This presentation is created by Dr. Nizar Saleh Abdelfattah in 2017. He used it in his episodes of "Research Fundamentals For Dummies" on YouTube. https://www.youtube.com/playlist?list=PLuDFktFSWZ_XVufo7h9bDIerKoo7s3ouA * The original presentation on Mediafire: http://www.mediafire.com/file/mu5dml695g5r8qf/How-to-Research-by-Nizar-Abdelfattah.pptx/file

1. How to Read a Research
Article?
Nizar Saleh Abdelfattah, MD
Assistant Scientist in Ophthalmology, UCLA
July 30, 2017

2. What is a Research Article?
 Research Article = Manuscript = Research Paper = Journal Article
 Research is published through
1. Journal: peer-reviewed (as Full study)
2. Conference: International (as Abstract)
It is presented in conferences as a Paper (oral presentation) or a Poster.
 Research articles are like Facebook posts! You write down what you did, and post it for everyone to see.
 Research articles are always peer-reviewed. This makes them the most respected and well-evidenced
type of research publications
 Research articles are not restricted to medicine or science. Economics, agriculture, astronomy, music,
history, religion, engineering, law…etc.
 Researchers write their study details, send it to a research journal, a board of experts review the study,
then write their scientific analysis about it. If the study is strong, it is published as a research article. If
not, it is rejected from being published.
 The main cause of rejection is stretch of conclusions.

3. How to find a senior to work with?
https://www.ncbi.nlm.nih.gov/pubmed/advanced

4. Why Is It Important to Read an Article?
 For every field, people may be divided into 2 types:
specialists and lay people.
• Lay people only read breaking-news articles! Like “New Study Suggests that Chocolate
causes Cancer”.
• Specialists should read nearly all articles related to their specialty, especially if their field
constantly changes e.g. clinical medicine.
 Specialists may be divided into 2 types:
research creators and research consumers.
• Creators read all relevant articles to help them with their research studies.
• Consumers read relevant articles to help them update their knowledge and work habits
e.g. prescribing doses differently to patients, or asking for different lab tests to reach
diagnosis.
 Reading articles is the most important skill in order to write articles.

5. Types of Research Articles
In medicine, there are 4 major types:
Primary (Original)
1. Clinical research articles include:
prospective studies, case-control studies, clinical trials, cross-sectional studies,
methodology studies …etc.
2. Bench/lab research articles (Basic science research) include:
laboratory experiments whether in-vitro or in-vivo on animal models.
Secondary
3. Review articles include:
literature reviews, systematic reviews, meta-analyses ..etc.
4. Other mini-articles include:
letters to editor, opinion piece/perspective, case reports/series, clinical image…etc.

6. Original Research Articles
 Title
 Authors:
1st author, Middle/contributing author,
Statistician, Senior author
 Abstract
 Introduction
 Methods
 Results
 Discussion
 References

7. Abstract
 A 250-words summary of the whole study.
 First part read in an article. Usually it is the free part.
 Usually the only part to be read by research consumers.
 Gives only the big picture, but no details, no mentioning of all the findings.
 Divided into:
• Purpose
• Methods
• Results
• Conclusions

8. Example
 Purpose = What are you
trying to do?
 Methods = What are the steps
you took (in order to reach
your purpose)?
& exclude the confounding
factors
 Results = What did you find
(without giving your opinion
or interpretation)?
 Conclusions = What do these
results mean?

9. Should I Read The Whole Article?
 The rule is to always see the whole article, but only read the important parts!
 Abstract is NEVER enough.
 The exception is when you are looking for something specific, only here you can
just read the abstract to know whether this article may have what you are looking
for.

