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DR. Miswar Fattah, SSi, MSi
th June 1978
Makassar, 6th

: SMAK Depkes Makassar

: Chemistry - UNHAS
: Master of Science in Clinical Chemistry, Biomedicine- UNHAS
: Doctor of Medicine Clinical chemistry, UNHAS

1. Research & Esoteric laboratory Head, Prodia Clinical Laboratory
2. Vice President of The Indonesian Assoctioatin Medical
Laboratory Technologist
3. Scientific division of immunoassay & Molecular Diagnostic
(2011-20130, Reference interval & Decision limit (2013 Now)
Indonesian Association for Clinical Chemistry (IACC-HKKI)
4. Corresponding Members Scientific Committee Asia Pacific
Federation for Clinical Chemistry (APFCB) 2010 - Now
5. Council member of ASEANAssociation For Clinical Laboratory
Sciences 2010 2012

Preparation of Manuscript
for Publication

Seminar Publikasi
USU Medan April 22, 2015

DR. Miswar Fattah, MSi

Research & Esoteric Laboratory Head

Prodia Clinical Laboratory

Guide to Scientific Writing

How to design and write scientific

research papers for publication

These Presentation will help authors,

educators, researchers, training program
directors, and other professionals write
more clearly and effectively, thereby
improving their chances for success

List Journal (Scopus)

Acta Medika Indonesia

Asia Pacific Journal of Public Health
Journal of University of Malaya Medical
Centre (Malaysia)
Medical Journal of Malaysia
Asian Pacific Journal of Tropical Medicine
Asian Pacific Journal of Tropical
Asian Pacific Journal of Reproduction

The Avoidable Downfall

Carefully planned
Flawlessly designed and executed
Poorly designed and writtenrejected or
The loss or delay of disseminating
important critical information to the
science community

Manuscript Deficiencies
57 articles evaluated to Emerg Med28 accepted, 29
rejected/pending, Of these 29:
Ambiguous methods
Ambiguous results
Conclusions not warranted by data
Poor referencing
Inadequate study design description
Unclear tables
Overly long discussion
Inadequate definition of terms
Deficiencies in manuscript preparation are more
frequent than mistakes in study design and execution.
Specific trainingin manuscript preparation is

Top 10 Reasons Manuscripts


Wrong journal, format, preparation

Disorganized study design
Defective tables, figures
Poor organization throughout, writing, spelling
No hypothesis or problem statement
No or insufficient conclusion
Overinterpretation of results
Article unfocused, too verbose and long
Inappropriate statistical methods; methods not
sufficient to repeat study
10. Poorly written abstract/title
Pierson DJ, Respiratory Care 49(10), 2004
Byrne DW, Publishing Medical Research Papers, Williams and Wilkins, 1998

Manuscript Reviews
Peer Reviewers

No - DOA



Masked review

Decision Editor
Rejection - Outright
Revise-Acceptance ?

Receipt of
manuscript by
editorial asst

Appropriate to
Conform to

Title &
& Abstract
Read Through

Editor Reports
Summary of
of peer
peer reviews
Summary of
of editors
editors review

Christoper Dant,

Acceptance - Outright

The Title Says It All

Titles are the first thing readers see,

Often the final part of writing a manuscript

Recommend writing starting with : the Methods


The title is the component that closes the circle

Like a billboard, it is your 10-second opportunity

to connect with the reader

Annesley, T.M., 2010. The Title Says It All. Clinical Chemistry 56, 357360. doi:10.1373/clinchem.2009.141523

The Title Says It All

Be Concise / short
Avoid using wasted words such as a study of,

investigation of, development of, or observations on

Be Clear
H1N1 Virus Testing on Mice Using Polymerase Chain Reaction
Polymerase Chain Reaction Testing of Mice for the H1N1 Virus

