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Writing Introduction for Manuscript (scientific writing)

To introduce participants to the details of communication and writing scientific papers.
To guide researchers in the writing of scientific paper to increase its acceptability for publication in a journal; and
To upgrade the pre-existing knowledge of writing skills in a scientific manner.

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Writing Introduction for Manuscript (scientific writing)

  1. 1. Writing Introduction Section Training Workshop on Scientific Research, Communication and Publication Ashok Pandey Research Officer NHRC 7/2/2019 1
  2. 2. Before start writing Be sure to select appropriate journal Follow the instructions of journal Keep research ethics in mind 7/2/2019 2
  3. 3. Essential information 1. Number of articles had already crossed 50 million by 2009. 2. Since then on an average 2.5 million new scientific papers are published each year. 3. 34,400+ peer-reviewed journal in late 2014 4. No. of article increases at a rate of approximately 4% per year. 5. Number of researchers was 8.4 million in 2011 (Full time 6.3 million) 6. A researcher reads on an average 270 articles per year, depending on discipline (more in medicine and science) 7. Average time spent on reading an article was 50 min in 1990 and 30 min now. 8. If you read less than 270 articles per year, its likely that an average researcher writes better than you do. 7/2/2019 3
  4. 4. "Hell is sitting on a hot stone reading your own scientific publications" - Erik Ursin ‘‘There are many exceptions in ecology. The author has summarized them in four books’’ - Jens Borum, ecologist 7/2/2019 4
  5. 5. Scimago Journal and country rank (1996-2018) Accessed date: July 1, 2019 Rank Country Documents Citable documents Citations Self- Citations Citations per Document H index 1 USA 12070144 10701848 297655815 134368758 24.66 2222 2 China 5901404 5785424 48833849 27480980 8.27 794 91 Nepal 14965 13382 166841 20487 11.15 129 239 Heard Island and McDonald Islands 2 2 9 0 4.50 1 Source: 7/2/2019 5
  6. 6. Scimago Journal & Country Rank (Among 31971 journal) Accessed date: July 1, 2019 Rank Title SJR H inde x Total Docs. (2018) Total Docs. (3years) Total Refs. (2018) Total Cites (3years) Citable Docs. (3years) Cites / Doc. (2years) Ref. / Doc. (2018) 1 CA - A Cancer Journal for Clinicians 72.57 6 144 45 127 3078 20088 103 206.85 68.40 14409 Journal of Nepal Health Research Council 0.253 Q3 9 23 92 0 55 88 0.26 0.00 17441 Kathmandu University medical journal (KUMJ) 0.174 Q3 21 53 259 879 86 238 0.31 16.58 7/2/2019 6
  7. 7. Scimago Journal & Country Rank (Among 31971 journal) Accessed date: July 1, 2019 Rank Title SJR H inde x Total Docs. (2018) Total Docs. (3years) Total Refs. (2018) Total Cites (3years) Citable Docs. (3years) Cites / Doc. (2years) Ref. / Doc. (2018) 1 CA - A Cancer Journal for Clinicians 72.57 6 144 45 127 3078 20088 103 206.85 68.40 14409 Journal of Nepal Health Research Council 0.253 Q3 9 23 92 0 55 88 0.26 0.00 17441 Kathmandu University medical journal (KUMJ) 0.174 Q3 21 53 259 879 86 238 0.31 16.58 7/2/2019 7
  8. 8. 7/2/2019 Scimago journal ranking of Nepal There are 152 journals listed on NepJOL. There are 1349 Tables of Contents listing 17,476 articles. 16,725 of the articles are available in full text (PDF). Assessed date: 2nd July 2019 8
  9. 9. 7/2/2019 Never try to be infamous 9
  10. 10. 7/2/2019 Never try to be infamous 10
  11. 11. Difference between Introduction and Background • Both an introduction, as well as, background is necessary and integral parts of a document • Introduction is like showing a trailer of a movie to entice a reader to go through the entire document • Background is to make a reader understand the reasons of conducting a study and the incidents leading up to the study. Example • Intro: Known worldwide for it's magnificent Eiffel Tower, France has so much more to offer in magnificence. • Background: France is a European country situated between England and Spain. The dominant language is, of course, French. The country also borders the Pyrenees Mountains to the southwest, and Italy to the southeast. 7/2/2019 11
  12. 12. The difference is that introduction is like the universal set while background is a subset of the universal set. The introduction contains the background of the study as well as other elements. • statement of the problem • goal and deliverables of the research • justification/significance/rationale • scope of the study • aim and objectives 7/2/2019 12
  13. 13. Example URL: URL: 7/2/2019 13
  14. 14. Example Source: Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F: Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002,3:RESEARCH0034. Background Gene-expression analysis is increasingly important in many fields of biological research. Understanding patterns of expressed genes is expected to provide insight into complex regulatory networks and will most probably lead to the identification of genes relevant to new biological processes, or implicated in disease. Two recently developed methods to measure transcript abundance have gained much popularity and are frequently applied. Microarrays allow the parallel analysis of thousands of genes in two differentially labeled RNA populations [1], while real-time RT-PCR provides the simultaneous measurement of gene expression in many different samples for a limited number of genes, and is especially suitable when only a small number of cells are available [2,3,4]. Both techniques have the advantage of speed, throughput and a high degree of potential automation compared to conventional quantification methods, such as northern-blot analysis, ribonuclease protection assay, or competitive RT-PCR. Nevertheless, these new approaches require the same kind of normalization as the traditional methods of mRNA quantification. Several variables need to be controlled for in gene-expression analysis, such as the amount of starting material, enzymatic efficiencies, and differences between tissues or cells in overall transcriptional activity. Various strategies have been applied to normalize these variations. Under controlled conditions of reproducible extraction of good-quality RNA, the gene transcript number is ideally standardized to the number of cells, but accurate enumeration of cells is often precluded, for example when starting with solid tissue. Another frequently applied normalization scalar is the RNA mass