Dr. Ashraf Abdel Basset Prof. of Pediatrics Mansoura Faculty of Medicine Writing a Scientific Manuscript

Dr. Ashraf Abdel BassetProf. of Pediatrics

Mansoura Faculty of Medicine

Writing a Scientific Manuscript

Writing a Scientific Manuscript

•Scientific Writing Overview

•Why a Scientific Format?

•Before Writing

•Format of a Scientific Paper



•Before Writing


Scientific Writing Overview

Scientific WritingOverview

Island ofHuman

Knowledge

OCEAN OF IGNORANCE

yourpaper

Sharks(reviewers)

• Scientific writing is the reporting of new results in scientific journals r to disseminate that information to the larger community of scientists.

• Communication of your results contributes to the pool of knowledge within your discipline provides information that helps others interpret their own experimental results.

• Most journals accept papers for publication only after peer review.

Sending your manuscript for publication

Sending your manuscript for publication

PaperAccepted!

Reviewer 1

Reviewer 2

Reviewer 3Editors

Author’s feelings…

AUTHO

R

Editors

• I expect the editor to accept all my papers, accept them as they are submitted, and publish them promptly. I also expect him to scrutinize all other papers with the utmost care, especially those of my competitors.

• Dr E H Wood, Mayo Clinic

Publication Procedure

MEDICAL JOURNALISMThe quintessential arm of biomedical research

Whoever tells the truth, sooner or later will be caught doing it—Oscar Wilde

The role of scientific publications

BALAJI RAVICHANDRANEditor, studentBMJ



•Before Writing


Why a Scientific Format?Why a Scientific Format?

• It is a means of efficiently communicating

scientific findings to the broad community

scientists in a uniform manner.

• It allows the paper to be read at several

different levels. At whatever level a

person reads your paper, they will likely get

the key results and conclusions.



•Before Writing


Before WritingBefore Writing

Where to submit the manuscriptWhere to submit the manuscript• The prestige factorThe prestige factor• The circulation factorThe circulation factor• The frequency factorThe frequency factor• The audience factorThe audience factor

– A narrow, highly technical, A narrow, highly technical, disciplinary journaldisciplinary journal

– A broad range of discipline A broad range of discipline – An audience of other biologyAn audience of other biology

• Professional publishers – Elsevier– Pergamon Press– Springer Verlag– J Wiley & Sons– Kluwer Academic

Publishing– MCB University Press– IOP Publishing– Academic Press

• Professional publishers – Elsevier– Pergamon Press– Springer Verlag– J Wiley & Sons– Kluwer Academic

Publishing– MCB University Press– IOP Publishing– Academic Press

Journals - PublishersJournals - Publishers

• Professional societies– AIAA– ASCE– ASME– IEEE– SIAM

• Professional societies– AIAA– ASCE– ASME– IEEE– SIAM

Before WritingBefore Writing

Searching scientific literature• Explore ideas to your subject

– Gaps in research on a subject of interest

– Existence of any duplication to your work

• Conduct a specific search– Manually in the library

– On-line searching

• Keep up-to-date with the specific subject

Before WritingGetting statred• Some people work well from an outline, others do not.• Some people write first to discover the points, then

rearrange them using an after-the-fact outline.

Experimental process Section of Paper

What did I do in a nutshell? Abstract

What is the problem?Introduction

How did I solve the problem? Materials and Methods

What did I find out? Results

What does it mean? Discussion

Who helped me out? Acknowledgments

(optional)

Whose work did I refer to? Literature Cited

Extra InformationAppendices (optional)



•Before Writing


Format of Scientific PaperFormat of Scientific Paper

Front Matter•Title (fewest possible words that describe the contents)•Author’s (co-authors) name and address•Abstract (miniversion of the paper, no citations)•Keywords

Article Body

Introduction

Material & Methods

Results

Analysis

Discussion/Conclusion

End Matter•Acknowledgment (technical help and financial assistance)•References (at 52 journals were found 33 different styles for listing)•Appendixes

Write in What Order?

TitleAbstractIntroductionMethodsResultsDiscussionAcknowledgementsReferences

Format of Scientific Paper Format of Scientific Paper

TitleTitle

AbstractAbstract

IntroductionIntroduction

MethodsMethods

ResultsResults

AnalysisAnalysis

DiscussionDiscussion


TitleTitle

AbstractAbstract


MethodsMethods

ResultsResults

AnalysisAnalysis


TitleTitle

• Criteria

• Frame

• Tips

• Examples

CriteriaCriteria

• Concise and descriptive.