Treatment of Pediatric Melanoma Patients with Lasers

Laser Treatment for Pediatric Melanoma
A good practice is to show the title to colleagues who are not
coauthors and ask them to tell you what message they take away
from your words
Annesley, T.M., 2010. The Title Says It All. Clinical Chemistry 56, 357360. doi:10.1373/clinchem.2009.141523

The Title Says It All

Be Informative

The Title Says It All

Use Key Words and Terms Wisely

Avoid Abbreviations
Know the Journal and the Target Audience
Learning Exercise
Final Thoughts

Learning Exercise
Development and Evaluation of a New ELISA for the
Improved Detection of Lupus-Specific Antinuclear
Revised title:
ELISA with Improved Detection of Lupus-Specific
Antinuclear Antibodies
A Validated Method for the Sensitive Quantification of
Sirolimus in Whole Blood by the Use of Online Extraction
Connected to Liquid ChromatographyMass
Revised title:
Quantification of Whole-Blood Sirolimus by On-line
Extraction Liquid ChromatographyMass Spectrometry

Learning Exercise
Evaluation of siRNA Molecules Reveals Them to Be Sensitive
and Specific Biomarkers of Sepsis
Revised title:
Plasma siRNA Are Biomarkers of Sepsis
Reduction of Viral Load in Blood after Albinovir Treatment of
HIV-Infected Patients
Running title:
HIV Viral Load Reduction with Albinovir Treatment (49
Albinovir Treatment and HIV Viral Load (38 characters)
HIV Treatment with Albinovir (28 characters)

The Abstract and the Elevator Talk:

A Tale of Two Summaries

1st Impression to journal editor and the reader!

Follow the Journals Guidelines

Most abstracts are often too long: 250 words:

Cannot upload your paper!

Structure it (outline it)

The abstract is the single most important part of a manuscript,

yet the most often poorly written
-JAMA Editor

The Abstract

First looked at by editors/sometimes only thing read

by readers

Sometimes only part available electronicallyKEY


Summarizes the main points succinctly:

Study design, method
Primary germane results
Principal conclusions, implications

Do NOT be vaguebe substantive and brief

NOT The implications are summarized


Emphasize methods, main results, and


Introduction/purpose: 1 short sentence

Put objective as imperative style:

Objective: To evaluate whether zinc

supplementation during pregnancy affects infant

birth measures.

Methods, Results: 2-4 sentences

Conclusion: 1-2 sentences

Structured Abstract

IntroductionWhat problem, question, or hypothesis is

being studied? Why would it be of interest to the reader?

MethodsHow did you perform the study, test the

hypothesis, or answer the question?

ResultsWhat did you find? Did you solve the problem,

prove the hypothesis, or answer the question?

DiscussionWhat do your results mean? What value do

they add to the scientific literature?

Structured Abstract
ContextSummarize the study rationale and provide
clinical (or other) reason for the study question.
ObjectiveState the purpose or question asked. If more
than one objective, state primary objective and key
secondary objectives.
DesignDescribe basic design, including relevant details.
SettingGeneral community, primary care, hospital, etc.
Patient or other populationdescribe demographics,
disorders, inclusion/exclusion criteria, etc.
Interventionsname, dose, dosage
Main outcome measure(s)

The Effect of Zinc Supplementation on

Pregnancy Outcome
ObjectiveTo evaluate whether zinc supplementation during pregnancy affects
infant birth measures.
DesignRandomized, double-blind, placebo-controlled trial.
SettingOutpatient clinic at University of Alabama at Birmingham.
Patients580 healthy African-American pregnant women with plasma zinc levels
below normal levels, randomized at 19 weeks gestational age and divided by
median body mass of 26 kg/m2 into placebo and zinc supplement groups.
InterventionWomen receiving a non-zinc-containing prenatal vitamin tablet
were randomized to 25 mg/day zinc or placebo.
Outcome MeasuresBirth weight, gestational age at birth, head circumference
at birth.
ResultsInfants from zinc supplement group had greater birth weight (p<0.01)
and head circumference (p=0.02) than those in placebo group. Women with
body mass 26 kg/m2 had infants with significantly higher birth weights
(median 245 g, p<0.001) and larger head circumference (median 0.7 cm,
ConclusionsDaily zinc supplementation in women with low plasma zinc
concentrations in early pregnancy is associated with greater birth weights and
head circumferences, with the effect occurring in women with body mass
index 26 kg/m2. The specific effects of zinc on the fetus are unknown, and
future work is focusing on zinc effects on embryonic cells in vitro.

