Writing and Publishing a Scientific Research Paper (eBook)

Subhash Chandra Parija is the Director of the Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER), Pondicherry, India, and has nearly three and half decades of teaching and research experience in Medical Microbiology. Prof. Parija is a Food and Agriculture Organization (FAO) expert, and has been consulted to draft guidelines on food safety for parasites. Prof. Parija was on the Board of MD Examination at Colombo University, Sri Lanka, Sultan Quaboos University, Oman, University of Malaya, Malaysia. He was conferred a D.Sc. for his contributions in the field of Medical Parasitology by Madras University. The author of ten books including the “Text Book of Medical Parasitology,” he has published more than 300 papers in both national and international journals of repute. Prof. Parija has been honored with more than 25 awards including the Medical Council of India’s Dr. BC Roy National Award and the National Academy of Medical Sciences’ Dr. PN Chuttani Oration Award. Prof. Parija founded the Indian Academy of Tropical Parasitology (IATP), the only professional organization of Medical Parasitologists in India, and initiated the journal Tropical Parasitology. Vikram Kate is currently the Professor and Head, Department of the Surgery and Senior Consultant General and Gastrointestinal Surgeon at Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER), Puducherry. He has contributed more than 25 chapters in reputed surgical gastroenterology and surgery textbooks, and has more than 140 papers to his credit. He is a Past President of the Indian Association of Surgical Gastroenterology. He was awarded the Membership Diploma of the Faculty of Surgical Trainers by the Royal College of Surgeons, Edinburgh. Further, he currently serves as the Editor-in-Chief of The International Journal of Advanced Medical and Health Research, the official journal of JIPMER. Professor Kate is Examiner for the M.S./M.Ch./DNB and Ph.D. program for Surgery, Surgical Gastroenterology and Intercollegiate Membership of the Royal College of Surgeons, Edinburgh. He is a Fellow of Royal College of Surgeons of England, Edinburgh and Glasgow (FRCS, FRCS Ed., FRCS Glasg.), and of the American College of Surgeons (FACS) and the American College of Gastroenterology (FACG). He has been honored with many awards, including the Dr. Mathias Oration (2010), the Prof. N. Rangabashyam Oration (2015), by the Tamil Nadu and Pondicherry Chapter of the Association of Surgeons of India and the Silver Jubilee MASICON Oration (2016) by the Nagpur Branch of the Association of Surgeons of India. 

Foreword 5
Writing and publishing a scientific research paper 5
Preface 7
Acknowledgements 8
Contents 9
Editors and Contributors 11
About the Editors 14
Part I: Writing a Scientific Research Paper 15
1: Why Write a Scientific Research Paper 16
1.1 History of Scientific Writing 17
1.2 Need for Scientific Research Paper 18
1.2.1 To Develop a Scientific Writing Skill 19
1.2.2 To Connect with Senior Colleagues 19
1.2.3 To Enhance Academic Career 19
1.2.4 Improves Job Opportunity 19
1.2.5 Benefits for Senior Researchers 20
1.2.6 Guides Future Research 20
1.2.7 Provide Reliable Scientific Information 20
1.3 Moral Responsibility of the Researcher 20
References 21
2: Components and Structure of a Manuscript 22
2.1 Background 23
2.2 Introduction 24
2.3 Methodology 24
2.4 Results 26
2.5 Discussion 26
2.6 Acknowledgment 26
2.7 References 27
Case Scenario 28
References 28
3: Title 29
3.1 Introduction 30
3.2 Title 30
3.3 Importance of Writing a Relevant Title 31
3.4 There Are Three Basic Rules to Be Followed While Writing a Title 31
3.5 Types of Titles 32
3.6 Running Title 33
3.7 Title Page 34
3.8 Covering Letter 35
3.9 Attributes of a Good Title, Running Title, and Covering Letter 36
3.10 Conclusions 36
Case Scenario 37
