How to Write the Thesis and Thesis Protocol: A Primer for Medical, Dental, and Nursing Courses Piyush Gupta, Dheeraj Shah
Abbreviations 175
glossary of 21
in the title 47
Acknowledgments 20
Acronyms 175
Accountability 98
Aim 13, 60
vs. objectives 60, 61t
Aim and objectives 13, 6065
aligning with title 62
in a manuscript-based thesis 210
in protocol 199
steps to formulate 64t
translating research question to 61
Allocation concealment 40, 80
Alpha error 87
Alternate hypothesis 28
Analytical studies 36
Ancillary data 128, 129
Animations 190
Annexure 16
in protocol 201
Appendices 16, 21
Applied research 26
Area under the curve 38
Assent 99
Authorship 169b, 205
in a graph 135
Bar chart 136f
Baseline data 80, 124
Basic research 26
Beneficence 97
Beta error 87
Bibliography 154
in a manuscript-based thesis 211
Binary logistic regression analysis 115
Binding 22
Blinding 40, 80
Block randomization 40
Boolean operators 55, 56
Boxplot 135f
of a graph 135
Case record form 22, 106108, 200, 212
Case studies 44t
Case-control study 36, 37f, 44t
objective of 63
Categorical data 110
Central tendency
measures of 111
of consent 102b
of participation 99
of thesis 20f
Charts 189
Citing 154
Clinical informatics 58
Clinical Trials Registry India (CTRI)
ClipArt 190
Clipboard 55
Cluster randomization 40
Cochrane collaboration 41
Cochrane database of systematic reviews 57
Cochrane library 57
Cohen's d 89
Cohort 36
Cohort study 36, 37f, 44t
objective of 63
Collective nouns 178
Columns 134
Comma 176
Comma separated lists 177
Comparison group 79
Complete plagiarism 167t
Conclusion 15, 143147
do's and don'ts 144
errors in writing 145
essential elements of 143
sample 144
styles of 146t
using tense in 145t
in a manuscript-based thesis 211
Confidence interval 86, 120
Confidence level 120
Confidence limits
for calculating sample size 92
Confidentiality 101b
Confounder 37
Consent form 22
CONSORT 44, 77
flow diagram 126f
Consortium for academic and research ethics (CARE) 58
Continuous data 110
Control group 79
selection of 37
Convenience sampling 79
Correlation 113
and regression 115b
Correlation coefficient 113, 114b
Cover design 19f, 22
Cover page 197
Crossover study design 42
Cross-reference 154
Cross-sectional study 36, 37, 37f, 44t
Cryptomnesia 166
acquisition of 103
categorical vs. numerical 110
collection 81
fabrication 168
falsification 168
management 200
monitoring 81
ownership 103
paired vs. unpaired 110
type of 124
Data Safety Monitoring Board (DSMB) 104
Data sheet 22
Data slicing 206
Data-based manuscripts 210
Databases 53t
Decimal 129
Declaration 19, 20f
Declaration of Helsinki 104
Demographic data 125
Descriptive research question 28
Descriptive studies 35
Diagnostic studies 37, 43t, 77
Diagnostic test 121
Digital presenter 194f
Direct plagiarism 167t
Discussion 138142
checklist 141
components of 15
contents of 138
elements of 139
how to organize 140
in a manuscript-based thesis 211
of thesis paper 205
purpose of 138
about mean 88
measures of 111
Dissertation 2
Distributive justice 98
Dropout rates 90
Effect size 43t, 88, 89
Efficacy studies 43t
Electronic case record form 108
Embase 53t
Environmental protection 98
elements of writing 175184
problems in writing 182
Epi Info 91, 91f
Essentiality 98
Ethics 97105
in methods 78
in patient care and research 103
Ethics committee 104
Ethical writing 166
levels of 42
Exclusion criteria 79
Expected frequency
for calculating sample size 91
Experimental studies 34, 44t
Experimental study design 39
Exposure 36
Fabrication 168
False negative 38t, 121
False positive 38t, 121
Falsification 168
examples of 169b
Feasibility sampling 79
Filters 54
serif vs. sans-serif 188f
size, for slides 188
of table 134
Forest plot 42
Gaussian distribution 112f
Ghost authorship 169
Glossary 21
Good clinical practice guidelines 104
Google 51
Google Scholar 52, 53t, 57
Google slides 196
Grab bag conclusion 146t