Characteristics of a well-written

Set the Scene with a Good Introduction

Starts by what is happening or has

happened (the context), ends by giving the
reader a glimpse of what follows in the
remainder of the artice
The Conical Introduction
Goal : demonstrate to the reader that
there are important missing pieces of
the puzzle that need to be filled in.


Why did you carry out this research? State the specific
purpose or rationale for the study.

What is the existing state of knowledge of this topic?

Synthesize information tracing the development of the
problem and summarize its current stateie, the background.
You ask (with citations):
Whats known?
Whats unknown?
What are the gaps in knowledge this study will fill?

What are you going to do and what do you expect to find?

State your hypothesis or question clearly (Objectives, Aims)

Give only strictly pertinent references.


This is a vital part of your paperit convinces (or not) the

reader whether your study:
Has merit and asks important research questions
Is focused and supported by relevant recent citations
Is ultimately important to human health and human disease

Reviewers and editors will judge the papers importance in the


You will better focus your introduction AFTER you construct

your findings (results) and consider them (discussion).

Your research question is the most important partin your

discussion, you will address whether the question or
hypothesis was answered based on your data.

Introduction Structure



What is the general problem or current situation?

Zinc plays a critical role in many biochemical functions, including nucleic acid
metabolism and is critical in early development.

What is the specific problem or controversy? Its significance?

Zinc deficiency is associated with increase metabolic problems in fetuses.

Studies evaluating relationship between zinc intake and pregnancy
outcomes have produced conflicting results for many reasons

What are our hypotheses/questions, and how will we answer them?

To clarify the relationship between zinc levels in the mothers diet and
pregnancy outcomes, we undertook a randomized placebo-controlled
trial of zinc supplementation.
Our objective was to determine if zinc supplementation was associated with
higher birth weight.
Our findings will help to provide continuing nutritional guidelines in

The introduction: a cone or funnel

Go from large to small

Background, known information

Knowledge gap, unknown information
Hypothesis, question, purpose statement
Approach, plan of attack, proposed solution


The text must provide a clear rationale. The reasons

for doing research are limited. to test a hypothesis,
answer a question, solve a problem, or fulfill a
purpose. The text should include something like the
We hypothesized that . . .
We tested the hypothesis that . . .
We asked whether . . .
To answer this question, . . .
This prompted us to investigate whether . . .
To resolve this apparent difference . . .
We solved this problem by . . .
The purpose of our study was . . .


Transition Phrases

Different Study Types,

These prior studies show that . . .
Same Model
Supporting the theory that . . .
Length, Detail, and
These studies are important because . . . Overlap
Consistency with Other
Interestingly, . . .
More importantly, . . .

Using this information, . . .

Yet, . . .
Unlike . . .
Whereas it has been shown that . . .
On the other hand, . . .
It is unclear . . .
The question remains, however, . . .
Although prior studies demonstrated . . .

Methods are Critical: Editors

What section contains the most flaws?

What section responsible for outright rejection?


How frequently do Editors encounter manuscript problems?

