Publishing Articles in Medical journals and guide for writing dissertations (thesis).

1. How to write Articles & Protocol
formulation for Dissertations &
Thesis writing (Dos & Don’ts)
Dr. Debarshi Lahiri, Kolkata

2. Part 1:
• Research Article submission
Part 2:
• Writing thesis/protocol

3. PART 1

4. Why to Publish
• Diligent research during thesis (2-3 years) needs to be published
• Learning/developing a new skill set.
• Helps in building up academic career.
• Satisfaction of contributing to the field

5. How to find journal to publish
• PubMed search (all the relevant articles and associated journals)
• NLM catalogue- Provide the list of journals on the topic (focused results)
• Compile a list of possible journals.
Selecting the journal
Lower impact factor may be easier to publish, Article type, Free
• Register online at journal website for author instructions
• Read the author guidelines (what type of articles/ word limits etc.)
• Not mandatory to only publish in a PubMed indexed journal. The journals
indexed with Embase/SCOPUS etc. can be equally good for publishing.

6. Impact Factor
• Reflects the yearly average number of citations that articles published
in the last two years in a given journal received.
• Proxy for the relative importance of a journal within its field
• New journals, which are indexed from their first published issue, will
receive an impact factor at the end of 3 years.
• Not a measure of quality of articles published in a journal.
• A journal with lower impact factor not necessarily inferior and can have
good quality articles.
• It is useful to target a journal with relatively lower impact factor
initially for publishing papers.
• IJROBP: 5.859, Radiotherapy and Oncology: 4.856, JCRT: 1.326

7. Manuscript Submission
Follow journal instructions to authors carefully
• Format
• Length of text and number of figures/tables
• References-correct format
Abstract (summary)
• Entire gist of the article needs to be reflected in the abstract. This implies that
you should write your abstract in such a way that it tells your entire story in a
minimal number of words without changing the overall message of your paper
to be published.
• Abstract is the part of manuscript that is copied by reference systems. Hence, it is
more broadly published than your manuscript in total. Should be Attractive.
• Stick to word limit.

8. Manuscript Submission
Cover Letter, Title page, Main Article (plus figures, tables), References
Cover Letter
• Very important, often not appreciated
• Describes why the article needs to be published, but be concise.
• This is a great opportunity to highlight to the journal editor what makes your
research new and important. The cover letter should explain why your work is
perfect for their journal and why it will be of interest to the journal’s readers.
• Be sure to revise if you send article to a new journal.
Recommending Reviewer
• You can give suggestions for reviewers (you can also request to exclude some
reviewer, if you suspect bias on the ground that he is a competitor).
• Suggest appropriate reviewers:
Not your prior mentors/coworkers
and with required expertise and experience
Ideally best not to suggest anyone (Personal view)

9. Manuscript Submission
Title Page
• Title/Running title (short version of the title)
• Authors- Degrees, Affiliations/Institutions, Contact info, Disclosures
• Keywords
• Funding
• Article not submitted anywhere
• All authors approve submission (the corresponding author may do for
all others during submission)- Signatures of all authors usually
required at some point.
• Acknowledgements

10. Submission Authorship
Authorship
• Negotiate in advance
• All authors now usually notified at the time of submission
• Journal will not intervene
ICMJE Recommendations ( International Committee of Medical Journal Editors
www.icmje.org )
• Substantial contributions to the conception or design of the work; or the
acquisition, analysis, or interpretation of data for the work;
AND
• Drafting the work or revising it critically for important intellectual content;
AND
• Final approval of the version to be published;
AND
• Agreement to be accountable for all aspects of the work in ensuring that
questions related to the accuracy or integrity of any part of the work are
appropriately investigated and resolved.