• Stated in terms of a functional

relationship.

• Informative and catchy.

FrameFrame• Either 1 or 2 parts

• 2 part titles with main topic first then

precise specification of research focus

• Typically packed with information

• Verbs – not used; mostly nouns/dense

noun groups with some adjectives

• Noun groups- often 2 or even 3 groups

separated with prepositions [‘Position’

words: in/of/on etc]

Stimulus-induced oscillations (Group1)

in (Preposition)

plant cell cytosolic free calcium (Group 2)(Group 2)

• 2 part titles often give broader topic area 2 part titles often give broader topic area

first, then specific focus, angle or method first, then specific focus, angle or method

e.g.e.g.

• Compliance in an anti-hypertension trial: a

latent process model for binary

longitudinal data

Frame….

TipsTips

• Pricks the reader's interest.

• Predisposes him/her favorably

towards the proposal

ExamplesExamples

• Which, if any, of the 3 titles would be appropriate for a paper you’re writing? – An Investigation of Hormone

Secretion and Weight in Rats – Fat Rats: Are Their Hormones

Different?– The Relationship of Luteinizing

Hormone to Obesity in the Zucker Rat

Examples.…Examples.…

• An Investigation of Hormone Secretion and Weight in Rats

• Fat Rats : Are Their Hormones Different?

• The Relationship of Luteinizing Hormone to Obesity in the Zucker Rat

[delete-no added meaning]

[A little vague- Which hormone? What effect on weight- increased or decreased?]

[catchy journalistic style]

[2 part title–commonly used in journals; relationship between obese rats & specific hormone not identified]

[Clear relationship & precise description]

Examples.…Examples.…


TitleTitle

AbstractAbstract


MethodsMethods

ResultsResults

AnalysisAnalysis


AbstractAbstract

• Purposes

• Criteria

• Frame

• Tips

• Mistakes

• Examples

PurposesPurposes

• An abstract is a shortened version of

the paper and should contain all

information necessary for the reader

to determine:

1. What the objectives of the study were?

2. How the study was done?

3. What results were obtained?

4. And the significance of the results.

Criteria…..Criteria…..• Usually 1 paragraph for reports, journal articles

& sometimes 2 paragraphs for longer papers such as dissertations and theses.

• They generally follow the order of the work they are condensing

• They should provide a well balanced account of the original study i.e. not focusing disproportionately on 1 or 2 sections of the article

• Should read seamlessly moving smoothly from section to section, rather than mechanically devoting a sentence to each section

Criteria …..

• Descriptive abstract (topical abstract)– Describes the contents but contains

too little substance and detail• Informative abstract

– Self-explanatory report on a scientific investigation (research objectives for conducting the investigation, the basic method used, and the results and significant conclusions)

• Extended abstract (conference proceedings)

FrameFrame• 200-300 Words

• Written in a formal, impersonal scientific style.

However 'we' is commonly used.

• Passive or active constructions can be used [passive

e.g. Measurements were made.. Object, to be + past

participle]

• Should use a level of language that will be

understood by those for whom the report is intended.

• Often packed with a considerable amount of

information but should not overload the reader.

• Should be succinct, avoiding redundancy .

• Written in complete sentences with effective

punctuation.

TipsTips• Murray describes the process of writing an

abstract: ‘.. as if someone had taken a

yellow marker and highlighted all the key

points in the body of the report into a [1-

page] document' [David Murray, Online

Technical Handbook] Though he points out

the need for further editing and revision to

ensure readability

Tips……. Tips…….

Ask a critical friend to read it. • Can they explain to you the scope and structure of

your abstract?

• Does it flow and establish a clear connection between ideas?

• Can you cut any superfluous information?

• Have you written it succinctly? Is it free from wordiness?

• Is it a well-balanced representation of the original paper?

• Has any key information been omitted?

Tips…….Tips…….Is it appropriately paragraphed?

• Have you checked that it does not contain cross references to

graphical or other information in the report?

• Is free from errors: grammatical, non-scientific style, sentence structure

and punctuation?

• Have you kept to the word limit?

• Have you made sure that it does not includes

• information, ideas or claims

that are not included in your paper?