Graph 132f, 134
components of 135
considerations for 134
in PowerPoint 189
selecting appropriate 135
Guru 5
Haiku deck 195
Harvard style 157
Headers and footers 191
and subheadings 23
of table 134
Health informatics 58
Hypothesis 26, 28
elements of 28
framing of 29
studies to test 86
types of 28b
Hypothesis testing
concept of 116
steps of 117
ICMJE style 157, 158
Inclusion criteria 78
Index 21
Index test 38
IndMED 58
Inferential research question 28
Informed consent 98
Informed consent document 99
Informed consent form 100b
in protocol 200
Institutional arrangements 98
Institutional Ethics Committee (IEC) 104
Intellectual theft 167t
International conference on harmonization (ICH) 104
as source of literature 51
citation 159
Interquartile range (IQR) 111
Intervention 48, 80
Interventional studies 77
components of 13
funnel approach 67
in a manuscript-based thesis 210
in summary 149
of protocol 198
of thesis paper 204
purpose of 66
structure of 67
what not to include in 67
when to write 66
name, abbreviating 159
selection of 203
Keyboard shortcuts 192
Keynote 196
Law 97
Legally acceptable/authorized representative (LAR) 99
of graph 135
Levels of evidence (LOE) 42
for different research questions 43t
hierarchy of 43f
Linear correlation 113
Lists 177
critical analysis of 73
primary, secondary, tertiary 51, 69
scholarly vs. nonscholarly 51
sorting and prioritizing 72
sources of 51
Literature review. Also See Review of literature
chronological 71
conceptual 71
goal of 71
methodological 71
organization of 71
writing the 73
Literature search 5159
Logistic regression 115
Manipulation 166
Manuscript based thesis 203, 208211
components of 210b
format of 209
traditional thesis vs. 209t
Margin of error 87
Master chart 22
Matched control 110
Material and methods 14, 7684
checklist for 83b
components of 76
in a manuscript-based thesis 210
in protocol 199
in summary 149
of thesis paper 204
tips for writing 14, 82
what not be include in 84
Mathew effect 52
Maximization of benefit 98
Mean 111
Measures of dispersion 88
Median 111
Medical information 52f
Medical informatics 58
Medline 53
Mendeley 160162
Mentee 7
Mentor 7
Mentoring 5, 6t,
Mentor–Mentee relationship 29
do's and don'ts of 7
Mentorship program 7
MeSH 56
MeSH database 56
MeSH-based search 54f, 56
Meta-analysis 41, 77
Methodology oriented literature review 70
Misattribution 167t
Misquotation 166
Misrepresentation 166
Mixed-methods study 42
Mode 111
Model protocol 197
Modifiers 179
Morals 97
Multinomial logistic regression analysis 115
Multiple regression 115
My bibliography 55
National Center for Biotechnology Information (NCBI) 54
National guidelines for biomedical and health research in 2017 104
National institute of health (NIH) 54
National library of medicine (NLM) 54
Negative predictive value (NPV) 38t, 122
Nested case–control study 42
NLM catalog 57
Non-linear correlation 113
Nonexploitation 98
Nonmaleficence 97
Nonrandomized study 39
Nonresponse rate 90
Null hypothesis 28, 117
Numbers 178
Nuremberg code of 1947 103
Objectives 60
essential elements of 63
primary and secondary 61
SMART 13, 63
Observational studies 33, 35, 77
Odds ratio (OR) 115
Optional thesis 24
Outcome 36
Outcome data 126, 129
of a single group 126
of categorical variables 127
of more than one group 127
Outcome measures 81
in protocol 200
estimated value of 87
Outcome oriented literature review 70
P value 117, 128
Pagination 23
Paired data 110
Paragraph 182
Paraphrasing 165, 171
appropriate and inappropriate 171b
Parenthesis 55
Participant 78
Participant data 124, 129
Participant flow 125, 126f
Patient information sheet 22, 99
Patient information sheet, additional elements 102
essential elements of 101
Photographs 136
Photomicrographs 136
comparison in 29f
in conclusion 143
in objectives 63
intervention on 29f
outcome in 29f
population in 29f
Picture 190
Pilson's law 12
