Introduction to quantitative research (whole course)

• Professor ABDULAZIZ ALKAABBA
Professor of Family Medicine and Bioethics, AL-Imam University - College of Medicine
Board member of the Saudi Healthcare Ethics Society
• Dr. Ghaiath Hussein
Assistant professor of Bioethics and Community Medicine
Board member of the Saudi Healthcare Ethics Society
• Dr. Abdullah Adlan
Consultant Biomedical Ethics and Health-care Governance, Adjunct Assistant Professor,
KSAU-HS
Head of the Biomedical Ethics Department, King Abdullah International Medical Research
Center (KAIMRC), Riyadh, KSA

• Describe the Research
Publication Cycle
• Describe the steps in
constructing, revising, editing
and submitting a manuscript
for publication in a peer-
reviewed journal
• Explain the IMRAD structure
approach of scientific
publications
• Define reference management
software (RMS)
• List examples of the main RMS
• Install and apply the basic
functions of Mendeley
• Describe and apply criteria of
choosing journals for
publication
• List the reasons for rejecting
the submitted manuscripts
1 2

Date & time Topics Speaker
Day 1: Prepare your manuscript
8.00 - 8.30 Registration
8.30 – 9.00 The research-publication cycle
- The Knowledge Management Cycle
- Overview on research steps from idea to
publication
Prof. Alkabba
9.00 – 9.30 How to structure your paper? IMRAD: Part I
- Title, Abstract and Keywords
- Introduction, Methods and Results
Dr. Adlan
9.30 – 10.10 How to structure your paper? IMRAD: Part II
- Discussion and Conclusions
- Figures and tables
- Acknowledgments and References
Dr. Ghaiath
10.10 – 10.20 Coffee break
10.20 – 11.00 Formatting your manuscript
- IMRaD structure
- Author’s guidelines
- Online submission systems
Dr. Adlan
Dr. Ghaiath
11.00 – 11.30 Ethical considerations in scientific publications
- Authorship and authors' responsibilities
- Falsification, fabrication and plagiarism
Prof. Alkabba
11.30 – 12.00 Tips for using reference management
software (Mendeley)
- What is the RMS?
- How RMS can help in your research
& publication?
- Practical tips to Mendeley
Dr. Ghaiath
Dr. Adlan
12.00 – 1.00 Prayer & lunch break
1.00 – 4.00 Practical sessions: groups will have the
following tasks
- Critically read a publication (does it
follow IMRaD structure?)
- Outline a (mock) manuscript you
developed from your research report
- How to search and cite using
Mendeley?
Prof. Alkabba
Dr. Ghaiath
Dr. Adlan
4.00 – 4.20 Work group presentations Groups
4.20 – 4.30 Wrap-up and tasks for Day 2 Prof. Alkabba
Dr. Ghaiath
Dr. Adlan
1 2

Day 2: Publish your manuscript
8.30 – 9.00 Selecting a journal & submitting your paper for publication Prof.Alkabba
9.00 – 9.30 What do journal editors want? Dr. Adlan
9.30 – 10.00 Cover letters and supplementary documents for manuscript submission Dr. Adlan /Dr. Ghaiath
10.10 – 10.20 Coffee break
10.20 – 11.00 Understanding peer review process & Journal decisions - I Dr. Adlan
11.00 – 11.30 Understanding peer review process & Journal decisions - II Dr. Ghaiath Hussein
11.30 – 12.00 Reference management and manuscript preparation) Dr. Abdullah Adlan
Dr. Ghaiath Hussein
12.00 – 1.00 Prayer & lunch break
1.00 – 4.00 Practical sessions- groups will have the following tasks:
- Critically read a published article – if you were a reviewer, what would
you suggest?
- Respond to a (mock) reviewer’s comments on their manuscript.
Prof. Abdulaziz Alkabba
Dr. Ghaiath Hussein
Dr. Abdullah Adlan
4.00 – 4.20 Work group presentations Groups
4.20 – 4.30 Wrap-up and end of workshop (certificates)

The Research-
Publication Cycle
Prof. Abdulaziz Alkabba
The Knowledge Management Cycle
Overview on research steps from
idea to publication

“Good” research: Good Science & Good Ethics
“Good” Evidence: near-top to hierarchy of
Evidence
Evidence-Based Healthcare: Better
practice that is based on best evidence
Better health status
Why do we need research?

Research planning - implementation cycle
Planning
Conducting
Data
Management
ReportingDissemination
Evidence
synthesis
New research
questions

Generation
Dissemination
SynthesisUtilization
Assessment
Statistics
Research in Context
Evidence-based
Guidelines
Evidence-informed
policy
Knowledge
Management
Cycle

Research Life Cycle
Credit: https://images.app.goo.gl/NR6Fa9Y82JyErUHf9

• Contribute to the body of knowledge
• To become a recognized expert in your field
• To help develop or improve on existing practice or policy
• To advance your career (promotions)
• Gain inner satisfaction
https://simplyeducate.me/2013/07/20/why-publish-research-findings/

What are
the
you faced
when you
tried to
publish?
• Group A • Group B
Tasks:
1. Divide yourselves into two groups.
2. Share your experiences about scientific publications
3. What are the main challenges you faced when you tried to publish?

Essential Research Skills
Before conduct (Prepare) During conduct (Do) After conduct (Disseminate)
Review of literature Research methods (Q&Q) Reference management
Proposal writing Designing data collection tools Scientific writing
Grant writing (and hunting) Data analysis (Quan. & Qual.) Writing for publication
Research ethics Plagiarism Publication ethics
Cross-cutting skills:
• Critical thinking
• Leadership skills
• Project management
• Presentation (communication) skills
• Resource (Time) management
• Scientific writing

How to structure your paper? IMRAD: Part I
Dr. Abdullah Adlan
- Title, Abstract and Keywords
- Introduction, Methods and Results
Source: https://www.enago.com/academy/

What to
read an article?
• Reflect on your latest online literature search …
• What made you stop at a specific article to click it?

Titles matter!
Nicola Di Girolamo and Reint M. Reynders (2016) found
that:
• Titles in the Altmetric Top 100 were 102.6 characters
long, included 3.4 uncommon words, and 29.6% were
declarative
• Declarative titles having lesser uncommon words were
significantly more represented in the Altmetric Top 100
• Declarative titles had 2.8 times the odds in the top list
• For every extra uncommon word used in the title, there
was a 1.4 increase in the odds to be non-Altmetric Top
100 article
• The conclusion of the study showed that an
informative and easy to understand title might help in
bridging the gap between scholarly and social media
dissemination.

• Declarative
State the main conclusions.
Example: Mixed strains of probiotics improve
antibiotic associated diarrhea.
• Descriptive
Describe the subject.
Example: Effects of mixed strains of
probiotics on antibiotic associated diarrhea.
• Interrogative
Use a question for the subject.
Example: Do mixed strains of probiotics
improve antibiotic associated diarrhea?

Tips for an
Attractive Title
•Be concise
• Convey the main topics
• Highlight the importance
• Be concise
•Be descriptive
•Use a low word count (5-15
words)
•Check journal guidelines
•Avoid jargon and symbols

Why did it
become #1?
https://www.cebm.net/wp-content/uploads/sites/3/2016/06/Nicola-Di-Girolamo.pdf

Problematic Titles
• Does Vaccinating Children and Adolescents with Inactivated
Influenza Virus Inhibit the Spread of Influenza in
Unimmunized Residents of Rural Communities?
This title has too many unnecessary words.
• Influenza Vaccination of Children: A Randomized Trial
This title doesn’t give enough information about what makes
the manuscript interesting.
• Effect of Child Influenza Vaccination on Infection Rates in
Rural Communities: A Randomized Trial
This is an effective title. It is short, easy to understand, and
conveys the important aspects of the research.
TIP: Write down a few possible titles, and then select the best to
refine further. Ask your colleagues their opinion. Spending the
time needed to do this will result in a better title.Photo Credit

Abstracts and Keywords … What & Why?
• An abstract is a self-contained, short, and precise summary that
describes a larger work.
• Components vary according to discipline (IMRaC ± Limitations)
• The abstract is an original content rather than an excerpted passage.
Why write an abstract?
• Selection and Indexing:
• To allow readers who may be interested in a longer work to quickly decide
whether it is worth their time to read it.
• many online databases use abstracts to index larger works.
• Therefore, abstracts should contain keywords and phrases that allow for easy
searching.
https://writingcenter.unc.edu/tips-and-tools/abstracts/

Abstract format
• Depending on the author guidelines of the
journal, it can be:
• The structured abstract
• has distinct sections with headings(objective,
methods, results, and conclusion), which
enables a reader to easily find the relevant
information under clear headings
• Think of each section as a question and provide
a concise but detailed answer under each
heading.
• The unstructured abstract
• is a narrative paragraph of your research.
• It is similar to the structured abstract but does
not contain headings.
• It gives the context, findings, conclusion, and
implications of your paper.