10. So How Should I Read the Article?
 If the article is in your field of experience (for example, you are a cardiologist specialized in
arrhythmias, and the article is about comparing 2 new anti-arrhythmic drugs), then you can
only read the methods and results section. You are experienced enough to draw your own
conclusions based on what the researchers did.
 If the article is not in your immediate field of experience (for example, you are the same
cardiologist, but the article is about comparing 2 new drugs for hypertrophic cardiomyopathy
“HCM”). Here, cardiology might be your “big specialty” but you do not spend everyday
reading about HCM! So here you need to also read the discussion part to understand what
should be the conclusions drawn from the results of this study.
 If the article is completely outside your field of experience (for example, you are a student or
non-specialist), then you will benefit the most from the introduction section of the article
because it will tell you why researchers thought about this study from the start.

11. Why A Specialist Needs to Read the
Methods?
 Fact: Researchers are humans, and they can be biased!
 Reading only the results may cause you to (for example) think that Drug-A is way
better than Drug-B because patients got better.
 But, methods can be weak, and don’t mean that these results are valid.
 How?
 The sample size of the study may be too small!
 Or the diagnostic test used to judge drug effectiveness is a non-specific test!
 Or some patients had a big confounding factor!
 Or patients taking Drug-A were mildly sick compared to patients taking Drug-B!

12. Anatomy of the
Research Article
 Title Field
 Abstract
 Introduction
 Methods
 Results
 Discussion
 References

13. Anatomy of the Research Article (Title Field)

14. Authorship
 Authors of any research study
are defined as people who
fulfill 4 criteria:
http://www.icmje.org/recommendations/browse/roles-and-
responsibilities/defining-the-role-of-authors-and-contributors.html

15. Authorship
• Vancouver protocol 1979

16. Authorship https://www.ncbi.nlm.nih.gov/pmc/2544445/
Co-first author: *These authors contributed equally to this manuscript

17. Journals
 Good journals vs. Bad journals
• According to:
1)Editorial board
2)Impact factor
3)Fame of journal
 Open access vs. restricted access
• Usually bad journals offers open access ONLY
 Impact factor: reflects the yearly average number of citations that articles published in
the last 2 years
 Citation: a reference to a published or unpublished source
 List of journals you should target (reading & writing for):
• Journal Citation Reports
• Scimago Journal & Country Rank

18. Anatomy of the Research
Article (Introduction)
 Introduction of a research article is composed of 3 sections:
the past, the present, and the future.
 It provides the reader with a sequence of events 
1. General information about the disease/problem.
2. Currently available knowledge
3. Currently missing knowledge
4. Importance of finding the “currently missing knowledge”
5. Stating which piece of “currently missing knowledge” we will
study.

19. Anatomy of the Research Article (Introduction)
 Example-1:
It is known that several general anesthetics, including barbiturates, depress the
bronchomotor response to vagus nerve stimulation. However, the site of this
depression has not been determined. Identifying these sites is crucial for research
studies and clinical trials comparing different pharmaceutical agents. The purpose of
this study is to determine which site in the vagal motor pathway to the bronchioles is
most sensitive to depression by barbiturates.

20. Anatomy of the Research Article (Introduction)
 Example-2:
Previous investigations have demonstrated that metabolic alkalosis during exercise
increases blood lactate concentrations substantially beyond the concentrations
observed during exercise in the absence of metabolic alkalosis. Conversely, metabolic
acidosis decreases blood lactate concentrations. However, for these investigations,
alkali was ingested or infused, which is an artificial situation. More important clinically
is the effect of respiratory alkalosis that occurs during exercise in a variety of
circumstances that involve increased respiratory drive. These circumstances include
interstitial lung disease and congestive heart failure. This study aims to determine the
effect of respiratory alkalosis during exercise on blood lactate concentrations.

21. Anatomy of the Research Article (Introduction)
 Example-2:
Previous investigations have demonstrated that metabolic alkalosis during exercise
increases blood lactate concentrations substantially beyond the concentrations
observed during exercise in the absence of metabolic alkalosis. Conversely, metabolic
acidosis decreases blood lactate concentrations. However, for these investigations,
alkali was ingested or infused, which is an artificial situation. More important clinically
is the effect of respiratory alkalosis that occurs during exercise in a variety of
circumstances that involve increased respiratory drive. These circumstances include
interstitial lung disease and congestive heart failure. This study aims to determine the
effect of respiratory alkalosis during exercise on blood lactate concentrations.