Poorly written, excessive jargon
Inadequate/inappropriate presentation
Poor description of design
Excessive zeal and self promotion
Rationale confused, contradictory
Essential data omitted, ignored
Important work of others ignored
Byrne DW, Publishing Medical Research Papers, Williams and Wilkins, 1998




Editors judge the study on whether your methods

are adequate to answer your specific aim or

Rationale for choosing procedures/tests

The pivotal point to judge whether the results are valid

Dont suggest a method you have no expertise with

Your peer reviewer may uncover this

Use consultants for methods you have no experience with, stating this
in paper

Methods usually the weakest section

Often deficient in detail, not providing enough information to

replicate the study
Statistical shortcomings


Study design or analysis type and period of study

Condition or disease studied

Human subjects approval

Details of sample (number, recruiting methods of study subjects,

patients, how organized)

Interventions, outcome measures, statistical analyses

Include the locations and times that data were collected

Give enough information to replicate the study; dont assume

only the specialist in your field will read it


Balance between brevity and completeness

Sometimes reference an often-used method

Use figures and tables (eg, flow diagram)

Naming thingsbe consistent

Acronymsspell out first time, use consistently throughout
Specialized tests, termsuse identical name in text, figs, tables

Develop list of frequently used terms

Present in logical order and your subsequent results

should follow that same order


Method diagrams communicate schedule of procedures, enrollment, study design,

mechanisms of action, guidelines, algorithms to reduce text and increase

ResultsThe Beginning

The heart of the paper

Write after figures and tables are
Consider your data critically
Construct tables, figures and include them in

Write the results
Use subheadings

Results determine
Whether youve answered your original

Your direction for future studies
Both of which belong in the discussion

ResultsThe Beginning

State ALL the findings

Whether significant or not
Without bias or interpretation
Do not include weaknesses, strengths of study, ie dont discuss


List experiments in order listed in methods

Use logical headers and group your findings

Characteristics of study subjects
Findings in order listed in methods
General to specific

Use past tense

Results confirm or reject your hypothesis: they do not prove


Short and to the pointMain or most important

findings first
Present only data directly relevant to the study
Dont repeat methods but you may remind the
reader briefly how you measured something.
Allow the data to speak for itselfuse tables/figures
construct them first and use as a basis for writing
In Tables and Figures, be descriptive, specific. Do
not repeat the obvious:
NO: Results of the kidney lead analysis are shown in Table 1.
YES: Kidney lead concentrations increased in group 1 over the

first 10 study weeks (Table 1).

Present absolute numbers and percentages so

reviewers can judge the significance of the findings.
Statistical significance clinical significance

Results or Data?
Mean translational movements in the X (left to
right), Y (back to front) and Z (bottom to top)
head directions were 0.10 0.11 mm, 0.16
0.03 mm, and 0.65 0.58 mm, respectively.
Mean rotational movements about the three axes
were 0.44 0.42 degrees, 0.24 0.26 degrees,
and 0.18 0.17 degrees, respectively. Movement
was not significantly correlated with age for
translation in the X (r = -0.09; p = 0.69), Y (r =
0.21; p = 0.35) or Z (r = -1.02; p = 0.64)
directions. Movement was not significantly
correlated with age for rotation in the X (r = 0.15;
p = 0.51), Y (r = -0.20; p = 0.35) or Z (r = 0.02; p
= 0.94) directions.


ResultsDont Regurgitate

As shown in Table 1, the mean age of participants was 20.4 2

years, and 80% of patients were Caucasian. Treatment group
contained 40 patients, whereas control group contained 45
patients. Table 2 shows the demographics of women in these
groups. There were 24 women in the control group, and 33
women in the treatment group...

There were no significant differences in treatment and control

patient intake demographics (Table 1), although a significantly
greater number of patients in the treatment group dropped from
the study for a variety of reasons, mostly relating to adverse
reactions. However, analysis of patients in this group later
revealed that those dropped patients had significant disease at
intake (Table 2). In comparing the two treatment groups (Figure
1), we found that...

Dont State the Obvious

Figure 1 is a graph illustrating
the plasma zinc levels
(moL/L) over the 37 weeks
versus gestational age in both
the zinc supplement group
and placebo group. The
placebo and the zinc group
both decreased over the 37
weeks of the study, but the
differences were significant for
the zinc group.

