Qureshi Manual of Scientific Manuscript Writing for Medical Journals: An Essential Guide for Medical Students, Residents, Fellows, and Junior Faculty
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About this ebook
Adnan I. Qureshi MD
Dr. Qureshi is recognized as a leader in research pertaining to interventional neurological procedures and acute stroke management. He has written over 300 scientific publications in prestigious journals such as the New England Journal of Medicine, Lancet, Archives of Internal Medicine, Critical Care Medicine, Neurology, Stroke, and Circulation. Dr. Qureshi has made over 500 presentations in various national and international meetings. He has been a speaker at numerous national and international forums, plus has been invited as a visiting professor to universities in the USA and abroad. The attributes with specific relevance to the project are described below: Leadership in interventional neurology Dr. Qureshi is one of the first neurologists in the world to train in neurointerventional procedures. He subsequently established the first interventional neurology service and training program at University of Medicine and Dentistry of New Jersey (UMDNJ) in 2002. He served as the Chair-elect and Chair of the Interventional Section at the American Academy of Neurology (AAN) from 2003 through 2007. In 2006, he founded and has since served as the President of the Society of Vascular and Interventional Neurology. He is also the Chair of Research Subcommittee, American Society of Interventional Therapeutic Neuroradiology, and Ex-officio Member, Executive Council of the American Association of Neurological Surgeons/Congress of Neurological Surgeons, Cerebrovascular Section. He was a representative from the AAN for the carotid artery stenting multi-specialty working group. He is the neurointerventional section editor of the Journal of Neuroimaging and the chief editor of both the Journal of Vascular and Interventional Neurology and the International Journal of Biomedical Sciences.
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Qureshi Manual of Scientific Manuscript Writing for Medical Journals - Adnan I. Qureshi MD
Contents
Acknowledgement
Chapter 1
Chapter 2
Chapter 3
Chapter 4
Chapter 5
Chapter 6
Chapter 7
Chapter 8
Chapter 9
Chapter 10
Chapter 11
Chapter 12
Chapter 13
Acknowledgement
I would like to express my deep and sincere gratitude to Cathie Witzel for her secretarial assistance, detailed review, and constructive comments, throughout the preparation of this book. I would also like to thank numerous medical students, researchers, residents, and fellows who gave me the motivation to strive to be a better educator over the years. Over the years, nothing has paralleled for me the joy that I felt in witnessing the success of my trainees and thank all of them to allow me to be a part of their success. I recite the quotation by my trainees inscribed on a plaque that states Let Each of Us Aspire to Inspire, Before We Expire
that should serve as a guiding light for all of us.
Chapter 1
PRINCIPLES OF SCIENTIFIC
MANUSCRIPT PREPARATION
Why should you publish
Sharing of medical knowledge is an essential component of responsibilities jointly shared by all physicians. The prompt and widespread dissemination of medical knowledge derived from a variety of sources alert scientists to the potential of new areas of research and facilitate the training of new physicians and researchers. Public availability of such findings allows independent testing and ultimate verification or rejection by other practitioners and researchers. Campbell and Blumenthal stated The free and open sharing of scientific information, data, and materials is a fundamental ideal underlying the social structure of science. The importance of data sharing is clearly illustrated by the inscription on the statue of Albert Einstein in front of the National Academy of Sciences:
The right to search for truth implies also a duty: one must not conceal any part of what one has recognized to be true." ¹
http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2002_05_31/noDOI.5822398718525511595
The American Medical Association policy emphasizes the same issues and states
In the ethical tradition expressed by Hippocrates and continuously affirmed thereafter, the role of the physician has been that of a healer who serves patients, a teacher who imparts knowledge of skills and techniques to colleagues, and a student who constantly seeks to keep abreast of new medical knowledge. Physicians have an obligation to share their knowledge and skills and to report the results of clinical and laboratory research. Both positive and negative studies should be included even though they may not support the author’s hypothesis. This tradition enhances patient care, leads to the early evaluation of new technologies, and permits the rapid dissemination of improved techniques. The intentional withholding of new medical knowledge, skills, and techniques from colleagues for reasons of personal gain is detrimental to the medical profession and to society and is to be condemned. Prompt presentation before scientific organizations and timely publication of clinical and laboratory research in scientific journals are essential elements in the foundation of good medical care.
²
The National Institutes of Health (NIH) defines research data as recorded factual material commonly accepted in the scientific community as necessary to validate research findings.
NIH affirms its support for the concept of data sharing and states data sharing is essential for expedited translation of research which results into knowledge, products, and procedures to improve human health.