11. Timeline
Preparing the work (after the study is over)
• Many weeks to months
Finding the right journal
• One day to a week or two
Submitting the work
• One to two days
Decision (peer review process)
• One to three months

12. Peer Review
• Process takes 1-3 months
• Manuscript is usually sent to at-least two reviewers who are experts
in the field and well known researchers with many peer reviewed
publications.
• It is ideally double blinded (Reviewer also does not know the names
of the authors/institutions). For double blinded peer reviews, it is
essential that name of the institution comes nowhere in the main
manuscript.

13. Post-Submission issues
Decisions: Acceptance/ Minor revisions/ Major Revisions/ Rejected
(Strategies to get acceptance: Cover letter/Recommend Reviewers/
Become editor  )
“Revision Invited”- how to respond to reviewer comments?
• If new information/analysis from the available raw data is not
feasible or if you feel strongly that it is not required, contact editor
for clarification.
• Otherwise comply substantively with every comment/request
• Prepare a succinct and polite point by point response to each
comment in the review.

14. Post-Submission issues
What to do if your paper is rejected?
• Accept decision if clearly justified by reviewer comments (and get
ready to submit to a new journal with the suggested corrections of
the mistakes that led to rejection here).
• Accept decision if based on priority/novelty (and look for another
journal that will give value and priority to your hard work and
research)
• Consider rebuttal if reviewers clearly misunderstood or
misrepresented the paper
Appeals
• Be polite , unemotional, succinct and clear
• Wait at least one week for a response before submitting elsewhere

15. Post-Submission issues
The paper has been accepted!!
Copyright transfer form is sent to the corresponding author for signing
(usually needs signature of all the authors)
Accepted article sent back by the publisher for checking Proofs
• The 48 hour turnaround is a suggestion, not a requirement.
• Important to check proofs carefully with senior author.
• DO NOT want to miss a problem and later have to publish a correction
How to get more citations?
• High impact journal, strategic titles, keywords (MeSH terms), open
access

16. Plagiarism
It is the unacknowledged use of work of another person as one’s
own: “use of others’ published and unpublished ideas or words (or
other intellectual property) without attribution or permission, and
presenting them as new and original rather than derived from an
existing source”-World Association of Medical Editors (WAME)
Considered unethical “stealing” with serious consequences
• At journal and institution
• Retraction, public shaming, ban on publishing in journal etc.
• Avoid inadvertent plagiarism- when taking notes always paraphrase
• Plagiarism detection tools are used by all reputed journals.

17. PART 2

18. Utility of Thesis
• Mandatory for academic degree
• First experience in research (for most students)
• Learning: Ask research questions /conceive and
design scientific studies/ use appropriate methodology/
generate and handle large volumes of data/ valid & logical
conclusions.
• Research trains mind for critical reviews of published articles.
• Encourages further research, and contributes to the science

19. Fields of Research
• Intracellular and biological processes, genetic studies, studies on
properties of drugs, radiobiological research, animal experiments
(Basic Research).
• Distribution of diseases and/or health related characteristics in the
population; Profile of cases of a specific disease; Risk factors and their
contribution to a condition (Epidemiological Research).
• Efficacy of treatment: Drugs/ Radiation therapy/ Procedures.
• Health economics, cost-effectiveness
• Quality of healthcare, and quality of life.
• Health policy, health systems, health services.
• Reviews, meta-analysis.
Time/available resources to be considered for deciding the field.

20. Research question
Research Question:
• Unfamiliar and difficult task for a new PG student
• Time is of extreme importance for PG Thesis
• Well built research question usually contains 4 PICO elements to make it
clear, specific, focused and achievable.
P- Patient/Population/Problem
I- Intervention/procedure/treatment etc.
C- Comparator
O- Outcome
I/C- represent independent variables; O- dependent variable
• Keep number of questions restricted
• Can be completed using available resources: Time/subjects/material/tools
• Ethically sound

21. Developing a Research Question
• First Choose a broad topic first (specific area where you want to do your
research in).
• Extend your knowledge on the topic by consulting resources
(literature)/seniors/colleagues.
• Try to identify the areas of deficiency/lack of clarity of information which
require further research.
• Narrow the topic to suit your specific research interest & frame research
query.
• Check for PICO elements.
• Test for Goodness: novelty, clear, ethically sound, feasible.