State Whats Important

We measured mothers plasma
zinc levels before randomization
(week 19) and at 26, 32, and 37
weeks gestational age (Fig 1).
Beginning as early as 26
weeks and at each timepoint,
differences in plasma zinc levels
between placebo and zinc
supplement groups were
statistically significant (P0.05)
after randomization.

ResultsMajor Mistakes

Failure to provide all the data critical to

answering the research question

Interpreting or commenting on results

Six of the 20 patients required intubation, illustrating the

seriousness of this problem (belongs in Discussion)

Over 40% of treated rats exhibited a decreased inflammatory
response, an unexpected finding (belongs in Discussion)

Failure to adequately address statistical


Tables and figures inappropriate, unbalanced

Tables and figures poorly constructed

Discussion Construction

Summarize major findings1st paragraph

Explain how your findings relate to those of
otherswhat do they mean?
Clinical relevance of the findings?
Limitations and how this influenced your
How will you overcome these in the next studies?

Explain the implications of findings

What future direction(s) will you take?

Discussion: Getting Carried Away

Few studies make discoveries changing the course of

scientific direction, and so authors:
Attempt to overly state or the importance of their findings
Come to erroneous or unsupported conclusions
Uncritically accept statistical results

This all distracts from works importance and signals to

the reviewer problems with the research

Also results in excessive length, a common problem

Authors should let the data speak for themselves

DiscussionCommon Mistakes

Unwarranted speculations


Injecting tangential issues


Conclusions not supported by the data


Not suggesting future directions for research

hypothesis study data/results conclusions

Sections Unbalanced
Article 3650 words

Tables and Figures

Critical to a paperEditors and readers look at these

before reading the paper!

Editors judge your paper on how well these are


Stand alone and tell a complete story

Unambiguousimmediately clear

Eliminate numerical data and long explanations in text

Figures display important trends, procedures, simplify

detailed data, and show basic methodologies.

This requires a table!

This result does NOT require a table!

Growth medium aeration was essential for the growth

of S. coelicolor. At room temperature (24C), no growth
was measurable in stationary cultures, whereas in
aerated cultures, we measured substantial growth (78
Klett units).

Tables & Result

In women with BMI <26
kg/m2, zinc
supplementation was
associated with a
significant increase in
birth weight of 248 g
(P=0.005), an increase in
head circumference of
0.7 cm (P=0.005), and
increase in arm length of
0.3 cm (P=0.03). The
other outcome measures
all favored the zinc
supplement group but
the differences were not
statistically significant
(Table 2).

Table & Result

Table 3 shows the mean birth weight by the BMI categories recommended
by the NIH Institute of Medicine. The lower the BMI, the greater the
effect of zinc supplementation on birth weight.

Patient Disposition
Study Design

Bar or Line Graphs-Colors?

This graph

will appear in the journal like this:

Journals DO NOT allow color graphs unless they are

necessary for understanding the graph

This series of 3 hypothetical KaplanMeier curves demonstrates the importance of scale.

David R. Holmes, Jr et al. Circulation. 2009;120:906-913

Copyright American Heart Association, Inc. All rights reserved.

Simple Graph

Use graphing software in word/powerpoint to create: KISS

No more than 3-4 groups
Keep all lines solid, few symbols
Put in SD and P values if relevant

Typical researcher writing a paper

Source: flickr/toennessen

Managing References

Recomeendeed : Using the free

reference management tool (Zotero)


Problem statement
Your topic:

Your paper


Lots of typing
Lost references

reference list/bibliography

Use a reference management


Your article


reference list/bibliography

Zotero is compatible with many databases,

including PubMed. Note: you can open
HINARI/PubMed or regular PubMed
If you are looking at PubMed search results,
a Save to Zotero icon will appear in the
address bar of your browser.
If you click on this icon, the citation
information will be immediately added to
your Zotero library.