³
The failure to communicate medical knowledge through effective means and its adverse consequences were highlighted in the failure to prevent and treat Caisson disease during the building of Brooklyn Bridge. Dr. Andrew Smith first utilized the term Caisson disease
in 1873 describing 110 cases of decompression sickness including chief engineer Washington Roeblingas the physician in charge during construction of the Brooklyn Bridge. A lack of recognition and appropriate treatment at that time resulted in several instances of permanent disabilities and deaths. Ironically, in 1872, Friedburg had already recognized that intravascular gas was released by rapid decompression and recommended: slow compression and decompression; four-hour working shifts; limit to maximum depth 44.1 psig (4 ATA); using only healthy workers; and recompression treatment for severe cases. If such information was disseminated in a timely fashion through publications, perhaps some of those cases and permanent sequelae could have been prevented.
Apart from the broader implications, scientific publications are an important venue for academic recognition and one of the metrics used for advancement along the academic ranks. For example, most academic institutions require at least 18 peer reviewed publications (at least a third of them first authored by the candidate) for advancement from Assistant Professor to Associate Professor. While no clear numeric criteria exist, most applicants who are being considered for promotion from Associate to Full Professor have 50 or greater peer reviewed publications. Publications also represent a mode for immortalizing ones contribution in the eyes of current and incoming generations of medical professionals.
Why most medical professionals do not publish scientific manuscripts
A crude observation would suggest that most of the medical literature is written by less than 10% of medical professionals. Such an observation appears paradoxical given the importance of scientific manuscripts discussed in the previous section. In my experience, nine out of every ten medical students, residents, and fellows will attempt to write a manuscript during their training. Yet, after finishing their training, only 1 or 2 will continue to write scientific manuscripts. Such a dramatic attrition is based on two reasons:
1. The effort involved in preparing a manuscript
Most medical students, residents, fellows, and even junior faculty consider writing a scientific manuscript harder than working grueling hours on the clinical service. The average novice takes between 3 and 6 months to complete a manuscript. I am surprised by the highly prevalent mind block
most trainees or even junior faculty experience in their early years of publishing. There are two methods by which most authors overcome the mind block
. Either they prepare a very scanty draft which is considered an outline rather than the desired product, or they prepare an extensive draft based on compilation of summaries of previous studies without a cohesive theme or even a clear relationship to the theme of the manuscript. Unfortunately, such efforts result in alienating the senior co-authors and even may result in the author quitting prior to manuscript completion. An organized method of approaching writing of manuscript would result in focused effort with a much higher yield.
2. Misplaced expectations
Most medical students, residents, and fellows expect that the manuscript they prepare and submit will be followed by an acceptance letter from the Journal. However, the reality even for long-standing authors is quite different. Most submissions (≈80%) will be rejected by the first journal of submission. Approximately 20% will be returned with a recommendation for revision. In my experience, 1-2% of publications may be accepted as a first submission. In my portfolio, 80% of published articles are a result of acceptance after revision in the second or third journal of submission. Unfortunately, my years of experience have not influenced these statistics to any significant magnitude. I am appalled that one third of the medical students, residents, and fellows would not consider submitting a rejected manuscript to another journal. An appropriate set of expectations would have prevented crippling disappointment.
Types of manuscripts
The manuscripts are broadly divided into Original research and Reviews. The details and subdivisions are provided in the Table below:
The definitions of various forms of Reviews are based on definitions provided by AHRQ⁴ http://www.effectivehealthcare.ahrq.gov/index.cfm/glossary-of-terms/?pageaction=showterm_and_termid=39
Basic principles of manuscript quality
I recommend that the authors consider the quality of the manuscript in the following domains:
The judgment categories are not defined as such in the Reviewers’ comments but can be deduced from the content of the comments.
Theme/objectives:
The least quantitative of the four elements is theme or objectives. A Journal may make the decision based on novelty standard, level of evidence, and/or reader interest. For example, the New England Journal of Medicine, JAMA, Lancet, and Nature are going to require a much higher standard for novelty than other journals where confirmatory studies may be acceptable. Similarly, level of evidence that is not based on a randomized controlled clinical trial is unlikely to change major practices and thus may not reach the priority required for the Journals with the highest impact factor. Similarly, a manuscript describing the extracellular ion shifts in an experimental model is unlikely to be considered of high reader interest for any journal with predominant readership of clinicians. However, I have found that most authors by review of previously published articles in the Journal, are good at identifying the readership interest in target journal. I have found that resubmission to another journal with a more favorable outlook is required to address the fatal flaw.