Plagiarism 166
Delhi University Guidelines 173b
how to avoid 170
types of 167
UGC guidelines 172t
Plagiarism check software 171
Plurals 178
Population 48, 78, 109
for calculating sample size 91
Positive predictive value (PPV) 38t, 122
Post-hoc analysis 128
Power 88,120
PowerPoint 185196
alternatives to 195
Predictive value 122
defining contents of 186
finalization of 195
preparing 192
Prevalence study 43t
Prezi 195
Primary literature 51, 69
Primary outcome 81
and sample size 87
Primum non nocere 97
Privacy 98
Professional competence 98
Protocol. See Thesis Protocol
PS2 software 92, 93f
Publication ethics 206
Publication misconduct 165174
reasons for 170b
types of 166
PubMed 53
clipboard in 55
filters in 54
my bibliography in 55
opening page 54f
other features of 57
parentheses in 55
quotation marks in 55
search 53, 55f
truncation in 55
PubMed mobile 57
Qualitative research 26
Qualitative studies 33
Quantitative data 110
Quantitative studies 33
Quotation marks 55
Randomization 39, 80
Randomized controlled trial 40
objectives of 63
parallel group 41f
Receiver operating characteristic (RoC) curve 38, 39f
References 15, 154164
for a book chapter 159
for a journal article 158
Harvard style 157
how to write 156
ICMJE style
importance of 154
in protocol 200
key-terms for 154
numbering of 158
of thesis paper 205
selection of 156
sources of 155
styles for writing 157
Vancouver style 157
Reference list 154
Reference managers 160
Referencing software 58
Regression analysis 114
Rehearsing 194
Relative risk (RR) 116
Reporting guidelines 43
categories of 27t
fields of 27
for the practicing physician 1
importance of 1
in postgraduate courses 14
opportunities for 2
planning and conducting 103
reporting of 103
responsible conduct of 103
types of 26
Research question 11, 2632
characteristics of 30b
descriptive vs. inferential 28
developing a 31f
elements of 28
framing 29
good vs. bad 30
Respect for autonomy 97
Results 124130
components of 14
in a manuscript-based thesis 211
in discussion 139
in summary 149
of thesis paper 205
presentation of 129f
sequence of presentation 128
structure of 132
what to include in 131
Review of literature 6975
components of 70
in a manuscript-based thesis 210
in protocol 199
mistakes in writing 74
process of 72
tips for writing 13
Right to refuse or withdraw 101b
Risk minimization 98
ROC curve 38
Rows 134
Salami publication 206
Sample 109
Sample size 81, 82, 8596
adjusting the 89
Epi Info for calculating 94
for a case-control study 93f
for a randomized trial 94f
for prevalence study 86
for studies involving hypothesis testing 88
formulae for 90
how to calculate 86
PS2 software for calculating 93
software for calculating 90, 90b
why to calculate 85
Sampling 79
in graph 135
Scatter plot 136f
Scholarly literature 51
Secondary literature 51
Secondary outcome measures 81
Self-plagiarism 167t
Semicolon 177
Sensitivity 38t, 121
Sentence 181
Sequence generation 80
Sequential sampling 79
Setting 48
Sherlock Holmes conclusion 146t
Shishya 5
Simple randomization 39, 79
Simple regression 114
Six by six rule 188
Skewed data 112
Slides 185
10 points for making 192b
background of 189
bad 193f
editing of 192
layout 187
Smart art graphic 190
Social data 125
Social responsibility 98
for literature search 53
for plagiarism check 171
for sample size 90, 93, 94
Source-based plagiarism 167t
Specificity 38t, 121
Spelling 176
Standard deviation (SD) 111
for calculating sample size 88
Standard test 38
STARD 43, 77
Statistical analysis 82, 109123
in the text 133
in protocol 200
Statistical tests 118, 119f
significance of 128
Stop words 56
Stratified randomization 39
Stratified sampling 79
STROBE 43, 77
Structured summary 148
Studies of diagnostic accuracy 37
Study design 3344, 76
additional 41
case–control vs. cohort 35t
choosing the 34
limitations and strengths 44t
outline of 34f
qualitative vs. quantitative 33