A full overview of databases and

publishers supported by Zotero
is available at:

If you open an individual PubMed

entry, you will see a Save to Zotero
icon in the address bar of the browser.
By clicking on the icon, the Saving to
My Library... message will appear and
save the record to the open collection.

If you are on a page with a list of PubMed

results, you will see a Save to Folder icon in the
address bar of the browser.
If you click on the icon, a box will appear with a
list of all records to import. Select the records
you would like to import and click on OK.

In the new dialog box:

From the drop down menu,
choose the Citation Style
you would like to use
Choose the Format (RTF or
HTML) to save your
Click on OK

This is an example of a Zotero

bibliography that was created
using the Harvard citation style
and RTF as format.

Prepare Your Manuscript Carefully

Incorrect style irritates reviewers and editors, and

the wrong style suggests that another journal
previously rejected the paper.
Edit carefully
Eliminate spelling, punctuation, and grammar errors
Good writing requires rewriting

Check accuracy of references with original


Incorrect citations inconvenience the publisher and are a

disservice to the reader

Double-check numerical data!

Numbers in abstract, text, tables, figures, ledends, and

text must be consistent and correct

Avoid Repetition

Do not disclose results in introduction

Do not repeat the Introduction in
In text
Do not repeat figure legends, table titles, or contents of

the tables themselves

Use tables sparingly

Presenting a few facts in text takes less space than a

Do not use tables for presenting simple lists

Abbreviations, definitions, symbols in figures and

tables must be explained in legends and footnotes

Journal Review
Full review and decision takes ~1 month
Editors make decision based on arguments; they dont
count votes from Peer Reviewers
Most papers undergo 2 rounds before publication
For borderline decisions, a goal is to avoid multiple rounds
of review
Pressure to publish quickly may lead to rejection if further
experiments are needed

What Helps or Hinders the Paper?

What Helps?

New data to a point

Referee or Editor made factual errors (easy to prove)
Careful and accurate response to criticisms (table)
Telling the editor that reviews were helpful in improving the
Knowing how to submit to the journal electronically

What Doesnt?

Referees were unfair and the criticisms were largely not

Guesses at referee identity followed by personal attacks
Specific evidence of bias by referee (difficult to prove)
Endorsements or (positive) statements about your standing
and reputation

Evaluate Your Paper

To understand and evaluate your

paper, the editor will ask (and so
What specific
questions/aims does the paper address?

Are the methods/design adequate to answer your questions?

What are the main conclusions?
What specific evidence (data) supports those conclusions?
What is the quality of that evidence?
Conclusions: what is the studys significancewhat insights or new
directions are evident?

My Suggestions

Put the manuscript away for a couple of days

Read troublesome areas aloud

Dont try to edit a mangled paragraphdelete

and rewrite it

Your colleagues reviews of writing and

table/figures are valuabledont be defensive
about edits

Let go of academic writing habits and dont

imitate others writing. Develop your own clear,
direct style

Writing Deficiencies
Most commonly cited by journal editors
Wordiness and

Cut, condense, combine


Outline to catch logic problems

Poor flow of ideas

Consult an editor

Poor syntax and grammar

Excessive abstraction

Be specific and descriptive

Keep it simple and direct

Do not overly compress writing

Qualify statements as necessary

Unnecessary complexity

Excessive compression

Unnecessary qualification
Byrne, D. Science Editor 23:2, 2000

Outline your paper
Start early as your data is being analyzed
Look at your data and decide how to organize and
present your results: tables, figures, text
Patterns and clues will emerge to guide your argument
Start with results then introduction and
Write title and abstract last
Put it away, re-read, give to your colleagues to read
Revise, revise, and re-revise
Adhere to journal guidelines!
Critically evaluate your paper with an editors eye
Write clearly, logically, and simply!
Use tools loke zotero, medeley, etc