Methods used:
Any flaw identified during conduct of study or data collection is very difficult to address because redoing the study is not practical. Any flaw identified in the analysis plan is remediable because the study conduct or data collection does not require repetition. A fatal flaw is where the reviewer either requires part or all of the study to be redone or does not believe that the current methodology provides any valid information (even short of the primary objectives). If a reviewer has identified a fatal flaw, it is unlikely the Journal that requests the review is going to accept the manuscript. The author has to identify what valid information the study provided and focus on the valid components in the resubmission to another journal. The most daunting task for Reviewers is the use of Complex statistical methods in the manuscript. The Reviewers or Editors may request an independent statistical review and send the manuscript for review by a statistician. Alternatively, the Editor may request that authors to have a statistician at their institution review the manuscript and write a letter supporting the methodology. The authors should only use complex statistics if no other method would suffice. Using complex statistics is unlikely to increase the credibility of findings in most cases but raises the scrutiny in the Review process.
Accuracy of results:
If the reviewer has any question about the accuracy of the data, the article is doomed except in infrequent circumstances where the Reviewer may not be entirely definite about his concerns for accuracy and wants to give the author the benefit of doubt. An impression of providing inaccurate results may affect the credibility of the authors for future submissions so the importance of avoiding such a situation cannot be overemphasized.
Now the question becomes how does a Reviewer identify the flaws in accuracy of results. I present details because such methods can be used by the authors to confirm the validity of their work prior to submission. The Reviewer does not have the raw data to perform an independent statistical analysis. However, the Reviewer can make assessment of the quality of data by comparing numbers between Abstract, Results, and Tables. If there is any incongruence, the Reviewer will be understandably concerned. The Reviewer can also add the numbers in various subgroups to ensure that the total numbers are matching the numbers. For example, a statement like A total of 63 patients were included in the study, of which 22 were treated with surgery and 40 were treated using best medical management,
would prompt an astute Reviewer to recognize that 22 and 40 do not add up to 63. The Reviewer may also use the event rates in treated and control groups to assess the estimates provided in the Results or Tables. Such a second estimate is based more on the direction and magnitude of association because in the absence of raw data in the multivariate analysis, the precision of estimate cannot be estimated. For example, if the event rate for death in medically treated patients was 25% and the event rate in surgically treated patients was 12%, the odds ratio or relative ratio of 1.1 instead of values between 1.7 and 2.1 will raise concerns. The last tool the Reviewer has is the value and precision of estimates from previous literature. In every instance, when the values are markedly different from those identified in previous studies, the Reviewer is bound to look at the Results more carefully. For most instances, each analysis will include co-variates that have been studied in previous studies. For example, while the study may be identifying the contribution of a new risk factor in determining death in a cohort of elderly individuals, the analysis may include cigarette smoking as a co-variate and the direction and magnitude of association between cigarette smoking and death is known from previous studies. Infrequently, the authors may have published previous articles from the same cohort and comparison between values for common endpoints between the two manuscripts is available for validation to the Reviewer. For example, if the authors report a 10% rate of 1 month mortality in the first 100 patients and 25% in the first 150 patients (including the first 100 patients), an astute Reviewer is bound to recognize that there is an atypical aggregation of deaths in the last 50 patients. Therefore, the authors must make every attempt possible to ensure that the Results are accurate.
Interpretation of results
Of all the sins that an author can commit, the Reviewer is most likely to forgive a different interpretation of the results. The most common reason for deficiencies in interpretation are based on either drawing conclusions that are not directly supported by the results or claiming the impact of the results to be more than what can be justified after consideration of various limitations of the study. Let us discuss each of these items, which overlap in some regards.
The figure below summarizes the sequence of any observation that moves from description through various cascades. If any of the steps are eliminated in the cascade, the consequences are outlined below:
image001.gifA. Drawing conclusions that are not directly supported by the results
If a study found that patients with elevated blood pressure are more likely to die after myocardial infarction and interpret the data to state that elevated blood pressure should be lowered aggressively in patients with myocardial infarction, such interpretation is not justified. The authors must always make sure that associated
in not confused with resulted
. Any association between two factors could be either a cause-effect relationship (one factor resulted in occurrence of the other) or simultaneous effect relationship (both are consequences of an unknown cause) or bystander relationship (both were present at the same place and time by chance). Infrequently, the association may be a mixed relationship. Thus the author has converted an association into a cause effect relationship without appropriate data. The correct interpretation would be that elevated blood pressure may be a therapeutic target that needs to be evaluated in future studies.
B. Claiming the impact of the results to be greater than what can be justified after consideration of various limitations of the study
Infrequently, authors may use a retrospective or observational study and derive recommendations that most other investigators would consider appropriate only after a randomized controlled clinical trial. An example is when a retrospective study found that patients who received intravenous antihypertensive medication after acute myocardial infarction were more likely to die, and concluded that, antihypertensive medications should be avoided in such patients. Without adequate assurance that patients who received antihypertensive medication were similar to those who did not receive antihypertensive medication and elimination of other factors that may be responsible, the statement is OVERCLAIMING the impact. Such balance among treated and untreated patients and adjustment for other confounders is not possible in retrospective studies. Another issue can be the number of subjects or events that may preclude a definitive statement.