quantity, especially in northern blot analysis. There are several arguments against the use of mass quantity. The quality of RNA and related efficiency of the enzymatic reactions are not taken into account. Moreover, in some instances it is impossible to quantify this parameter, for example, when only minimal amounts of RNA are available from microdissected tissues. Probably the strongest argument against the use of total RNA mass for normalization is the fact that it consists predominantly of rRNA molecules, and is not always representative of the mRNA fraction. This was recently evidenced by a significant imbalance between rRNA and mRNA content in approximately 7.5% of mammary adenocarcinomas [5]. Also, it has been reported that rRNA transcription is affected by biological factors and drugs [6,7,8]. Further drawbacks to the use of 18S or 28S rRNA molecules as standards are their absence in purified mRNA samples, and their high abundance compared to target mRNA transcripts. The latter makes it difficult to accurately subtract the baseline value in real-time RT-PCR data analysis. Statement of the problem To date, internal control genes are most frequently used to normalize the mRNA fraction. This internal control - often referred to as a housekeeping gene - should not vary in the tissues or cells under investigation, or in response to experimental treatment. However, many studies make use of these constitutively expressed control genes without proper validation of their presumed stability of expression. But the literature shows that housekeeping gene expression - although occasionally constant in a given cell type or experimental condition - can vary considerably (reviewed in [9,10,11,12]). With the increased sensitivity, reproducibility and large dynamic range of real-time RT-PCR methods, the requirements for a proper internal control gene have become increasingly stringent. Purpose and what was done In this study, we carried out an extensive evaluation of 10 commonly used housekeeping genes in 13 different human tissues, and outlined a procedure for calculating a normalization factor based on multiple control genes for more accurate and reliable normalization of gene-expression data. Furthermore, this normalization factor was validated in a comparative study with frequently applied microarray scaling factors using publicly available microarray data. 7/2/2019 14
  15. 15. While writing the Background, make sure your citations are: Well balanced: If experiments have found conflicting results on a question, have you cited studies with both kinds of results? Current: Every field is different, but you should aim to cite references that are not more than 10 years old if possible. Relevant: This is the most important requirement. The studies you cite should be strongly related to your research question. • DO NOT write a literature review in your Background, but • DO cite reviews where readers can find more information if they want it. 7/2/2019 15
  16. 16. Once you have provided background material and stated the problem or question for your study, tell the reader the purpose of your study. Usually the reason is to fill a gap in the knowledge or to answer a previously unanswered question. Eg. if a drug is known to work well in one population, but has never been tested in a different population, the purpose of a study could be to test the efficacy and safety of the drug in the second population. The final thing to include at the end of your Background is a clear and exact statement of your study aims. You might also explain (very briefly!) how you conducted the study. 7/2/2019 16
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  18. 18. The Introduction Primary goal: Build the rationale for your study Is the topic important? Will the paper advance knowledge? Secondary goal: Sell your paper to reviewers/readers Is the topic appropriate for the journal? 7/2/2019 18
  19. 19. The Introduction Move from broad to narrow The big picture your study Why your study question is important? Will the paper advance knowledge in the field? Objectives and brief description of study Do not assume that need for your study is obvious-Sell it to your readers and reviewers 7/2/2019 19
  20. 20. Appearing first = The importance of the topic Appearing second = Highlights of relevant previous research Appearing third = Identification of unanswered question(s) Appearing fourth = Your hypotheses, if any Appearing last = Approach you used to seek the answer(s) 7/2/2019 20
  21. 21. Outline for an Introduction Why did you do this study? 1. Define the general area of the problem. 2. Develop the background of the problem. Include previous studies. 3. State the basis for your study (limited data, a new phenomenon, side- effects, conflicting previous observations, additional investigation, a new problem) 4. State why the question your study addressed is important. 5. State the specific problem you studied. 7/2/2019 21
  22. 22. Criteria of writing introduction in The lancet Systematic reviews and meta-analyses • Give the background to your study, providing references for data presented and all previous studies mentioned. • State why now is an appropriate time to do a systematic review/meta- analysis? • End with the aim of your study Source: Systematic reviews and meta-analyses in The Lancet: formatting guidelines 7/2/2019 22
  23. 23. Criteria of writing introduction in BMC Background The Background should provide readers with the information needed to understand your study, and the reasons why you conducted your experiments. • The Background should answer the question: • What question/problem was studied? Source: BMC 7/2/2019 23
  24. 24. Criteria of writing introduction in NHRC Provide a context or background for the study (that is, the nature of the problem and its significance). State the specific purpose or research objective of, or hypothesis tested by, the study or observation; the research objective is often more sharply focused when stated as a question. Both the main and secondary objectives should be clear, and any pre- specified subgroup analyses should be described. Provide only directly pertinent references, and do not include data or conclusions from the work being reported. The word limit for introduction is 150. Source: 7/2/2019 24
  25. 25. Take home message Just by following the instructions closely, you can increase your chances of getting published. Write to inform not to impress 7/2/2019 Thank you 25