reporting guidelines for 77
Study period 78
Study setting 78
Summary 148153
4-point checklist 149t
10-point checklist 149t
attributes of a good 152
do's and don'ts of 152
elements of 149
format for writing 148
in the thesis 152
of protocol 198
structured vs. unstructured
and supervisee 6
as a mentor 6
expectations from 6,8
expectations of 8
Swag 196
Systematic random sampling 79
Systematic reviews 41, 77
2 × 2 38t
components of 134
considerations for 134
in PowerPoint 189
presentation of 134
Table of contents 21
sample of 21f
Tertiary literature 51, 70
Text 132
Text-based search 54f, 55, 56
Thesis protocol 12, 197201
elements of 198
summary of 198
Thesis 1025
10 essential components of 18
advantages and disadvantages of 3
author names in 158
content of 13
converting into a scientific paper 3, 16, 202207
in postgraduate courses 3
margins of 23
optional 24
paper quality of 22
preparing final 23
rationale for 14
rectification in 24
role of 3
spine of 22f
submission of 23
time guidelines for submission 24
timetable for 12
typing and formatting 22
vs. dissertation 2
vs. scientific paper 202t
Three-word challenge 188
Title 4550
abbreviations in 47
elements of 47, 48
importance of 45
of thesis paper 204
what all to include 48
when to write 49
Title page 19, 198
sample of 19f
selection of 11
Totality of responsibility 98
Translation plagiarism 167t
Transparency 98
Trial registration 104
True negative 38t, 121
True positive 38t, 121
Truncation 55
Type I error 87, 118, 119t, 119f
Type II error 88, 118, 119t, 119f
Typographical errors 176
UGC guidelines on academic integrity 172
UGC guidelines on prevention of plagiarism 172
Universal declaration on bioethics and human rights (2005) 104
University grants commission regulation 2018 172
Unpaired data 110
Unstructured summary 148
of conducting research 103
Vancouver style 157, 158
and data 110
dependent vs. independent 111
Visme 195
Voluntariness 98
Writing malpractice 166
Chapter Notes

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Rationale for Thesis and Research in Postgraduate CoursesCHAPTER 1

Siddarth Ramji
As a medical practitioner we would always have to query ourselves about the whys, hows, whats, and whens related to problems people present with or situations that arise as part of the discharge of our professional responsibilities. How does one get answers to these concerns and queries? The easiest way is search for published material on the subject (which nowadays is just a few taps away in this digitalized world). If we do manage to find a solution, we feel happy and get on with our lives. But, how many of us pause for a moment and give a thought to the quality of evidence for this solution; most of us take the information obtained as the “gospel truth.” Decisions based on low-quality evidence could have the potential to adversely impact the outcome—either by not improving the person's condition or hurtling him/her down the abyss of death or disability—though both being the result of a decision that was unintentional on the part of the medical practitioner.
There are several reasons for the need of research in medical sciences; the most salient ones are outlined below.
For the Practicing Physician
Imagine a physician deciding to use prophylactic daily aspirin therapy to prevent myocardial infarction (MI) in a 50-year-old postmenopausal woman because her father had history of MI at 60 years, based on the result of a single randomized control study.
  • If with this treatment, the woman does not develop MI, can one conclude that the physician's decision validates the study results?
  • On the other hand, if the woman was to develop MI, would it refute the study results?
  • Or if she was to develop serious gastrointestinal bleeding without developing MI, would it mean aspirin therapy is unsafe for use for prevention of MI in postmenopausal women?