Good abstract should be
• A summary of the content of the journal manuscript
• A time-saving shortcut for busy researchers
• A guide to the most important parts of your manuscript
• Able to stand alone (the only part of your article that appears in indexing)
• Helping to speed up the peer-review process.
• Answering these questions about your manuscript:
• What was done?
• Why did you do it?
• What did you find?
• Why are these findings useful and important?
TIP: Journals often set a maximum word count for Abstracts, often 250 words,
and no citations. This is to ensure that the full Abstract appears in indexing
services.

All abstracts include:
• A full citation of the source, preceding the
abstract.
• The most important information first.
• The same type and style of language found in
the original, including technical language.
• Key words and phrases that quickly identify
the content and focus of the work.
• Clear, concise, and powerful language.
Abstracts may include:
• The thesis of the work, usually in the first
sentence.
• Background information that places the
work in the larger body of literature.
• The same chronological structure as the
original work.
How not to write an abstract:
• Do not refer extensively to other works.
• Do not add information not contained in the
original work.
• Do not define terms.
https://writingcenter.unc.edu/tips-and-tools/abstracts/

Keywords
• Keywords are a tool to help indexers and
search engines find relevant papers.
• If database search engines can find your
journal manuscript, readers will be able to find
it too.
• This will increase the number of people
reading your manuscript, and likely lead to
more citations.
• They should:
• Represent the content of your manuscript
• Be specific to your field or sub-field

Examples of Keywords
• Manuscript title: Direct observation of nonlinear optics in an isolated carbon
nanotube
Poor keywords: molecule, optics, lasers, energy lifetime
Better keywords: single-molecule interaction, Kerr effect, carbon nanotubes,
energy level structure
• Manuscript title: Region-specific neuronal degeneration after okadaic acid
administration
Poor keywords: neuron, brain, OA (an abbreviation), regional-specific neuronal
degeneration, signaling
Better keywords: neurodegenerative diseases; CA1 region, hippocampal; okadaic
acid; neurotoxins; MAP kinase signaling system; cell death
• Manuscript title: Increases in levels of sediment transport at former glacial-
interglacial transitions
• Poor keywords: climate change, erosion, plant effects
• Better keywords: quaternary climate change, soil erosion, bioturbation

Give your
study an
attractive
and
effective
• Group A • Group B
Tasks:
1. Divide yourselves into two groups.
2. Share your titles
3. Classify your title
4. Write 3 – 5 keywords that best describes your study

What is an ?
• The section that introduces your
research in the context of the knowledge
in the field.
• First introduce:
• the topic including the problem you are
addressing,
• the importance of solving this problem, and
• known research and gaps in the knowledge.
• Then narrow it down to your research
questions and hypothesis.
https://www.enago.com/academy/top-three-tips-for-writing-a-good-introduction/

Tips to an effective
introduction
• Give broad background
information about the problem.
• Write it in a logical manner so that
the reader can follow your
thought process.
• Focus on the problem you intend
to solve with your research
• Note any solutions in the
literature thus far.
• Propose your study as solution to
the problem with reasons.

LITERATURE REVIEW
WRITTEN AND COMPILED BY COURSE COMMITTEE 31

Objectives
• Define literature review
• Explain aim of literature review
• Describe of good characteristics of literature review
• Discuss steps of a literature review

I- Definition of a literature review
• Research literature review is a systematic, precise, critical method
for reading, analyzing, evaluating and summarizing, the existing
body of completed and recorded work produced by researchers,
scholars, and practitioners .
• It is one of the most important early steps prior to initiating any
research study.

What LR is NOT?
• It is not just a descriptive list of the material available, or a set of summaries
• A literature review is more than the search for information, and goes
beyond being a descriptive annotated bibliography.
• The following is NOT a LR:
Annotated bibliography List in text format
Ibrahim , S. D. (1995). Outcomes of Intervention X on
Pregnant women, Soba Hospital." BMJ 2/3, 34-38.
This article discusses the effect of the intervention X
on pregnant women delivering in Soba Teaching
Hospital. It also discusses the implications for
reducing factor Y on these women.
IBRAHIM and BANNAGA (1965) conducted
experiments on pregnant women in STH, basing on
the theoretical investigation of X interaction
complemented by type Y. It showed that the
numerical results were in reasonable agreement with
laboratory experimental data."

Why/When do we need LR?
•LR can help in finding, developing, and/or fine-tuning your RQ.
•Determine the nature/method of your research
Find Research questions
•What is not known/established?
•What is not well known?
•What was not well-studied?
•Cross-referencing
Define gaps & references
•Strengths & weaknesses
•Theoretical base
•Comparison of findings
•Critical appraisal
Establish relations

II- The aim of a literature review
1. It helps the researcher understand the existing body of knowledge in a
specific medical field. Moreover, the researcher will be updated on the
most recent findings in that field.
2. It identifies areas of consensus and debate among different studies,
and highlights the gaps in knowledge that exist in the literature, which
in turn justifies carrying out the research project.
3. It provides details of different research methodology that were
adopted by different researchers, which in turn helps in adopting the
most appropriate study methodology in the proposed study.
4. It identifies other researchers who share the same research interests,
who might act as support for future queries.

III- Characteristics of a good literature review
A good review should have the following characteristics which make it of value:
1- Comprehensive: Evidence should be gathered from all relevant sources.
2-Referenced: Providing full references for reviewed papers.
3- Selective: Using appropriate search strategies to find the most important
evidence.
4- Relevant: Focusing on related studies.
5- Balanced: Providing objective evidence from papers with different findings.
6- Critical: Following valid scientific critical appraisal of the literature.
7- Analytical: Developing new ideas and understandings from the evidence.

Search Strategy

IV- Steps of a literature review
1- Develop a research question
• The first step is to define a specific research question, which
identifies the research or clinical problem the research is aiming to
solve.
• For example, a sample research question is:
• What strategies can healthcare workers use to communicate effectively
with clients with a hearing disability?
• Evidence based practice proponents advice using four elements in
building the research question, specifically, the PICO (Patient,
Intervention, Comparison, and Outcome).

Steps of a literature review
2- Types of the sources used in a literature review
THREE TYPES:
i. Primary source: Is a direct description of a research study written
by a researcher who conducted the study.
ii. Secondary source: Is a review of studies summarizing and
providing new interpretations built from and often extending
beyond the original study.
iii. Tertiary source: Include perceptions, conclusions, opinions, and
interpretations that are informally shared.

Literature sources available

Where to search?
•Library (institutional,
professional,
organizational)
•Archives
•Reports
Offline
•Journals websites
•Publishers’ databases
•Institutional
databases
•Institutional libraries
Online

Before going online… remember!
• The printed resources have almost always been thoroughly ‘peer-reviewed’, and
systematically catalogued and cross-referenced
• On the Internet "anything goes."
• Don't rely exclusively on Internet resources.
• Narrow your research topic before logging on.
• Before you start your search, think about what you're looking for, and if
possible formulate some very specific questions to direct and limit your
search
• Know your subject directories and search engines.
• There are several high quality peer-reviewed subject directories containing
links selected by subject experts
• Keep a detailed record of sites you visit and the sites you use (Ctrl+H).
• Keeping track is necessary so that you can revisit the useful ones later, and

3- Search engines used in a literature review
Universal Resource Locator

4. Establish the keywords and search strategy
• To effectively conduct a search, keywords to be used in the search
need to be identified, which are mainly the PICO elements.
• Moreover, a specific search strategy using the Boolean operators
(AND, OR, and NOT) should be developed, which can be used to
combine the keywords and concept in a search.

5. Conducting the search
• PubMed is the primary database for researchers in the fields of
biochemistry, molecular biology, and related life sciences. It comprises
over 20 million references to articles published in more than 5,200
current biomedical journals from the United States and over 80 foreign
countries.
• It was developed by the National Center for Biotechnology Information
(NCBI) at the National Library of Medicine (NLM). It is one of several
databases under NCBI‟s Entrez retrieval system (the text-based search
and retrieval system used at NCBI for all of the major databases,
including PubMed, and many others).
• PubMed can be directly accessed at: http://pubmed.gov or the National
Library of Medicine's homepage: http://www.nlm.nih.gov.

The main screens of Pubmed
• The most important features in PubMed which a researcher needs
to be familiarized with are: the main page (including database
selection menu, search box, and advanced search link), the search
results page, and the My NCBI.

The main screens of PubMed
The main page includes a database selection menu, a search box,
and
an advanced search link.

