    • Coverage andTissue Pathology Figures – Tips Staffing Plan 16-bit vs. 8-bit 16-bit 8-bit 6.5 MB 3.3 MB
    • Coverage andTissue Pathology Figures – Tips Staffing Plan 16-bit vs. 8-bit 16-bit 8-bit Started with 65,000 Started with 256 shades of gray shades of gray Still have ~40,000 (60%) Now have only 152 (60%)
    • Coverage andTissue Pathology Staffing Plan Figures - Tips ppi: pixels per inch For online/monitor use, 72 ppi is fine For printing, need at least 300 ppi Most journals require that final figures are atleast 300 ppi for printing purposes
    • Coverage andTissue Pathology Staffing Plan Figures - Tips • Colors used in printing • Primary colors of light • Most journals require CMYK images • Used in TVs and monitors RGB → CMYK can be unclear • • Most microscopes take pictures into make sure your image looks • Check RGB good in CMYK (Photoshop Ctrl+Y for CMYK preview mode)
    • Coverage andTissue Pathology Staffing Plan Figures - Tips
    • Coverage andTissue Pathology Staffing Plan Conclusions What is unique or novel? Geographically/ethnically specific? What does this pathology mean? Does it affect treatment? What does it teach us about disease pathophysiology?
    • Today’s presentation …Section One: Scientific publication The publication process General Considerations Manuscript structureSection Two: Case studies Clinical case reports Genetic analysis studies Tissue pathology reports
    • Thank you for your attention! Questions?