22. Searching Literature
• Prerequisite for any research (from finding a relevant topic to
reaching a conclusion).
• Good literature review will help build knowledge and identify
methodologies.
• Focus your research and refine your research question.
• Helps justifying the results.

23. Sources of Literature
• Scholarly articles: written by experts and peer reviewed: Textbooks,
journals, theses, e-books, govt. publications, systematic reviews etc.
• Non-scholarly articles: for general public, not peer reviewed: have a
doubtful credibility
Internet as a source of literature:
• Google (www.google.com): most commonly used website for searching
any kind of literature
• Google Scholar (www.scholar.google.com): The results are more focused
than google
• MEDLINE/PubMed: Database of articles from academic journals in the
field of biomedical sciences. Accessed through internet via PubMed
interface (maintained by NLM, NIH, USA)
• Other important databases: EMBASE, SCOPUS, CINAHL, Cochrane Library
(for systematic reviews) etc.

24. What constitutes the literature
• Primary Literature: Published work of original researcher (Research
papers, conference proceedings, case reports etc.)
• Secondary Literature: Review articles published in scientific journals,
literature reviews from thesis/dissertations.
• Tertiary Literature: Textbooks and guidelines issued by competent
bodies. These present the currently acceptable knowledge, rather
than contribute to it.

25. Literature Search
• Open PubMed- www.pubmed.gov , type the words in the search box
to search the database.
• Avoid stop-words: filters out important search articles which may
not contain these words (e.g. a, it, these, about, its, they, any, as, at,
using, upon, used, various, another, are, may, also, was, were, an etc.)
• Boolean Operators: AND/OR/NOT
• Identify keywords: Keywords help other researchers find the
paper when they are conducting a search on the topic. Try to
identify keywords relevant to the research question.
• Limits: Using Filters is a way of narrowing down search even further.
On the left of all search results, there are many filter options
available.

27. Review of Literature
Follows the introduction and precedes the objectives, methodology,
results and discussion, but introduction can only be written after
reviewing the literature
Definition: The process of reading, analyzing, evaluating and
summarizing scholarly material about the topic.
Why review of literature?
• To provide background information needed to understand the study.
• 1st step to understand the current level of knowledge and identify the
areas of deficiency/conflict/lack of clarity of information
• To justify your choice of research question, conceptual framework
and methodology.
• Brings clarity and focus to the research problem.

28. Writing the Introduction
• Serves the purpose of acquainting the topic to the reader.
• What is being studied? Why is it an important question? What is
already known? How will this study advance our knowledge?
• Should provide basic information that the reader will need to
understand the topic.
Structure:
• Background: Present the more general aspects of the topic early in
the introduction.
• Statement of problem and rationale: Narrow down towards the
more specific information that provides context.
• End with the research question/hypothesis.

29. Writing the Review
1. Start with historical overview of research literature, with a special
emphasis on literature specific to the research question (should be
selective based on the relevance to the topic).
2. For protocol writing, only selected articles directly related to the
research question may be summarized.
3. For thesis, summarize all the relevant articles. Do not simply state
the findings of other studies, one after the other. Each article should
be summarized in own words with brief comments of your own.
4. The review is like an inverted pyramid- widest to start with (an
overview), and narrowest in the end (discussing the research that
relates to your specific topic).