6. Choosing the material to be included in the literature review
• In narrowing the literature selection, more focused screening criteria are taken into
consideration, such as:
• Date of publication: e.g. only studies conducted between 2005 and 2012
• Participants or subjects: e.g. children 6 to 12 years of age
• Publication language: e.g. documents written in English
• Research design: e.g. clinical trials
• Authors: e.g. well-known author in a specific field
• Journal: e.g. high impact journal, such as New England Journal of Medicine
• Relevance: e.g. similar objectives addressed and methodologies adopted
• Country of origin: Are you looking for UK only based information? Most databases
will
allow you to limit your search by country, such as; UK, US or Europe.

Practical tips
• Wildcards are a way of searching for alternative spellings of the same words,
e.g. organisation (organization in the US) and paediatric (pediatric in the US).
To use the wildcard feature, you just need to substitute the wildcard symbol,
which is often ? , to replace a missing letter. For example, you could search for
'organi?ation' to capture both "organization" and "organisation".
• Truncation is a way to try and capture all relevant material by searching for
words or phrases which use the same root.
To use the truncation feature, you just need to put the truncation symbol,
which is often either $ or * at the root of a word. For example: If you were
looking for information on "elderly people" you could use elder$ as this would
bring up; elder, elderly, elderly people
• Note: Use truncation with caution as it can sometimes bring up irrelevant
results. For example a search on commission$ would bring up references on
commissioning but also references on the "Commission for health
improvement".

Practical tips: Boolean operators
• After identifying all the keywords, synonyms and phrases within a search, use the Boolean operators
'AND', 'OR' and 'NOT' to combine your topics areas together.
• Using OR
You can combine all the individual synonym searches together into one search using the OR operator
For example:
'old$' OR 'age$' OR 'elderly' OR 'geriatric$'
The OR operator broadens your results by including references that have ANY ONE of the search terms
within it.
• Using AND
You can focus the search by combining searches using the AND operator.
For example: {'old$' OR 'aged' OR 'geratric$'} AND {'care home$' OR 'residential home$' OR
'residential care$' }
This search will find references that contain ALL of the three sets of synonyms.
• Using NOT
You can eliminate items from the search further using NOT
For example: {'old$' OR 'aged' OR 'geratric$'} AND {'care home$' OR 'residential home$' OR
'residential care$'} NOT {'United States' OR 'US' OR 'USA'}
This will remove all references relating to the USA from your results.

7.Critically analyze and evaluate the information
• Critical analyses of the chosen documents refer to the process of
looking at each document closely, reading the introduction,
methodology, results and discussion sections.
• As for the critical evaluation of the document, it refers to assessing
the validity of the methodology adopted, and relevance of the
results reported.
• Biases affecting each of the documents should be taken into
consideration, and evaluated accordingly.
• Finally, integrate the reported results into the scope of the
proposed research.

8. Cite literature properly
• There are four main reasons why it is important to cite literature
properly:
• To acknowledge the author(s) of the work that the researcher used.
• To provide context to the research and demonstrate that the research is
well-supported.
• To allow readers to find the original source and learn more about some
aspects mentioned in the document.
• Avoid plagiarism, which occurs when a writer deliberately uses
someone else's language, ideas, or other original material without
acknowledging its source.

V- Conclusion
• An effective review will increase likelihood of funding, generate
new ideas and directions for investigation, and improve the quality
of peer reviewed publication of primary research.
• At all stages of the process it is vital that the search process is
evaluated, since the inability to find relevant information can be
attributed to a poorly constructed search strategy, inappropriate
search terms, poor retrieval methods or inappropriate source.

Grey Literature
• Work that has not been published in
conventional books and journals.
• This includes reports, working
papers, theses and dissertations,
newsletters, many official
and governmental publications, and
conference papers.
• Gray Literature includes:
• hard to find studies, reports, or
dissertations
• conference abstracts or papers
• governmental or private sector
research
• clinical trials - ongoing or unpublished
• experts and researchers in the field
The AACODS checklist for appraisal
of GL
Main Sources
A Authority: Is the author credible? • WorldCat
A Accuracy: Is it supported
by documented and
authoritative references? Is there a
clearly stated methodology?
• Google Scholar
C Coverage: Have limitations been
imposed and are these stated clearly?
• World Health
Organization
O Objectivity: Can bias be detected? • Gray Source Index
D Date: Can't find the date? Rule of
the thumb is to avoid such material
Professional
association websites
S Significance: Is it relevant? Would it
enrich or have an impact on your
research?

Let’s go online!
Task:
In your laptops/computers, use the University of
Birmingham literature search strategy form to
conduct an online search of literature in your
relevant area of research.

REFERENCE BOOK
INTRODUCTION TO CLINICAL RESEARCH
FOR RESIDENTS, Hani Tamim, PhD
Saudi Commission for Health Specialties, 2014
Liverpool Hope University Doing a literature search: a step by step
guide. URL:
http://www.hope.ac.uk/media/liverpoolhope/contentassets/docum
ents/library/help/media,1256,en.pdf
Other helpful guides can be found on the following links:
https://becker.wustl.edu/sites/default/files/RespLitSearch.pdf
http://www.birmingham.ac.uk/facilities/hsmc-library/faqs/literature-
searching.aspx

OBJECTIVES
• What are the research objectives?
• How to make research objectives SMART?
• Research Questions:
1. What is a research question
2. Criteria of a good research question
3. Sources of research questions
4. Elements of a research question
5. Criteria for a bad research question
6. Example of a research question

OBJECTIVES: What? Why?
• Definition: These are the statements that establish what the
research project should achieve after its completion
• Properly formulated specific objectives will facilitate:
1. Development of the research methodology
2. Orientation of the data collection, analysis, interpretation and utilization.

Classification of OBJECTIVES

GOAL /AIM:
The goal is a short and general sentence defining:
• The overall aim of the project and the contribution of the project in a
bigger context; thereby describing the purpose of the project.
• It is therefore a very general statement.
WRITTEN AND COMPILED BY 67

EXAMPLE
• An example of a project goal may be: “TO STUDY THE FACTORS
THAT AFFECT THE STUDENTS’ ACADEMIC PERFORMANCE IN THE
COLLEGE OF MEDICINE FOR THE ACADEMIC YEAR 2018/2019".

General vs. specific Objectives
General objective (aka
goal/aim)
Specific objectives
It identifies in general terms:
• what is to be
accomplished by the
research project and why
• what is expected to be
achieved by the study in
general terms.
• Identify in greater details the
specific aims of the research
project;
• breaking down what is to be
accomplished into smaller
logical connected
parts/components.

specific objectives should be SMART
S Specific
M Measurable
A Achievable
R Realistic/Resource
T Time-specific.
It is good to include timelines in objective. However, If not in the objective,
timelines can be defined in the indicator(s) correspondent to that objective

EXAMPLE
• For the project goal : “TO STUDY THE EEFECT OF UTILIZING
THE LIBRARY SERVICES ON THE STUDENTS’ ACADEMIC
PERFORMANCE IN THE COLLEGE OF MEDICINE FOR THE
ACADEMIC YEAR 2017/2018".
• Examples of Specific objectives:
1. To compare the level of utilization of the library services
among various levels of academic performance groups;
2. To establish the pattern of utilization of the library
services in two semesters of the year;
3. To verify whether increasing use of library services
increased the students’ grades in the academic year 2017-
2018;
4. To describe students’ perception of the quality of the
library services provided at the college .

Quick TASK
• Divide yourselves in groups of 4-5
• Develop a research project goal
• LIST 3-5 specific objectives for your research project
• Present it to your colleagues

CLASSIFICATION OF OBEJCTIVES
Depending on the research questions to be answered by the study
specific objectives are either:
1. Estimation objectives:
Estimating certain features e.g. to determine incidence rates,
prevalence rates, level of utilization of services etc.,
2. Association objectives:
Investigation of the association between a factor of interest and a
particular incidence e.g. to identify whether there is association
between the utilization of child welfare clinics, and the different
seasons,
3. Evaluation objectives:
Evaluate the effect of an intervention

Formulating a research
question

1. What is a research question
• A research question is a concise question which expresses what
the research project aims to address;
• it is the question the researcher wishes to answer.
• it will be the basis for developing and conducting the research
project.

2. Criteria of a good research question
• Attempts to fill a knowledge gap in the literature,
• Enough to be answerable and researchable
• Should be relevant to the study’s objective
• Should avoid duplication of previous work
• Should be feasible and cost effective
• Should be doable within a specified time frame allocated for the
research project.
• Needs to meet the minimum ethical standards.