22. Anatomy of the Research Article (Introduction)
 Example-3:
Neovascular age-related macular degeneration is a leading cause of vision loss in
developed nations. The use of anti-VEGF agents led to improvement in visual
outcomes for patients. However, these outcomes can be limited by the development
of macular atrophy or fibrosis. There has been a significant interest in the hypothetical
neurotoxic relationship between anti-VEGF and development of macular atrophy. This
study utilizes multimodal imaging to better define the frequency and progression of
macular atrophy in eyes with neovascular AMD undergoing treatment with anti-VEGF
injections.

23. Anatomy of the Research Article (Introduction)
 Example-3:
Neovascular age-related macular degeneration is a leading cause of vision loss in
developed nations. The use of anti-VEGF agents led to improvement in visual
outcomes for patients. However, these outcomes can be limited by the development
of macular atrophy or fibrosis. There has been a significant interest in the hypothetical
neurotoxic relationship between anti-VEGF and development of macular atrophy. This
study utilizes multimodal imaging to better define the frequency and progression of
macular atrophy in eyes with neovascular AMD undergoing treatment with anti-VEGF
injections.

24. Anatomy of the Research Article (Introduction)
General information
about the
disease/problem.
Currently available
knowledge
Currently
missing
knowledge
Importance of
finding the
“currently missing
knowledge”
Stating which piece
of “currently
missing
knowledge” we will
study.

25. Anatomy of the Research Article (Methods)
 Methods of a research article is a step-by-step explanation of what the authors did in-detail.
Purpose of the “Methods”
1. To provide evidence for why the results are valid
2. To provide sufficient details for a trained scientist to exactly repeat the experiments
3. To prove external or internal validity
• Internal validity:
is the level of the study results accuracy (in a tightly-controlled population)
• External validity:
is the suitability of the study results to be generalized (on the general population)

26. Anatomy of the Research Article (Methods)
 It is composed of 3 sections: (the materials, the approach, and the analysis).
 It provides the reader with a sequence of events 
1. What were the materials / Who were the patients?
2. Study Design (Protocol)?
3. How the authors prevented potential biases?
4. How the authors measured each variable/conducted each experiment/performed each surgery?
5. Statistical Analysis of Data

27. Anatomy of the Research Article (Methods)
1. What were the materials / Who were the patients?
Detailed description about materials will be explained e.g.:
• Patients (diagnosis, age, sex, race, stage of disease, how data was obtained)
• Drugs (scientific name, dose, route of administration, manufacturer)
• Surgery (pre-operative evaluation, surgical materials, surgical technique)
2. Study Design (Protocol)?
Manipulations (done to induce a change) and Measurements (made to assess the change)

28. Anatomy of the Research Article (Methods)
3. How the authors prevented potential bias?
Bias Definition Rx
Flawed Study
Design bias
vague purpose, subjective outcome measures, variable data collection
methods
Standardize
Selection bias cherry picking some patients whose data can support the author’s
claim, but can not represent the general population. Or, just small
sample size.
Randomize
Detection bias
(Data fishing)
excessive testing for patients group more than control group,
hoping that some results will support the author’s claim.
Blind Doctor
Observer bias using author’s subjective evaluations as a tool to support their claims Blind Doctor/
adjudication/
principle
investigator/
Artificial
intelligence
Recall bias patients knew they were “control group”, so didn’t feel placebo effect.
Or, report what they “remember/believe” happened.
Blind Patient
Non-Response
bias
publishing data from only few people who responded to the survey Incentives