It should be noted that such claims may in fact be true after appropriate data is accrued, but is premature at this time. The Reviewers also recognize that the authors and even other individuals may feel that there is enough data to justify making such claims. Most Reviewers will accept a compromise by the authors or toning down
in a Revised version of the original manuscript.
Conforming to the journal formatting and style
The Editors of Clinical Chemistry ⁵ reported that about a third of submitted papers fail to fulfill at least one journal requirement as described in the Information for Authors and the detailed checklist for manuscript preparation. They also reported that even after peer review, roughly two-thirds of papers are returned to the authors by the Deputy Editors at the final stages of editing. The reasons varied from clarification of text, additional method information or clarification, additional results, revision or shortening of the abstract, unclear figures or tables, unjustified conclusions, and improper use of statistics. Therefore, it is absolutely mandatory that the author review the Instructions to Authors
and also previously published manuscripts in the intended Journal of submission. I have summarized the most common mistakes that the authors make in formatting the manuscript in the Table.
Common errors in manuscript formatting
Incorrect formatting of title page including display of author names and affiliations
Abstract’s subheadings are different from those recommended by journal style
Subheadings in the text are different from those recommended by journal style
The word count exceeds the word count recommended by the journal
Incorrect reference formatting
Too many references
Inclusion of tables, supplemental files, and figure legends in the main text of the paper as opposed to separate pages after completion of text. (this is a major difference between submitted and published form of the manuscript)
The resolution and format of figures does not conform to the journal instructions
References
¹ Eric Campbell, David Blumenthal The Selfish Gene: Data Sharing and Withholding in Academic Genetics http://sciencecareers.sciencemag.org/career_magazine/previous_ issues/articles/2002_05_31/noDOI.5822398718525511595 Accessed 01/18/2012
² America Medical Association Opinion 9.08—New Medical Procedures http://www.ama-assn.org/ama/pub/physician-resources/medical-ethics/code-medical-ethics/opinion908.page Accessed 01/18/2012
³ http://grants.nih.gov/grants/policy/data_sharing/ last accessed on 1/23/2012.
Chapter 2
TITLE
The title is the flag of the expedition. The title has to follow the general principles: 1/. As conspicuous as possible; 2/. Attract attention of as many persons as possible; and 3/. Relevant to the material presented in the subsequent sections. The reason that title should be selected carefully is because multiple search strategies rely on identification of words and phrases in the title. The title is also displayed in the table of contents of medical journals either as one of the initial pages or even on the cover page. Thus, the readers’ decision to read a particular article may be based or influenced by the title.
A title has two components as identified in the Table as follows:
Main title
The main title should be able to stand alone without the unique attribute. Some journals have a word limit for the title that influences the choice of the title. To prepare a title, identify three components of the study: 1/. Study population; 2/. Primary study intervention or variable that affects primary endpoint; and 3/. Primary endpoint.
The study population is usually included in the Title. The study population can be either patients with a particular disease or persons without a disease or experimental models. Examples are patients with grade III carcinoma
or person aged 80 years of greater in urban population
or canine model of myocardial infarction
. These terms can be made more concise as follows: advanced carcinoma
, urban octogenarian population
, or experimental myocardial infarction
. It is an acceptable practice to group primary study interventions or variables in one category. For example, if a study evaluated multiple doses of intravenous abciximab in persons undergoing percutaneous transluminal angioplasty/stent, the intervention can just be grouped as intravenous abciximab
in the title. Similarly, if a study is evaluating the effect of multiple risk factors including age, gender, hypertension, diabetes mellitus, cigarette smoking, hyperlipidemia, and cocaine use on formation of intracranial aneurysm, then grouping these variables of interest as risk factors
is appropriate. If the risk factors do not include age and gender as variables of interest, narrowing the variable to clinical risk factors
is appropriate. If the study is evaluating comparative efficacy between two treatment groups, the intervention may be expressed as intervention A versus intervention B
. An example of such as title is as follows: Plasma exchange versus intravenous immunoglobulin treatment in myasthenic crisis.
¹ The Title is expected to focus on primary endpoints. Infrequently, the study may have two endpoints of equal importance and the author may want reviewers and readers to know about this information. In such situations, terms like clinical and radiological outcomes
are acceptable terms in the Title.
A. Theme based
Theme based titles are the most common form of titles used for scientific manuscript. If the study is addressing either more than one question or evaluating the question in subgroups or reporting ancillary data, theme based titles are the best option. So let’s take an abstract to review the contents of the study ² and then develop the title.
Background: Habitual sleep patterns may independently affect morbidity and mortality. However, the effect of habitual sleep patterns on the risk for stroke and coronary heart disease is