30. Writing Aim and Objectives
• Aim is a broad term that tells the reader what the study intends to
achieve (general intentions with respect to long term expectations
from the research)
• Objectives- Specific steps taken to achieve the aim. Clearly defined,
measurable and specific, and must be aligned to the research
question/hypothesis
Example:
• Aim: To compare efficacy and toxicity profile of CCRT using weekly
versus three weekly Cisplatin in locally advanced head and neck
cancer and help define an optimal CCRT schedule with tolerable acute
toxicity
• Objectives: 1. Comparison of locoregional response between the two
arms, 2. Compare treatment compliance, 3. Assessment of toxicity
(acute and late) in both the arms

31. Primary and Secondary objectives
• Primary Objective: Objectives that are directly linked to the research
question and will be able to answer it are called Primary Objectives.
• Secondary Objective: Do not contribute to answering the research
question. They pertain to incidental by-products of the study.
• Essential elements of ‘good’ objectives (SMART)
Specific: Clear, well defined (denote precisely what you are going to do)
Measurable: Outcomes are measurable
Achievable: Achievable in terms of resources, knowledge and expertise
Relevant: In terms of current ongoing knowledge and advances
Time constrained: can be achieved in usual timeframe available to PG
students.

32. Material and Methods
• Material: Implies all items such as equipment/subjects
(human/animal)/proformas/questionnaires/medicines/computer
software etc.
• Methods: ‘How’, ‘when’, ‘where’ are you going to use this material
1. protocol writing can be started with this section.
2. This section is evaluated most carefully by experts evaluating the
protocol and thesis
3. This section should be written precisely so as to make it possible for
any competent researcher to reproduce exactly what was done.
4. The methodology mentioned in the protocol has to be strictly
followed.
5. Past tense (in thesis)

33. Components of Material and Methods
1. Study design (prospective/retrospective/observational/analytical) & Setting
2. Study period
3. Study subjects including details of the study arms and method of accrual
4. Sample size and its justification (take help of statistician)
5. Sampling technique (take help of statistician)
6. Inclusion and exclusion criteria
7. Intervention to be discussed in details
8. Details of follow-up
9. Method of measurement of the outcome of interest
10. Data collection methods and statistical analysis (take help of statistician)
11. Study proforma (case record form), informed consent form (also in native
language), patient information sheet (also in native language), IEC clearance

34. Obtain required Institutional Review Board approval/IEC
• All prospective studies, including observational studies involving
human subjects need IEC approval.
Registration of the study:
Before initiation at ICMJE approved trial registry (www.clinicaltrials.gov
or equivalent- CTRI (www.ctri.nic.in))
• Required for “any research study that prospectively assigns human
participants or groups of humans to one or more health-related
interventions to evaluate the effects on health outcomes”
• Not required for observational studies
• Any phase 2-4 trial that began enrollment after July 1, 2005
• www.icmje.org/faq clinical.html for more information

35. Writing the Title
Title:
Best be written at the end of the protocol writing
It is the packaging of the thesis. Readers should be able to get the
glimpse of the study from the thesis title.
(SPICD)
S- Setting, P-Population, I- Intervention, C- Comparator D- Design of
study
• Concise, informative & specific
• Avoid unnecessary phrases at the beginning- Role of/effects
of/treatment of/ a study on etc.
• Place keywords towards the beginning
• Avoid abbreviations/acronyms- CCRT/3DCRT/IMRT/IGRT etc.

36. Thesis Title examples
• Weekly versus three weekly concurrent cisplatin with radiotherapy in
locally advanced head & neck cancer in a Regional Cancer Centre of
Eastern India: A randomized comparative study.
• Concurrent chemoradiation using intensity modulated radiotherapy
versus laryngectomy in locally advanced laryngeal cancer: A
randomized comparative study.
• Estimation of set-up errors and optimization of planning target
volume margin in patients undergoing intensity modulated
radiotherapy for head & neck cancer: A prospective observational
study.