These and many similar questions require an understanding of how to evaluate the strength of evidence available to be able to translate the findings into clinical practice. Understanding of research principles and methods facilitates the physician to adopt evidence-based results into their medical practice, which would not only make it more scientific but also more ethical.2
For Problem-solving
Research is also needed to find a way forward to handle health problems afflicting humankind, which either have no solution, or a solution with low-moderate efficacy, or prevent the occurrence of such health maladies. The Coronavirus (COVID-19) epidemic which had its origins in China in the late part of 2019 is a case in point, where neither a vaccine for its prevention nor a drug for its treatment was available when the epidemic began. However, the attempts to characterize the virus genome and consequent efforts at vaccine development are good examples of how research is being used to address human health problems.
For Professional Qualifications and Academics
Research work is an integral part of any academic milieu, be it for award of a professional degree/qualification or for those who aspire to become part of the academic fraternity and grow within these academic institutions. The consequent academic recognition brings name and fame to the individual.
We have outlined the importance of research in medicine but for different people it probably means different things. While there are many ways of defining research, a useful way to define it is to say that it is a systematic inquiry into a particular concern or problem. The systematic inquiry process is essentially the research methodology. Understanding research methodology process is the key to one's successful journey as a practicing physician, researcher, or an academician.
The outputs of this systematic inquiry process are the thesis or dissertation. What do these terms mean?
Thesis and Dissertation
The word thesis has its origin from the Greek word “thesis” meaning “something put forth,” while the word dissertation has its origins from the Latin word “dissertare” meaning “continue to discuss.” Thesis or dissertation is a document of research findings in support of one's candidature for award of an academic degree/professional qualification. The terms have generally been used interchangeably for both award of a Masters’ degree and a doctoral degree.
The quantum and quality of research and the duration needed to complete the thesis/dissertation vary with country and university. However, there are those who wish to distinguish the two from one another. A thesis maybe understood as a tool to test the students’ understanding of their field of study/work wherein they formulate a proposition based on work done by others in the field and analyze it. In a dissertation, the student is expected to focus on an original research question and prove or disprove the hypothesis by doing the research work. A thesis submitted for postgraduate courses in medicine or nursing probably includes both the elements.
As stated earlier, key to translating evidence to practice lies in comprehending research methodology. Classroom or workshop exposure at best sensitizes the learner to the principles of research and its process, but being able to understand it sufficiently well to look at published evidence for translating into clinical practice requires one to engage in some actual research work, even though for a brief period.
Unlike overseas, where students have several opportunities for research exposure and experiences even during their graduate medical training period, these opportunities are limited in India. The Short Term Studentship (STS) offered by the Indian Council of Medical Research is probably the only opportunity that an undergraduate student has to carry out research projects under the supervision of a mentor in their own medical college without disrupting their ongoing medical training. However, not all undergraduate 3students get selected for the Studentship. The primary opportunity for medical graduates to experience research work in India is therefore during the pursuance of their postgraduate courses wherein the thesis related research work is an obligatory requirement for the award of their postgraduate degree.
The aim of postgraduate training is not restricted to ensuring the acquisition of clinical skills to work as specialist/consultant in the concerned specialty. The objectives are manifold. The thesis should empower the postgraduate student as follows:
  • Enable them to critically evaluate and synthesize evidence available in published medical literature.
  • To be able to translate available evidence into clinical practice.
  • To be able to ask probing questions to solve clinical problems.
  • To be able to enthuse some of the postgraduate students to enter the academia or research pathways.
The experience of thesis work hones the students’ skills to search medical literature systematically, synthesize available evidence, identify unanswered queries, plan a study for gathering appropriate data, get to know how to analyze their data, and finally present their work as a written document.
The thesis, eventually, will form the launching pad for those who may choose to spend a greater part of their career contributing to the growing body of medical literature by writing and publishing. The thesis also exposes them to the ethics of healthcare, which is often a neglected area in one's daily practice of clinical medicine.
How did my thesis affect me?
It improved my critical thinking, ability to look at data and its analysis, and infused a passion for academics and research and eventually launched me on that trajectory. My mentor (research guide) was an important factor in my transformation. I was also fortunate to have trained in a department which fostered and supported academic excellence, publication and research, and encouraged its postgraduate students to present papers in local and national conferences. It activated the dormant “competitive” spirit in us.