29. Bias Definition Rx
Response bias using leading questions, or long surveys (fatigue)  unreal
replies.
Standardize
Survivor bias analyzing only the healthy winner, ignoring the sick failures Randomize
Citation bias authors publish only +ve results, for fear of rejection Trial Registration
Confounding bias association is due to 3 factors
(exposure, outcome, and a 3rd independent variable)
Randomize
Publication bias collecting famous articles with +ve data only for a meta-analysis Wide Literature
Review
Hawthorne bias Change in behavior in response to awareness of being observed
e.g. White coat hypertension
Repeated
Observations
Channeling bias assigning cases to treatment groups based on their prognostic
factors.
Randomize
Transfer bias excessive patients lost to follow-up from one group compared
to other
Incentives
Performance bias using multiple surgeons to operate on study patients Clustering
Anatomy of the Research Article (Methods)
3. How the authors prevented potential bias?

30. Anatomy of the Research Article (Methods)
4. How the authors measured each variable, conducted each experiment, or
performed each surgery?
Famous
Method
Published
Method
New
Method
Zeiger M, 1991

31. Anatomy of the Research Article (Methods)
5. Statistical Analysis of the Data
a. Sample size and power of study.
b. How data were summarized.
c. Statistical tests used.
d. Statistical software used.
e. P value differences considered
significant.
• p-value or probability value is the
probability of obtaining test results
at least as extreme as the results
actually observed during the test,
assuming that the null hypothesis is
correct
 < 0.05 is good / significant
 > 0.05 is bad / not significant
Abdelfattah NS et al. 2016

32. Anatomy of the Research Article (Results)
a) Demographic Characteristics (applicability)
b) Main primary outcome measures findings (most important findings first)
c) Secondary outcome measures findings (least important findings next)
d) For every result reported, there should be a method described.

33. Anatomy of the Research Article (Results)
What is included in the results section?
 Relevant results only.
 Results included whether or not they support your hypothesis.
 Findings only with no comparisons to literature. So, No references!
 Results vs. Data (facts)
 Raw vs. Summarized vs. Transformed Data.
 Tables and Figures  to provide absolute clarity for results’ presentation.

34. Anatomy of the Research Article (Results)
Example of how results are written
 Data, but no Result Stated
In the 20 control subjects, the mean resting blood pressure was 85 +/- 5 (SD) mmHg. In comparison,
in the 30 tennis players, the mean resting blood pressure was 94 +/- 3 mmHg.
 Result Stated
The mean resting blood pressure was higher in the 30 tennis player than in the 20 control subjects
(94 +/- 3 vs. 85 +/- 5 mmHg, P < 0/0.2).
 Result Stated, with Magnitude
The mean resting blood pressure was 10% higher in the 30 tennis player than in the 20 control
subjects (94 +/- 3 vs. 85 +/- 5 mmHg, P < 0/0.2).

35. Anatomy of the Research Article (Discussion)
 Beginning:
 Most important research answers (Primary Outcome)
• Supporting Evidence of 1ry Research Answer (explanation of results)
 Less important research answers (Secondary Outcomes)
• Supporting Evidence of 2ry Research Answer (explanation of results)
 Middle:
• Notable remarks or complications in clinical trials  Atypical scenarios
(limitations i.e. Uncorrectable conditions & strengths)
• Interesting related points and relation to literature
 Ending:
• In summary
• Future directions

36. Anatomy of the Research Article (References)
 Reference to a journal publication:
1. Van der Geer J, Hanraads JAJ, Lupton RA. The art of writing a scientific article. J Sci Commun. 2010;163:51-
59.
 Reference to a book:
2. Strunk W Jr, White EB. The Elements of Style. 4th ed. New York, NY: Longman; 2000.
 Reference to a chapter in an edited book:
3. Mettam GR, Adams LB. How to prepare an electronic version of your article. In: Jones BS, Smith RZ,
eds. Introduction to the Electronic Age. New York, NY: E-Publishing Inc; 2009:281-304.
 Reference to a website:
4. Cancer Research UK. Cancer statistics reports for the UK.
http://www.cancerresearchuk.org/aboutcancer/statistics/cancerstatsreport/; 2003 Accessed 13.03.03.