3. Sources of research questions
• The researcher formulates a research question through different
means.
• Literature reading might help a researcher identify the areas that
need further study, and thus a hint towards a research question.
• Patients’ observation through clinical experience which might pose
different researchable
questions.
• Peers: previous research, journal clubs, and conferences

4. Elements of a research question
• A "well-built" research question should include four elements of a
research question that need to be addressed; referred to as PICO
• The PICO concept is important in narrowing down the research
question, providing search terms, and saving time in literature
search.

PICO
• PICO letters stand for:
a. P: Patient or Population.
• The first step in the PICO process is to identify the patients or population
to be studied.
• More specifically, it describes patients’ characteristics, such as age, gender,
disease status, or any other patient-related characteristic.

PICO (2)
• b. I: Intervention to be tested.
• Identifying the intervention is the second step in the PICO process.
• It is important to identify the exposure intended to be studied in the
research project.
• This may include the use of a specific diagnostic test, treatment, adjunctive
therapy, medication, etc.

PICO (3)
• c. C: Comparison used in the research project. It is the alternative exposure to
which the intervention will be compared, which might be the standard of care
or a placebo. The comparison component is the only optional one in the PICO
question, since the researcher might study the intervention alone because
either due to no interest in comparison or the lack of a comparable
group.
d. O: Outcome to be measured as a result of the intervention. It is the evaluation
of the intervention’s effect. This may include cure or level of control of a
disease, efficacy of a medication or a diagnostic test, etc.

6. Example of a research question
Topic of
interest:
Narrowed
topic:
Focused topic:
Women’s health
Women and cancer
Women smokers and breast
cancer
PICO:
P = Women (age more than 35)
I = Cigarette smoking
C = No smoking
O = Breast cancer

5. Criteria for a bad research question
a) Vagueness of the research question.
b) The research question is too broad to reach conclusive results.
c) The research question might fail to reveal the relevance of the
topic under investigation.
d) Other criteria: the time needed to carry out the study, high cost
with limited funding, limited resources such as availability of
expertise, special equipment, and/or information.
e) Research question might be limited by ethical considerations or
requirement of authorities’ approval.

Methods or Methodology?
• Methods means the practical activities that you have done to collect your
data e.g. interviews, surveys etc. o
• Methodology means the philosophy and theory behind what you’ve done.
• Typically, you would include both of these as indicated above. If you
haven’t discussed the theory and philosophy, don’t call it a ‘methodology’!
Call it a ‘methods’ chapter.

The methods section
• Provides the information by which a study's validity is judged
• requires a clear and precise description of how the study was
done, and the rationale for why specific procedures were
chosen.
• should describe what was done to answer the research
question, describe how it was done, justify the design, and
explain how the results were analyzed.
• Scientific writing is direct and orderly.

Definition (2)
• describes actions to be taken to investigate a research problem
and the rationale for the application of specific procedures or
techniques used to identify, select, process, and analyze
information applied to understanding the problem,
• thereby, allowing the reader to critically evaluate a study’s overall
validity and reliability.
• The methodology section of a research paper answers two main
questions:
• How was the data collected or generated?
• How was it analyzed?.
https://libguides.usc.edu/writingguide/methodology

Importance of a Good Methods Section (1)
• Readers need to know how the data was obtained because the
method you chose affects the results and, by extension, how you
interpreted their significance in the discussion section of your
paper.
• Methodology is crucial for any branch of scholarship because an
unreliable method produces unreliable results and, as a
consequence, undermines the value of your analysis of the
findings.
• In most cases, there are a variety of different methods you can
choose to investigate a research problem. The methodology
section of your paper should clearly articulate the reasons why
you have chosen a particular procedure or technique.
• The reader wants to know that the data was collected or
generated in a way that is consistent with accepted practice in the
field of study.
• For example, if you are using a multiple choice questionnaire, readershttps://libguides.usc.edu/writingguide/methodology

Importance of a Good Methods
Section (2)• The method must be appropriate to fulfilling the overall aims of
the study.
• For example, you need to ensure that you have a large enough
sample size to be able to generalize and make recommendations
based upon the findings.
• The methodology should discuss the problems that were
anticipated and the steps you took to prevent them from
occurring. For any problems that do arise, you must describe the
ways in which they were minimized or why these problems do not
impact in any meaningful way your interpretation of the findings.
• It is important to always provide sufficient information to allow
other researchers to adopt or replicate your methodology.
• This information is particularly important when a new method has
been developed or an innovative use of an existing method is utilized.
https://libguides.usc.edu/writingguide/methodology

Components of the Methodology section
Philosophy (±)
Study design (most
common?)
Study area
Study population
(participants)
Data collection &
analysis (tools &
methods)
Ethical considerations

Other components of the Methodology

The methods section should
• describe the materials used in the study,
• explain how the materials were prepared for the study,
• describe the research protocol, explain how measurements
were made and what calculations were performed, and state
which statistical tests were done to analyze the data.
• present those elements as clearly and logically as possibly. The
description of preparations, measurements, and the protocol
should be organized chronologically.
• For clarity, information should be presented in sub-sections
according to topic.
• Material in each section should be organized by topic from most
to least important.
Kallet RH. How to write the methods section of a research paper. Respir Care. 2004 Oct;49(10):1229-
32.

Points to cover in Methods Section (thesis)
Subheading Points to cover
Aims and
objectives
Re-state your aims and objectives here from the introduction.
Approach What is your philosophical standpoint? (e.g. interpretivist? Positivist?...etc.) (NOT Always)
Strategy /
research design
What are you using and why?
Setting Where will you do this research (don’t give away anonymity)? Describe it. Why and how have
you chosen this place? Is the timing relevant? (e.g. time of year in a school)
Participants /
sample / subjects
Who is your study about (research population)? Who is giving you data (sample)? How many
(sample size)? How are you accessing them? How are you selecting them (sampling approach)?
Are there any ethical issues?
Materials /
Instruments
What are you using to collect data, e.g. interview questions or questionnaires? How are you
designing these? What principles or previous research are you drawing on? Will you pilot it?
https://cpb-eu-w2.wpmucdn.com/mypad.northampton.ac.uk/dist/d/6334/files/2018/01/What-should-I-include-in-my-methodology-section-Jan-2018-2i6hwkm.pdf

Procedure Describe how you will conduct the interview or administer the survey, in as much detail as
possible. E.g. will you print it or do electronically? Will you email it or put it online? How long
will it be live? What if you don’t get enough responses?
Data
analysis
How will you make sense of the data? Will you have to process it (e.g. transcribe or input into
software)? What statistical tests or analytical techniques will you use and why are these
appropriate? Will you use software? If so, which one, why and how? Caution: software does
not do the analysis for you – you still need to tell it what to do, so the most important
question is what analytical techniques will you use.
Limitations If everything goes perfectly and you collect all the data you anticipated, what will you still
NOT be able to conclude because of your strategy and approach? E.g. in a case study, you will
not be able to generalise the results. Do not mention anything that you could have changed
in your materials or procedures, only intrinsic issues with particular research approaches. (NB
this section may make more sense in the results or discussion section in some dissertations)

Challenges What problems can you predict? How can you adapt your plans to deal with them? (NB make
sure this is consistent with what you wrote earlier – i.e. if you mention that you might get a
low response rate and suggest another way to recruit participants, this second way should be
covered in the sample section already. Use this section to explain why you have put in certain
back-up plans.)
Ethics Are your participants vulnerable in any way? Could your research cause them any personal or
professional problems? What can you do to make sure you do no harm? Are any of the issues
in your research sensitive or personal? How can you deal with this? How will you deal with
informed consent and data protection? (NB this may be a separate section, or you may
incorporate different elements into earlier sections)

Additional elements (1)
• Introduce the overall methodological approach for investigating your research
problem. Is your study qualitative or quantitative or a combination of both (mixed
method)? Are you going to take a special approach, such as action research, or a
more neutral stance?
• Indicate how the approach fits the overall research design. Your methods for
gathering data should have a clear connection to your research problem. In other
words, make sure that your methods will actually address the problem. One of the
most common deficiencies found in research papers is that the proposed
methodology is not suitable to achieving the stated objective of your paper.
• Describe the specific methods of data collection you are going to use, such as,
surveys, interviews, questionnaires, observation, archival research. If you are
analyzing existing data, such as a data set or archival documents, describe how it
was originally created or gathered and by whom. Also be sure to explain how older
data is still relevant to investigating the current research problem.
• Explain how you intend to analyze your results. Will you use statistical analysis?
Will you use specific theoretical perspectives to help you analyze a text or explain
observed behaviors? Describe how you plan to obtain an accurate assessment of
relationships, patterns, trends, distributions, and possible contradictions found in the
data.