37. Results and Discussion
Results:
• Present observations in a comprehensive and systematic manner so
that others understand them.
• Balanced mix of narration, tables, figures and graphs.
• Do not include your own interpretations/views/opinions.
• When summarizing, don’t include raw data or intermediate
calculations. Use appendix for providing the master chart.
• Past-tense while referring to your results.
Discussion:
• Interpret and explain your results.
• Answer the research question/hypothesis.
• Justify your approach.
• Critically evaluate the strengths/weaknesses of your methods

38. Discussion and Conclusion
Key elements of a good discussion:
• Explain whether your results prove or disprove your hypothesis.
• Discuss strengths, Limitations, possible sources of bias and how they might
affect generalizability of results.
• For every result you want to discuss, you should find results from other
publications that have bearing on your work.
• Note the similarities, differences, common or different trends.
• Provide implications for clinical practice and directions for future research.
• Don’t repeat detailed descriptions of data and results, or introduce
new results.
Conclusion:
• It provides the final message and proper perspective to the thesis as a
whole.
• Clearly state the principal findings and recommend future research areas.

39. References
• Acknowledgement of contribution of those who have already done
research on the subject.
• Lends credibility and precision to your work.
• Indicates that a meticulous search of existing literature relevant to the
study has been done
• Limit the number of references to 25-30 for thesis protocol, maximum
100 for thesis (some Universities have specific rules).
• Prefer references from indexed journal articles.
• Avoid references from conference abstracts, papers under submission
etc.

40. Writing references
• Vancouver (ICMJE) Style (Mostly used)- The name is derived from a
meeting of editors of prominent journals at Vancouver, Canada in 1988.
Further modified by the ICMJE.
• The Vancouver citation style uses a citation-sequence number system,
using a number to represent the reference, which the reader can find
under the corresponding number in the reference list.
• You can insert numbers as superscript or in parentheses.
• If you wish to cite two or more references together, place a comma
between the numbers, e.g. 1, 2 or (1, 2).
• If you wish to cite a series of consecutive references use a dash, e.g. 2-5 or
(2-5).

41. Writing Reference for a journal article
1. Name (s) of the Author (s): Surnames followed by initials, in the
same order as published in the original article (surname first for each
author followed by space and then his/her initials).
• If there is more than one author, separate author names from each
other by a comma and space.
• If there are more than 6 authors, write the names of only first 6
authors, suffixed by et al.
2. Complete title of the article (full stop)
3. Abbreviated name of the journal (all PubMed indexed journals have
standard abbreviations) (full stop)
4. Year and month of publication (semi colon)
5. volume and issue (issue no. in bracket, then a colon)
6. 1st – last page numbers

42. Article Reference examples
• Villa LL, Costa RL, Petta CA, Andrade RP, Ault KA, Guiliano AR, et al.
Prophylactic quadrivalent human papilloma virus (types 6, 11, 16, and
18) L1 virus-like particle vaccine in young women: a randomized
double-blind placebo-controlled multicenter phase II efficacy trial.
Lancet Oncol. 2005 May; 6 (5): 271-8
• Tyagi N, Lewis JH, Yashar CM, Vo D, Jiang SB, Mundt AJ, et al. Daily
online cone beam computed tomography to assess interfractional
motion in patients with intact cervical cancer. Int J Radiat Oncol Biol
Phys. 2011 May; 80 (1): 273-80

43. Textbook chapter
Textbook chapter reference:
• Author of part.
• Title of chapter or part.
• In: Editor A, Editor B, editors.
• Title: subtitle of book.
• Edition (if not the first).
• Place of publication:
• Publisher; Year. p. Page numbers.

44. Textbook reference examples
Ford HL, Sclafani RA, Degregori J. Cell cycle regulatory
cascades. In: Stein GS, Pardee AB, editors. Cell cycle and
growth control: biomolecular regulation and cancer. 2nd ed.
Hoboken (NJ): Wiley-Liss; 2004. p. 42-67.
Arora SS, Gupta P. Writing References. In: Gupta P, Singh N, editors.
How to Write the Thesis and Thesis Protocol: A Primer for Medical,
Dental and Nursing Courses. New Delhi: Jaypee Brothers Medical
Publishers (P) LTD; 2014. p. 145-152.

46. THANK
YOU