References 37
4: Abstract and Keywords 38
4.1 Abstract 39
4.1.1 Definition of Abstract 39
4.1.2 Why Is a Good Abstract Important? 39
4.1.3 Types of Abstracts 40
4.1.3.1 Descriptive Abstracts 40
4.1.3.2 Informative Abstracts 40
4.1.3.3 Unstructured Abstracts 40
4.1.3.4 Structured Abstracts 40
4.1.4 What Makes an Abstract “Effective”? 41
4.1.5 Components of an Abstract 42
4.1.6 Title 42
4.1.7 Background 42
4.1.8 Methods 43
4.1.9 Results 43
4.1.10 Conclusion 44
4.1.11 How to Write an Abstract? 44
4.1.12 How to Avoid Pitfalls? 46
4.2 Keywords 46
4.2.1 How to Select Keywords? 46
4.3 Summary 47
References 48
5: Introduction 49
5.1 Why Introduce? 50
5.2 Ingredients of Introduction 50
5.3 Structure of Introduction 51
5.4 Don’ts for Introduction 51
5.5 When to Write the Introduction 52
5.6 Conclusion 53
Case Scenario 53
References 55
6: Methods 56
6.1 Characteristics of Ideal Methods Section 57
6.1.1 Precise and Meticulous 57
6.1.2 Structured or Unstructured 58
6.1.3 Avoid Shifting of Voices (Active and Passive) Inside the Paragraph 58
6.2 Components of the Methods Section 58
6.3 Subjects Used in the Study 59
6.4 Study Environment, Time Span of Study, and Study Design 60
6.5 Materials Used in the Study 61
6.6 Ethical Clearance/Informed Consent 63
6.7 Research Protocol (Intervention and Outcome Measures) 64
6.7.1 Intervention 64
6.7.2 Outcome 64
6.7.3 Validity and Reproducibility 65
6.8 Data/Statistical Analysis 65
6.9 Conclusion 67
Scenario 67
References 67
7: Results 69
7.1 Results 70
7.1.1 Introduction 70
7.2 Tables 72
7.3 Charts 74
7.3.1 Bar Charts 74
7.3.1.1 Types of Bars 74
7.3.2 Histograms 75
7.3.3 Pie Charts 77
7.3.4 Line Graphs 77
7.3.5 Scatter Plot 78
7.3.6 Photographs and Photomicrographs 80
Case Scenario 81
Suggested References for Further Reading 81
8: Discussion and Conclusion 83
8.1 First Paragraph 85
8.2 Subsequent Paragraphs [2–5] 86
8.2.1 Knowledge Gap 86
8.2.2 Explanation of Results 86
8.2.3 Unexpected Results and Plausibility 87
8.2.4 Clinical Implications 87
8.2.5 Future Direction 88
8.3 Strength of the Study 89
8.4 Limitations of the Study 89
8.5 Conclusion 90
8.6 Common Errors 90
Case Scenario 91
References 92
9: References 93
9.1 Introduction 94
9.2 Bibliography and References 94
9.3 Referencing Styles 95
9.4 Vancouver Style 96
9.5 Difference Between Vancouver Style and Harvard Style 98
9.6 Electronic Sources 98
9.7 The Number Game 98
9.8 Organization of the Reference List 99
9.9 Special Considerations 99
Case Scenario 100
References 100
10: Figures, Tables and Supporting Material 102
10.1 Introduction 103
10.2 Tables Versus Charts 104
10.3 Tables 104
10.3.1 The Anatomy of a Table 105
10.3.2 Good and Not So Good Tables 105
10.4 Graphs/Charts 106
10.5 Explanatory Artwork 108
10.6 Photographs and Line Drawings 108
10.6.1 Ethical Considerations 110
10.6.2 Formatting 110
10.6.3 Color or Monochrome? 110
10.6.4 Sending Your Illustration 110
10.7 Using EndNote for Tables and Figures 111
References 112
Part II: Publishing a Scientific Research Paper 113
11: Choosing a Journal for Paper Submission and Methods of Submission 114
11.1 Aim and Scope of the Journal 117
11.2 Specialty/Multidisciplinary 117
11.3 Type of Manuscript: Original Research/Case Report/Review/Letter to Editor 118
11.4 Regional/International 118
11.5 Indexed/Non-indexed 119
11.6 Journal Impact Factor (JIF) and Citation Index (CI) 119
11.7 Language of the Journal 120
11.8 Online vs. Print and Number of Issues 120
11.9 Open Access 120
11.10 Quality of Peer Reviewing and Acceptance Rate 121
11.11 Prestige and Stability 121
11.12 Ethical and Legal Issue 121
11.13 Potential, Possible or Probable Predatory Open-Access Journals 122
11.14 Author Guidelines 122
11.15 Advantages of Online Manuscript Submission (OMS) 123
11.16 Conflict of Interest and Financial Disclosure 124
11.17 Copyright Transfer Agreement 124