Additional elements (2)
• Provide background and a rationale for methodologies that are unfamiliar for
your readers. Very often in the social sciences, research problems and the methods for
investigating them require more explanation/rationale than widely accepted rules
governing the natural and physical sciences. Be clear and concise in your explanation.
• Provide a justification for subject selection and sampling procedure. For instance,
if you propose to conduct interviews, how do you intend to select the sample
population? If you are analyzing texts, which texts have you chosen, and why? If you
are using statistics, why is this set of data being used? If other data sources exist,
explain why the data you chose is most appropriate to addressing the research
problem.
• Provide a justification for the design (e.g. case study) selection. A common
method of analyzing research problems in the social sciences is to analyze specific
cases. These can be a person, place, event, phenomenon, or other type of subject of
analysis that are either examined as a singular topic of in-depth investigation or multiple
topics of investigation studied for the purpose of comparing or contrasting findings. In
either method, you should explain why a case or cases were chosen and how they
specifically relate to the research problem.
• Describe potential limitations. Are there any practical limitations that could affect your
data collection? How will you attempt to control for potential confounding variables and
errors? If your methodology may lead to problems you can anticipate, state this openly
and show why pursuing this methodology outweighs the risk of these problems cropping
up.

Hints for good methodology section
• Give a brief description of other research design solutions and
• justify and give a clear explanation for the chosen design (better to
answer your RQ);
• Include relevant literature review related to Methodology;
• Include a brief discussion on the instruments you have used to
analyze that data. (attach when relevant)
• Some of these elements may be more or less relevant to your
topic. They can be combined, re-organised and emphasis can be
given to different sections.
https://writeanypapers.com/blog/how-to-write-a-methodology/

Hints for good Methods section
1. Write it in the past tense
2. Adhere to the specific guidelines: Read the author’s instruction
section of your target journal carefully and follow the specific
instructions.
3. Structure the section so that it tells the story of your research:
presented in a logical manner, e.g. setting and time of the study,
recruitment, study design, intervention, and describing the
techniques used to collect, measure, and analyse data.
4. Follow the order of the results: match the order of specific
methods to the order of the results that were achieved using those
methods
5. Use subheadings
6. Provide all details meticulouslyhttps://www.editage.com/insights/how-to-write-the-methods-section-of-a-research-paper

DON’Ts in Methods Section
1. Do not describe well-known methods in detail
2. Do not provide unnecessary details
3. Do not discuss the pros and cons of other methods

Refer to the notes section below for guidelines
on this topic.

• It is the section whose purpose is to explain the meaning of the
results to the reader.
• It helps in answering the following questions:
• Did you achieve your objectives?
• How do your results compare to other studies?
• Were there any limitations to your research?
• Before writing the Discussion, consider the following:
• How do your results answer your objectives?
• Why do you think your results are different to published data?
• Do you think further research would help clarify any issues with your data?
How to Write an Effective Discussion, Dean R Hess . [Respir Care 2004;49(10):1238–1241

Structure of
• Set out the context and main aims of the study
• Do this without repeating the introduction
• Discuss findings, compare to other studies
• How findings compare to other studies
• Limitations
• Practical implications: what they mean for the field
• Talk about the major outcomes of the study.
• Be careful not to write your conclusion here.
• Merely highlight the main themes emerging from your data

Include
 It is not a literature review.
Keep your comments relevant
to your results.
 Interpret your results.
 Be concise and remove
unnecessary words.
 Do not include results not
presented in the result
section.
 Ensure your conclusions are
supported by your data.
√ State the study’s major
findings
√ Explain the meaning and
importance of the findings
√ Relate the findings to other
studies
√ Alternative explanations of
the findings
√ An explanation for any
surprising, unexpected, or
inconclusive results
√ Acknowledge the study’s
limitations
√ Make suggestions for further
research
 Overpresentation of the
results
 Unwarranted speculation
 Inflation of the importance of
the findings
 Tangential issues
 The “bully pulpit”
 Conclusions not supported by
your data
 New results or data not
presented previously in the
paper
 Inclusion of the “take-home
message”; save this for the
conclusions section
How to Write an Effective Discussion, Dean R Hess . [Respir Care 2004;49(10):1238–1241
https://www.enago.com/academy/discussion-conclusion-know-difference-drafting-manuscript/

SHOULD
 State what you set out to
achieve.
 Tell the reader what your
major findings were.
 How has your study
contributed to the field?
 Mention any limitations.
 End with
recommendations for
future research.
 Restate your hypothesis or
research question
 Restate your major findings
 Tell the reader what
contribution your study has
made to the existing
literature
 Highlight any limitations of
your study
 State future directions for
research/recommendations
 Introduce new arguments
 Introduce new data
 Fail to include your research
question
 Fail to state your major results

Example of a
good
conclusion

Display items (Tables & Figures)
• The quickest way to communicate large amounts of complex information.
• Many readers will only look at your display items without reading the main
text
• Display items are also important for attracting readers to your work.
• High-quality display items give your work a professional appearance.
• Readers will assume that a professional-looking manuscript contains good
quality science
• Which of your results to present as display items consider the following
questions:
• Are there any data that readers might rather see as a display item rather than text?
• Do your figures supplement the text and not just repeat what you have already stated?
• Have you put data into a table that could easily be explained in the text such as simple
statistics or p values?
https://www.springer.com/gp/authors-editors/authorandreviewertutorials/writing-a-journal-manuscript/figures-and-tables/10285530

Tables & figures
• What is wrong with this table?
Men Group 1 men group 2 Rats
Serum Protein
A
100 158 -
Blood glucose
(mmol/L)
102 160 154
Weight
(average)
138.8989 150.8 1.6588887
Activity level 0 5 8
Data on different responses

Tables
• Concise and effective way to present large amounts of data.
• Design them carefully to clearly communicate your results to busy
researchers.
Clear and concise legend/caption
Data divided into categories for clarity
Sufficient spacing between columns and rows
Units are provided
Font type and size are legible
Source: Environmental Earth Sciences (2009) 59:529–536

Figures (Images, Data plots, Schematics)
• Images:
• Include scale bars
• Consider labeling
important items
• Indicate the
meaning of
different colours
and symbols used
• Data plots
• Label all axes
• Specify units for
quantities
• Label all curves and
data sets
• Use a legible font
size

Figures
(Images, Data
plots,
Schematics)
Source: Borrego et al. Cancer & Metabolism 2016 4:9

Figures (schematics & maps)
In maps:
 Include
latitude and
longitude
 Include scale
bars
 Label
important
items
 Consider
adding a map
legendSource: Nano Research (2011) 4:284–289

Why do we need to cite ?
• To give credibility to statements made
• To give credit to other scientists whose findings are being cited
• For use by readers to find further information
• Establish where ideas came from
• Give evidence for claims
• Connect readers to other research
• Provide a context for your work
• Show that there is interest in this field of research
Smart P., Maisonneuve H. and Polderman A. (eds) Science Editors’ Handbook. European Association of Science Editors.
www.ease.org.uk

Reference Management Software (RMS)
• It is software for scholars and authors to use for recording and utilising
bibliographic citations (references).
• These software packages normally consist of a database in which full
bibliographic references can be entered.
• It can usually be integrated with word processors so that a reference list
in the appropriate format is produced automatically
Source: http://en.wikipedia.org/wiki/Reference_management_software

RMS: What they do?
1. Import citations from bibliographic databases and websites
2. Allow organization of citations within the RM database
3. Allow annotation of citations
4. Allow sharing of the RM database with colleagues
5. Allow data interchange with other RMS through standard metadata
formats (e.g., RIS, BibTeX)
6. Produce formatted citations in a variety of styles
7. Work with word processing software to facilitate in-text citation
Source: (http://www.istl.org/11-summer/refereed2.html)

Examples of RMs
Reference Management Software
(http://en.wikipedia.org/wiki/Reference_management_software)
Open source Retail Web-based
•BibDesk
•Docear
•Ilibrarian
•JabRef
•KBibTeX
•Pybliographer
•Referencer
•Wikindx
•Zotero
• Biblioscape
• Bookends
• Citavi
• Papers
• Qiqqa
• Sente
•BibSonomy
•Qiqqa
•Wikindx
•WizFolio
•Zotero

1. Install your RM of choice
2.Do your online search
3. Build a new database
4.Transfer the reference from the web to your
database
5.Use the references you imported in your document

What are Author’s Instructions?
• All journals have certain requirements for publication in them
• These requirements are detailed in the ‘Author’s Instructions’
• They are important because:
• Facilitates the acceptance of your submission
• Editors can/will refuse submissions not following the instructions
• They make life easier (or harder?) for the author
The good news: many journals have ready-to-use templates.