Advantage and Disadvantage of Thesis
Working on a thesis bestows several advantages to the student. It improves critical thinking of the students, helps in problem solving, would facilitate adoption of evidence-based medical practice, and improves their medical writing skills. The only disadvantage that one may put forth is time spent on thesis is relatively large and could have been put to better use for acquiring their core subject specific skills. However, in the tradeoff between the pros and cons, the advantages outweigh the disadvantages.
One needs to understand the fate of the thesis after its completion. An important question is whether it should be viewed only as a passport to award of degree with the thesis left forgotten in the institutional archives? The answer to this is a definite “No.” Few theses get translated into a publication as they are not necessarily pursued any further thereafter. But there are examples wherein the thesis has become the beacon for ongoing research in the field which eventually changed practice and policy. The following experience of the author is an illustration of how thesis can translate into long-term research impacting practice and policy.
My first thesis as a mentor attempted to answer the question as to “whether room air could be used for resuscitation of newborns at birth instead of 100% oxygen”, which was driven by the observation that mouth to mouth resuscitation was being practiced 4successfully by primary health workers to revive asphyxiated newborns without supplemental oxygen. The question was relevant and novel but challenged by the ethical concerns of lack of any experimental or clinical data to support the proposed hypothesis. The search for this tenacious evidence to support the hypothesis led me to meet up with a researcher in another part of the world, who was independently attempting to unravel the answer to the same question in porcine models which was driven by the observation that use of excessive oxygen following hypoxia could be detrimental to the newborn due to its ability to generate free radicals. This thesis research effort was published (Ramji S et al. 1993) and translated into a journey of international collaborative research spanning three and half decades which eventually changed both practice and policy globally.
  • The existing practice at that time was to use 100% oxygen to resuscitate newborns at birth.
  • The thesis concluded that room air could be as effective as 100% oxygen for neonatal resuscitation, a finding that was confirmed by several clinical trials thereafter.
  • Today the current policy is to initiate resuscitation in newborns with room air.
There are also other examples wherein thesis work has contributed to ongoing research and change in policy. Some of the examples include delayed cord clamping at birth to improve iron stores in infancy, use of zinc in diarrhea, lack of maternal protection against rotavirus infection in newborns, iron supplementation in exclusively breastfed infants, and serum antigliadin antibody for diagnosis of celiac disease in tropical countries.
Postgraduate students must view the thesis as an educational tool to enhance their skills to practice medicine rationally. They must enjoy this learning experience which could launch them into a successful career. To make this a stimulating experience and rather than a drudgery of doing a thesis, teachers and institutions must strive to create a conducive ambience for learning and doing.
  1. Cheung BMY. Medical student research: is it necessary and beneficial? Postgrad Med J. 2018;94(1112):317.
  1. Dzirasa K, Krishnan RR, Williams RS. Incubating the research independence of a medical scientist training program graduate: a case study. Acad Med. 2015;90(2):176–9.
  1. Garg R, Goyal S, Singh K. Lack of research amongst undergraduate medical students in India: It's time to act and act now. Indian Pediatr. 2017;54(5):357–60.
  1. Morbitzer KA, Rao KV, Rhoney DH, Pappas AL, Durr EA, Sultan SM, et al. Implementation of the flipped residency research model to enhance residency research training. Am J Health Syst Pharm. 2019;76(9):608–12.
  1. O'Brien JM. Conceptualizing the research culture in postgraduate medical education: Implications for Leading Culture Change. J Med Humanit. 2015;36(4):291–307.
  1. Personett HA, Hammond DA, Frazee EN, Skrupky LP, Johnson TJ, Schramm GE. Road map for research training in the residency learning experience. J Pharm Pract. 2018;31(5):489–96.
  1. Ramji S, Ahuja S, Thirupuram S, Rootwelt T, Rooth G, Saugstad OD. Resuscitation of asphyxic newborn infants with room air or 100% oxygen. Pediatr Res. 1993;34:809–12.
  1. Tullu MS, Karande S. Quality research in Indian medical colleges and teaching institutions: the need of the hour. J Postgrad Med. 2016;62(4):213–5.