11.18 Manuscript Submission Process 124
11.19 Manuscript Tracking System 124
11.20 Withdrawal of the Manuscript and Its Consequences 126
Scenario 126
References 126
12: Revision of an Article and How to Deal with the Rejected Manuscript 128
12.1 Introduction 129
12.2 Editorial Decision on Paper: Types 129
12.3 Avoid Basic Mistakes 130
12.4 Respond to All Comments 131
12.5 Can Authors Disagree with Reviewer’s Comments? 131
12.6 How to Deal with the Rejected Manuscript 132
12.7 Appeal the Rejection and Resubmit It to the Same Journal 133
12.8 Submit It to a Different Journal 134
12.9 Filing the Manuscript Without Resubmission 135
12.10 Conclusion 136
Case Scenario 136
References 137
13: Authorship and Contributorship 138
13.1 Introduction and Definition 139
13.2 Importance of Authorship 140
13.3 Accountability and Duties of Author(s) 140
13.4 Authorship Policy 141
13.4.1 Order of Authors 142
13.4.2 Corresponding Author 142
13.5 Contributorship 142
13.6 Acknowledgments vs. Authorship 143
13.7 Gift Authorship 144
13.8 Ghost Authorship 144
13.9 Plagiarism 145
13.10 Summary 145
Case Scenario 146
References 146
14: Types of Manuscripts 147
14.1 Introduction 148
14.2 Letter to Editor/Brief Correspondences 150
14.3 Case Reports 150
14.4 Case Series 151
14.5 Original Articles/Scientific Articles 151
14.5.1 Publishing Clinical Trials 152
14.5.2 Helsinki Declaration and Human Trials 152
14.6 Review Articles 153
14.7 Levels of Evidence 154
14.8 Non-scientific Articles 154
Scenario 155
References 155
15: What Does a Reviewer Look into a Manuscript 156
15.1 Introduction 157
15.2 The Review Process 157
15.3 What Does a Reviewer See in a Manuscript? 159
15.3.1 General Considerations 159
15.3.2 Specific Considerations Related to the Scientific Merits of the Manuscript 160
15.3.2.1 Title and Abstract 160
15.3.2.2 Introduction 160
15.3.2.3 Methods 160
15.3.2.4 Data Analysis and Statistics 161
15.3.2.5 Results 161
15.3.2.6 Discussion 161
15.3.2.7 Conclusion 162
15.3.2.8 References 162
15.3.2.9 Standardized Checklist 162
15.3.3 Organization and Presentation of the Manuscript 163
15.4 Tips to Survive a Peer Review 163
15.5 Conclusion 163
Scenario 167
References 168
16: Open Access for Publication – Can It Be Chosen? 170
16.1 Introduction 171
16.2 How Does OA Compare to Other Publishing Models? 172
16.3 The Cost of OA 172
16.4 Specific Aspects of OA 173
16.5 Self-Archiving as Opposed to OA 174
16.6 Research Impact of OA 175
16.7 Which Journal Would You Publish in? 175
16.8 Conclusion 176
Scenario 177
References 177
17: Publishing Misconduct Including Plagiarism and Permissions 179
17.1 Introduction 180
17.2 Causes for Plagiarisms 180
17.3 Types of Plagiarisms 181
17.3.1 Verbatim Copy of Contents 181
17.3.2 Mosaic Plagiarism 181
17.3.3 Style Plagiarism 182
17.3.4 Idea Plagiarism 182
17.3.5 Metaphor Plagiarism 182
17.3.6 Self-Plagiarism or Auto-plagiarism 183
17.4 Copyright Protection 183
17.5 Consequences of Plagiarism and Copyright Violation 184
17.6 Committee on Publication Ethics (COPE) Guidelines on Plagiarism 185
17.7 Avoiding Plagiarism 185
17.7.1 Education and Awareness 185
17.7.2 Read, Understand, and Write Without Source Nearby 185
17.7.3 Write Notes from a Primary Source, and Prepare Manuscript from Notes 186
17.7.4 Follow the Guidelines for Scientific Writing 186
17.7.5 Self-Check for Plagiarism 186
17.7.6 Avoid Publication of One Research Work into Multiple Parts 187
17.8 Tools to Check Plagiarism 188
17.9 Other Publication Misconducts 188
17.10 Conclusion 189
Case Scenario 189
References 190
18: Ethical Dilemmas and Etiquettes of Scientific Publication 191
18.1 Introduction 192
18.2 Importance of Documentation 193
18.3 Ethical Issues and Dilemmas 193
18.3.1 Authorship Ethical Issues 193
18.3.2 Editorial Ethical Issues 194
18.4 Promising Newer Metrics 196
18.5 Conclusion 196
Case Scenario (Handling Plagiarism) 197
References 197