What’s usually included in the ?
• Scope and editorial policy
• Scope (areas of interest/focus), and types of submissions
• Ethical considerations:
• Ethical approval, Informed consent, authorship, conflict of interests
• Formatting:
• Font, Spacing, Numbers’ format
• Referencing style:
• Vancouver, Harvard, MLA,APA,
• There are templates in the main Reference Management Software (e.g. Endnote, Reference
Manager, etc.)
• Formatting guidelines
• Graphs and diagrams, accepted file types, photographic and scanned images, maps, etc.
Usually required to follow the Uniform Requirements for Manuscripts Submitted to Biomedical Journals
(International Committee of Medical Journal Editors, ICMJE).

What’s usually included in the ?
• Reporting of specific types of studies
Reporting format Usage and guidance
reports of randomized trials (http://www.consort-statement.org)
for systematic reviews and meta-analyses of randomized trials
(http://www.consort-statement.org/Evidence/evidence.html)
reporting of observational studies in epidemiology (http://www.strobe-
statement.org)
meta-analysis of observational studies
(http://www.consortstatement.org/News/news.html#moose)
for studies of diagnostic accuracy (http://www.consort-
statement.org/stardstatement.htm )
reports of non-randomized evaluations of interventions
(http://www.trend-statement.org/asp/trend.asp)

Publication Ethics
Ethical considerations in scientific publications
- Authorship and authors' responsibilities
- Falsification, fabrication and plagiarism

Who is an ?
• 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
• review manuscript drafts and approve the final version to be
published; AND
• Agreement to be accountable for all aspects of the work.
• An author should have made a substantial, direct, intellectual
contribution
• All authors should One author should take primary responsibility
for the whole work
• Authors should describe each author’s contributions and how
order was assigned to help readers interpret roles correctly
• The funding and provision of technical services, patients,
materials alone are not sufficient
ICMJE Guidelines | Harvard Medical School

Unethical forms of authorship
Authorship
misconduct
Definition
Ghost
Authors who contributed to the work but are not listed, generally to hide a conflict of
interest from editors, reviewers, and readers.
An author is paid to write an article but does not contribute to the article in any other way.
Guest
Individuals given authorship credit who have not contributed in any substantive way to the
research but are added to the author list by virtue of their stature in the organization.
Orphan
Authors who contributed materially to the work but are omitted from the author list
unfairly by the drafting team.
Forged/Gift
Unwitting authors who had no part in the work but whose names are appended to the
paper without their knowledge to increase the likelihood of publication.
https://www.internationalscienceediting.com/authorship/

How to
authorship ?
• Talk early and often about authorship
and authorship order for each
project’s manuscript(s)
• When gathering input about
contributions, ask everyone to put in
writing
• Create a culture of transparency and
collaboration and revisit the issue of
specific authorship periodically
• If a disagreement arises, make every
effort to resolve the dispute locally Harvard Medical School

Research Misconduct (FFP)
Definition: fabrication, falsification, or plagiarism in proposing,
performing, or reviewing research, or in reporting research results.
• Fabrication is making up data or results and recording or reporting
them.
• Falsification is manipulating research materials, equipment, or
processes, or changing or omitting data or results.
• Plagiarism is the appropriation of another person’s ideas, processes,
results, or words without giving appropriate credit.
• Research misconduct includes the destruction of, absence of, or
accused person's failure to provide research records accurately
documenting the questioned research.

Research Misconduct (FFP) – Wrongful Acts
Definition or research Misconduct:
is significant misbehaviour that improperly appropriates the intellectual property or
contributions of others, that intentionally impedes the progress of research, or that
risks corrupting the scientific record or compromising the integrity of scientific
practices. (US Commission on Research Integrity (1996) )
A wrongful act is defined as any act that may subvert the integrity of the review
process which includes, but not limited to the following:
• Submitting a fraudulent application, offering or promising a bribe or illegal
gratuity, or making an untrue statement.
• Submitting data that are otherwise unreliable due to, for example, a pattern of
errors, whether caused by incompetence, negligence, or a system-wide failure to
ensure the integrity of data submissions.

Other forms of
scientific misconduct
• Undeclared redundant publication or
submission
• Disputes over authorship
• Failure to obtain informed consent
• Performing unethical research
• Failure to gain approval from an ethics
committee

Definition of Plagiarism
• … plagiarism to include both the theft or
misappropriation of intellectual property (IP) and the
substantial unattributed textual copying of another's
work.
• … the unattributed copying of sentences and
paragraphs which materially mislead the ordinary
reader regarding the contributions of the author.
• The theft or misappropriation of IP includes the
unauthorized use of ideas or unique methods
obtained by a privileged communication, such as a
grant or manuscript review.
Office of Research Integrity (ORI)’s

Why care about the
choice of the journal?
Your thoughts?

Getting your research and
work to be published
The journal publishing process
Writing a paper
Ten rules for success

Deciding whether to publish
• Why publish?
• to add knowledge to your field
• to advance your career
• to see your name in print!
• It is my job as researcher
• For my promotion
• Have I got something worth publishing?
• Does the work add enough to existing knowledge?

Deciding where to publish
• Conference proceedings, book chapters and
journals
• 26,000 journals – how to choose?
• Different strategies
• topic and journal coverage (check website)
• Is it peer-reviewed?
• Most appropriate readership
• Length of time from submission to publication
• Highest ‘impact’
• Journal impact factors

How to
choose the
right journal?
Oxford Handbook of Clinical and Healthcare Research

What are the Scholarly Metrics?
• Scholarly metrics are away for the impact of an article, author, or
journal to be measured quantitatively.
https://www.lib.uwo.ca/files/scholarship/6-imtg-understanding_scholarly_metrics-final_en_0WL.pdf
Metric Definition
the impact factor represents the average number of
citations per article the journal received during the previous two years
Journals with high impact factors–where there are a high average number
of citations is considered to have greater impact and importance in that
field of study
focuses specifically on the individual researcher, quantifying the output
and impact of his or her work.
the calculation is cumulative and based on the distribution of citations
across the number of publications of an individual researcher.

What are impact factors?
• An impact factor attempts to provide a measure of
how frequently papers published in a journal are
cited in the scientific literature.
• Calculated as the average number of times an article
published in the journal in previous 2 years has been cited in
all scientific literature in the current year.
• So, if there were an average of 1000 citations in 2018 for 100
articles published in a journal in 2016 and 2017, the impact
factor would be 10.
• Most journals have impact factors that are below 2.
• e.g. Nature = 34,07, J. Applied Ecology = 4.5,
• Saudi annals 0.8

• Developed by Eugene Garfield in the 1950s
• Reflects average of number of citations to recent articles published in journals JCR tracks
• Proxy measure for importance of journal in the field
• Impact Factor
• Current and 5-year IFs
• Immediacy Index ( the journal it is cited for only one ans same year )
• Cites in 2012 to items published in 2012
Impact Factors and Immediacy
Formula
A = the number of times that articles published in that journal in
2006 and 2007, were cited by articles in indexed journals during
2008.
B = the total number of "citable items" published by that journal in
2006 and 2007.
2008 impact factor = A/B.

• Important notes
Any journal with an
impact factor is a good
journal.
• Social science journals
rank lower in impact
than science journals.
The higher the IF, the
more valued the journal.
Impact Factors
Of the 67 journals ranked in Health
Policy & Services, the top ranked
journal is Milbank Quarterly at 4.644,
the lowest is Sciences Sociales Et
Sante at 0.176.

What editors look for in a
manuscript
• Quality
• good science: well planned, well executed study
• good presentation
• Significance and originality
• Consistent with scope of journal
• Demonstrated broad interest to readership
• Will it cite?
• Well written ‘story’
• Author enthusiasm

Writing the paper: key points
• Strong Introduction
• Engage the reader
• Set the scene, explain why the work is important, and
state the aim of the study
• Clear, logically organised, complete Methods
• Provide enough information to allow assessment of
results (could someone else repeat the study?)
• Results
• Be clear and concise; avoid repetition between text,
tables and figures
• Relevant Discussion
• Start strongly – were aims achieved?
• Discuss significance and implications of results

Attracting the editor/reader
• There are lots of opportunities for rejection!
• Remember: your paper is competing with many others for the
attention of editors and readers
• Title
• Brief, interesting and accurate
• Abstract
• Attract readers to your paper
• Aim for 4 sections: why, how, what and implications
• Include important keywords for searching
• Make it clear and easy to read

The IMRAD Format
for Scientific Papers
• Introduction: What was the question?
• Methods: How did you try to answer it?
• Results: What did you find?
• And
• Discussion: What does it mean?

A More Complete View
• (Title)
• (Authors)
• (Abstract)
• Introduction
• Methods
• Results
• Discussion
• (Acknowledgments)
• (References)

Before you submit
 Internal review
• Ask your peers to read it to get an alternative perspective
• Ask someone outside your field to read it
• Read the Notice to Authors
• Follow format and submission instructions
• Write a covering letter to the editor
• Should clearly explain (but not overstate) the scientific advance
• Submit with the consent of all authors and to only one journal

Submitting the Paper
• Traditional submission (by mail)—now rare
• Electronic submission
• Commonly via online submission system
• Sometimes as e-mail attachment
• Inclusion of a cover letter (conventional or electronic)
• Completion of required forms

Journal publishing process
Submission Refereeing
Reject
Revision Acceptance Publication
More revision
Reject Reject
Reject

Peer Review
• Evaluation by experts in the field
• Purposes:
• To help the editor decide whether to publish the paper
• To help the authors improve the paper, whether or not the journal accepts
it

The Editor’s Decision
• Based on the peer reviewers’ advice, the editor’s own evaluation,
the amount of space in the journal, other factors
• Options:
• Accept as is (rare)
• Accept if suitably revised
• Reconsider if revised
• Reject

Revising a Paper
• Revise and resubmit promptly.
• Indicate what revisions were made.
• Include a letter saying what revisions were made. If you received a list of
requested revisions, address each in the letter.
• If requested, show revisions in Track Changes.
• If you disagree with a requested revision, explain why in your
letter. Try to find a different way to solve the problem that the
editor or reviewer noted.

Understanding reviews: what makes a good
review
• Good reviews provide the editor with the information on which a
decision can be based
• The best are articulate and constructive
• They tell the editor:
• What is interesting about the paper ?
• How the results are significant?
• What contribution the paper makes to the field ?
• What can be done to improve the paper ?
• If the paper is not publishable and why

Detailed comments in the review
•A good review answers the following
questions and provides suggestions for
improvement:
• Does the introduction explain why the
work was done and the hypothesis being
tested ?
• Is the experimental/study design
appropriate?
• Are the methods clearly described to
enable full assessment of the results ?
• Is the analysis appropriate ?

Detailed comments in the review
• A good review answers the following questions
and provides suggestions for improvement:
• Are the results presented effectively ?
• Is the work discussed in the context of all relevant
literature ?
• Does the discussion make clear the significance and
wider implications of the work ?
• Are the conclusions supported by the data presented?

Responding to referees’ reports
• Read the editor’s letter first for instruction
• Take a deep breath: proceed to the reports
• Put them aside for a day, or two, a week…
• Re-read reports and discuss with coauthors …
• Revise paper and prepare response document
• Remember –
• Even comments that seem aggressive or ignorant can be helpful
• Always view this as a chance to improve the paper

Good response to referees’ reports are ….
• Well organised
• Address common themes at start
• Use a ‘quote and response’ OR numbering system of points raised by each
referee
• Informative
• Provide full explanations
• Do not overlook or ignore any points
• Assertive (and polite)

• Questions going through the editor’s mind:
• How good is the science in this paper?
• Is an important issue/area of study being addressed?
• Is the experimental design appropriate and adequate?
• Are the analyses appropriate and competently done?
• Has the study been put in context?
• Does the paper contribute significantly to the literature?
• Does the paper tell an interesting story?
• Will it be read and cited?
The decision:
accept, re-review, reject

The decision
• Remember –
• The editor will make a final decision based on how well the
referees’ reports have been dealt with, so …
• Revise with care
• Respond fully to each of the referees’ comments
• Present cogent and complete arguments if you have not followed a
referee’s recommendation
• Make the editor’s job as easy as possible!

Summary
•Writing for successful publication
means
• having a well designed, original study to write about
• selecting an appropriate outlet/journal
• knowing what you want to write
• writing clearly
• making the story interesting
• highlighting the significance of the results
• responding carefully and positively to referees’ reports

Ten rules for getting published (1)
1. Read many papers, and learn from both the
good and the bad ones.
2. The more objective you can be about your work,
the better the work will ultimately become.
3. Good editors and reviewers will be objective
about your work.
4. If you do not write well in the English language,
take lessons early; it will be invaluable later.
5. Learn to live with rejection.

Ten rules for getting published (2)
6. Understand what makes good science and what makes good
science writing: be objective about them.
7. Start writing the paper the day you have the idea of what
questions to pursue
8. Become a reviewer early in your career.
9. Decide early on where to try to publish your paper.
10. Quality (not quantity) is everything.

Further information
• Getting your work published (Podcast)
• http://www.jobs.ac.uk/careers/whitepapers/640/Getting_your_academic_
work_published
• PLOS Computational Biology – ‘Ten simple rules for getting
published’
• http://compbiol.plosjournals.org/perlserv/?request=get-
document&doi=10.1371/journal.pcbi.0010057&ct=1
• ‘How to get published in LIS journals: a practical guide’
• http://www.elsevier.com/framework_librarians/LibraryConnect/lcpamphlet
2.pdf

Understanding peer review
process

Henry Oldenberg (1619-1677)
• A German Natural Philosopher
• A founding Member of the Royal society in
1660
• Founder Editor of:
Philosophical Transaction of Royal Society

Peer reviewed
Scholarly Journal articles
Books
Thesis
Grey Publication
Website
Daily news papers
None documented anecdotes opinions
Videos, films, presentations, word of the
mouth etc.

The importance of PR
• It is a cornerstone of contemporary science
and current medicine
• It is mainly relying on expert opinion
• It is objective review
• It is ensure the quality of the papers they
publish.
• It is usually done by group of volunteers yet
they are experts

PR Stake holders
Journal staff – oversees the receipt of manuscripts, manages communications
with authors and reviewers and processes accepted manuscripts for publication
Scientific editors - make the final decision as to whether a specific manuscript
will be accepted for publication, returned for revisions, or rejected
Members of the editorial board – read and review papers, select reviewers and
monitor quality of reviews, and recommend actions to editor
Reviewers – provide reviews of manuscripts, make recommendations concerning
publication

What is expected of your peer
• Expertise in one or more areas of paper
• Objectivity
• No conflicts of interest
• Good judgment
• Able to think clearly and logically
• Able to write a good critique
• Accurate
• Readable
• Helpful to editors and authors
• Reliable in returning reviews
• Able to do the review in the allotted time frame

Done by experts
Rate your work among other peers
Example: Grants writing or call for
paper
Done by experts
Insure the highest quality for the
final manuscript
Insure the availability of enough data
for reproducibility of the results
Merits Review
Versus
Peer Review

• Which journal should you publish in? (covered by Prof. Alkabba)
• How can you ensure you have the best chance of being accepted?
• Do you really need to bother with a cover letter?
• How do you respond to reviewers?

Aim at the !
• Journal editors:
• evaluate all submitted manuscripts,
• select those which they consider to be suitable for the journal,
• send for peer review, and
• consider peer reviewers’ advice to make a final decision about
what gets published.
• When first faced with a manuscript they usually look at the
cover letter, abstract, conclusion and references.
• Journal editors want to publish good quality science that is
of interest to their readers.
Submission is more likely to be accepted if it:
• Is within the scope of the journal
• Is novel and describes research that advances the field
• Adds to an active research field
• Is carefully prepared and formatted
• Uses clear and concise language
• Follows ethical standards
This Photo by Unknown Author is licensed under CC BY-NC

Why do papers?
Technical reasons
• Incomplete data such as too small a sample size
or missing or poor controls
• Poor analysis such as using inappropriate
statistical tests
• Inappropriate methodology for answering your
hypothesis or using old methodology that has
been surpassed
• Hypothesis is not clear or scientifically valid, or
your data does not answer the question posed
• Inaccurate conclusions on assumptions that are
not supported by your data
• Editorial reasons
• Out of scope for the journal
• Not enough of an advance or of enough impact for the
journal
• Research ethics ignored (e.g. IRB approval of consent)
• Lack of proper structure or not following journal
formatting requirements
• Lack of the necessary detail for readers to fully
understand and repeat the authors’ analysis and
experiments
• Lack of up-to-date references or references containing
a high proportion of self-citations
• Poor language quality (hardly understood by readers)
• Difficult to follow logic or poorly presented data.
• Violation of publication ethics
This Photo by Unknown Author is licensed under CC BY-NC
How to avoid them?

Document Details
Title page
Title
Authors—names, affiliations, addresses
Corresponding author’s contact details
Author roles
Conflict of interest statement
Funding sources if applicable
Manuscript
If the review is anonymous remember to include the manuscript title
The abstract should be at the start of the manuscript
Page numbers are essential
Line numbering may be useful
Tables Numbered and titled—tables should stand alone
Figures Numbered and titled—figures should stand alone
Covering letter
Addressed to the editor in chief
State the importance of the study without hyperbole.
Confirm that the work is original and not under consideration by another journal
Completed
copyright form
Table 27.5 example separate documents required for manuscript submission
Oxford Handbook of Clinical and Healthcare Research

The Title Page
The title page should contain the following contents:
• Main title and subtitle (if any).
• Authors (First Name, Middle Name, Family Name), listed in the order
in which they are to appear on the page of the published article.
• Highest qualification for each author.
• Institutional affiliation for each author.
• Financial support information.
• Short or ‘running’ title. Length should not exceed 58 characters.
• Name, address, number(s), and email address of the corresponding
author.

What is a Cover Letter?
• A letter you send to the editor to
‘sell’ your article along your
submission
• Your chance to introduce your
work to the editor AND explain
why the manuscript will be of
interest to a journal's readers.
• Make it persuasive!
• Is this a good letter?
Dear Editor-in-Chief,
I am sending you our manuscript
entitled “Large Scale Analysis of Cell
Cycle Regulators in bladder cancer” by
Researcher et al. We would like to have
the manuscript considered for
publication in Pathobiology.
Please let me know of your decision at
your earliest convenience.
With my best regards,
Sincerely yours,
A Researcher, PhD

What to include in the Cover Letter?
Where (in the letter)? What?
Beginning If known, address the editor who will be assessing your manuscript by their name.
Include the date of submission and the journal you are submitting to.
First paragraph: Include the title of your manuscript and its type of manuscript (e.g. review, research,
case study). Then briefly explain the background to your study, the question you sought
out to answer and why.
Second paragraph: Concisely explain what was done, the main findings and why they are significant.
Third paragraph: Indicate why the readers of the journal would be interested in the work, i.e. the
importance of the results to the field. Take your cues from the journal’s aims and scope,
Conclude State the corresponding author and any journal specific requirements that need to be
complied with (e.g. ethical standards).
Must include!
Cliché sentences
“We confirm that this manuscript has not been published elsewhere and is not under
consideration by another journal.
All authors have approved the manuscript and agree with its submission to [insert the
name of the target journal].”

What do reviewers assess in your article?
Do they clearly identify the need for this research, and its relevance?
Does it target the main question(s) appropriately?
Are they presented clearly and logically, and are they justified by the data
provided? Are the figures clear and fully described?
Does it justifiably respond to the main questions posed by the author(s) in
the Introduction?
Are they up-to-date and relevant?
Is it clear, correct and easy to read?

What to expect in a reviewer's response?
• Introduction: Mirror the article, state your expertise and whether
the paper is publishable, or whether there are fatal flaws;
• Major flaws;
• Minor flaws;
• Other, lesser suggestions and final comments.

How to respond to reviewers/editor?
• “Sleep on it” before starting to write your rebuttal. Take Your Time!
• Carefully read the accompanying letter
• Read the reviewers' comments again carefully and check the issues
raised by the reviewer
• Carefully discuss the comments – one by one
• The better you structure this, the easier it is for the editor and
reviewers to see what you have done.

Outline/framework for responding to editor
• Include a heading for every page with “Reply to the comments on
manuscript [title of your manuscript] [manuscript ID number]” and
“[your name] et al.”
• Write an introduction to your response to the comments and summarise
major changes you have made, and include this with this response or use
it for a separate cover letter for the Editor. Do not forget to thank the
editor and reviewers for their efforts.
• Organise the comments/questions from the editor and each reviewer
and your response, for example, as follows.
• 1) Comment 1.1. (for comment 1 from reviewer 1) followed by a copy–paste of the
comment or question, or a short summary of the point raised. If the reviewer's
comments are not numbered, split the review into individual comments. You can
use italics to highlight the comments from the reviewer.
• 2) Reply 1.1. (the reply to comment 1 from reviewer 1). This is why this is often
called a point-by-point reply to the comments.

Some ground rules for the content of your reply (1)
• Discuss the comments in detail in advance with your co-authors.
• Carefully read the requirements from the journal for submitting a revised
version (e.g. marked-up version).
• Realise that the reviewer has taken time to evaluate your manuscript and
aims to help you to improve it (although it may sometimes appear
otherwise).
• Be polite to the reviewer and editor, and do not be dismissive of their
comments.
• Always be very specific in your response and address all points raised
• an editorial comment or spelling error, you can answer “This has now been
amended”, “We agree” or “We apologise for this omission”.
• If more than one reviewer has raised the same point, refer to this (“this point has
been addressed in the reply to comment x of reviewer y”).

• Consider including additional information, data or figures for the
reviewer that were not included in the manuscript if it helps you to make
your point.
• If you cannot address a point raised by the reviewer, explain why. If you feel that
a certain comment is outside the scope of your study, please explain this.
• If you disagree with the reviewer (yes, this may happen) and/or think that an
additional experiment or analysis is not needed, explain why.
• Carefully consider also mentioning this in the Discussion, for example, in
the paragraph with limitations, since readers may share the reviewer's
opinion.
• Never claim to have made changes if you have not done so.

• If you have been asked to shorten some part of your manuscript, do so.
• Always indicate where you have made a change in your manuscript in
response to the question/comments: “This is now addressed in the
Discussion section of the revised manuscript on page x, line y.” If
appropriate, cite relevant references in your reply.
• Address your response and not to the Reviewers.
• You should write for instancto the Editor e “We agree with the reviewer
…”rather than “We agree with you”. Always refer to the reviewer in third
person.

Sample of response cover letter
Tuesday, May 12, 2019
Dear Mr. Jones,
Editor of BMC Medical Ethics
Re: Second Revision of the Manuscript reference No. METH-D-18-00176
It is our pleasure indeed to know that you consider our revised manuscript is potentially
acceptable for publication. Please find attached a revised version of our manuscript “Mention
of ethical review and informed consent in the reports of research undertaken during the
armed conflict in Darfur (2004-2012): a systematic review”, which we would like to resubmit
an updated and revised final version for publication in BMC Medical Ethics.
Please find, in the following pages, our point-by-point responses to each of the editorial
comments and those of the reviewers.
Revisions in the text are shown in details below with clear reference to where these changes
have taken place in the modified version of the manuscript. We hope that the revisions in the
manuscript and our accompanying responses will be sufficient to make our manuscript
suitable for publication in BMC Medical Ethics.
We shall look forward to hearing from you at your earliest convenience.
Yours sincerely,
On behalf of the authors
Ghaiath Hussein, PhD
Address: Slaman Farsi Rd., Khaleej Distr., Riyadh 7839-13224 , Saudi Arabia
Cell: +966-565565810
E-mail: ghaiathme@gmail.com
Editor Comments:
1. Please provide a list of all the abbreviations used in the manuscript. This list should be placed
just before the Declarations section. All abbreviations should still be defined in the text at first
use.
Response:
A list of abbreviations was added just before the Declarations section.
2. Please include a statement in the Authors' contributions section to the effect that all authors
have read and approved the manuscript, and ensure that this is the case.
Response:
The required statement is added.
3. Please ensure that the titles of each separate Table file are correct and that they are in
sequential order.
Response:
The tables were revised. This led to renaming adding the missing Table 4
4. At this stage, we ask that you submit a clean version of your manuscript and do not include
track changes or highlighting.
Response:
This will be done along the submission of the final version.
Reviewer reports:
1. Raffaella Ravinetto, PharmD, PhD (Reviewer 2): Thanks for a comprehensive and
accurate reply to our previous comments.
Concerning my previous remark that "Mortality and nutritional surveys may be primarily
undertaken for different purposes than research, e.g. exploratory assessments to further
plan field intervention, M&E of field intervention. When not conducted for a primary
research purposes, they still need to comply with essential ethical issues such as
consent, protection of privacy and confidentiality, etc. (by the way, is it possible that many
of the CRED studies belonged to the category?)", I wish to clarify that this was a
reflection on the fact that this kind of activity "should" comply with ethics requirements in
any case (even if not used for research). This was not at all an assumption that all
surveys "will" by default comply with ethics requirements.
Response:
We have added the following statement at the end of the “Possibility One”, which reads as:
“Moreover, it would be expected than even when these surveys are not done primarily for
research purposes may not need ethical approval; yet they would have complied with an
essential ethical requirement such as consent.”
2. Concerning the issue of pre-approved protocol, I wish to reiterate that for the MSF ERB
the pre-review of generic protocols still requires ethics approval of the final,
contextualized protocol, thus the relevant paper should still have mention of ethical
approval.
Response:
Under “Possibility Four”, we have added the following statement: “Moreover, the MSF ERB still
requires the ethical approval of the final protocols that used pre-reviewed generic
protocols. Thus, the studies under this category should have mention of ethical approval.”

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