Mistakes

• Too much background or methods information

• Figures or images• References to other literature, figures

or images• Abbreviations or acronyms

Evaluating abstracts: Abstract 1-Environmental Science about the Evaluating abstracts: Abstract 1-Environmental Science about the estimation of natural rechargeestimation of natural recharge

Natural ground water recharge is estimated using the injected tracer technique in

the Bairasagara watershed of Kolar district, Karnataka (India) comprising of

medium grained granite and granatic gneiss with weathering/fracturing up to 46 m

depth. On a macroscopic scale, it is estimated that the weathered granites act as a

uniform body having a recharge capacity of about six to 200 mm per annum for an

average value of rainfall of 968 mm. Marked differences of infiltration rates (nil to

130 cm/year) were observed under cultivated and dry areas. The water level

fluctuation and recharge are found to be minimum in the ayacut area as compared

to the catchment area. Studies helped in demarcating recharge and discharge

areas. Qualitative correlation studies of estimated natural ground water recharge

have been carried out with depth to basement, resistivity of subsurface layers, and

water level fluctuations.

An attempt has been made to get empirical relationships between the recharge

versus depth to basement, and recharge versus water level fluctuations. This paper

discusses the studies carried out, the results obtained the importance of such

studies in the evaluation of groundwater resources.

ExampleExample

Evaluating abstracts: Abstract 2- BiologyEvaluating abstracts: Abstract 2- BiologyStimulus-induced oscillations in plant cell cytosolic free calcium. Ca2+ is implicated

as a second messenger in the response of stomata to a range of stimuli. However,

the mechanism by which stimulus-induced increases in guard cell cytosolic free Ca2+

([Ca2+] are transduced into different physiological responses remains to be

explained. Oscillations in [Ca2+] may provide one way in which this can occur. We

used photometric and imaging techniques to examine this hypothesis in guard cells

of Commelina communis. External Ca2+ ([Ca2+]e), which causes an increase in [Ca2+],

was used as a closing stimulus. The total increase in [Ca2+] was directly related to

the concentration of [Ca2+]e, both of which correlated closely with the degree of

stomatal closure. Increases were oscillatory in nature, with the pattern of the

oscillations being dependent on the concentration of [Ca2+]e. At 0.1 mM, [Ca2+]e

induced symmetrical oscillations. In contrast, 1.0 mM [Ca2+]e induced asymmetric

oscillations. Oscillations were stimulus-dependent and modulated by changing

[Ca2+]e. Experiments using Ca2+ channel blockers and Mn2+-quenching studies

suggested a role for Ca2+ influx during the oscillatory behavior without excluding

the possible involvement of Ca2+ release from intracellular stores. These data

suggest a mechanism for encoding the information required to distinguish between

a number of different Ca2+-mobilizing stimuli in guard cells, using stimulus-specific

patterns of oscillations in [Ca2+].

ExampleExample

Evaluating abstracts: Abstract (3) StatisticsEvaluating abstracts: Abstract (3) Statistics

Non-parametric ecological regression and spatial variation Ecological studies aim

to analyse the variation of disease risk in relation to exposure variables that are

measured at an area unit level. In practice it is rarely possible to use the

exposure variables themselves, either because the corresponding data are not

available or because the causes of the disease are not fully understood. It is

therefore quite common to use crude proxies of the real exposure to the disease

in question. These proxies are rarely able to explain the disease variation and

hence additional area level random effects are introduced to account for the

residual variation. In this paper we investigate the possibility to model the effect

of ecological covariates non-parametrically, with and without additional random

effects for the residual spatial variation. We illustrate the issues arising through

analyses of simulated and real data on larynx cancer mortality in Germany,

during the years of 1986 to 1990, where we use the corresponding lung cancer

rates as a proxy for smoking consumption.

ExampleExample

Evaluating abstracts: Abstract 4-Environmental ScienceEvaluating abstracts: Abstract 4-Environmental Science

Geomorphology and pollution: the environmental impacts of lead mining,

Leadhills, Scotland The Glengonnar Water has experienced severe

environmental pollution resulting from historic lead mining operations.

Though now abandoned, the legacy of the mining era remains in the form of

river and floodplain sediments grossly polluted with metals, particularly lead

which exhibits surface concentrations in excess of 75 000 mg kg total Pb.

Geomorphological investigations link the most important mining period to a

major phase of floodplain degradation, which acted as an efficient sink for

particulate bound metals. The pattern of metal contamination within the

floodplain has been complicated by subsequent fluvial entrenchment.

However, preliminary evidence indicates that lateral and vertical variations of

metals [both total and available] can be accounted for in terms of the age of

deposit, distance downstream and local hydraulic conditions. The

effectiveness of floodplains to interrupt the delivery of sediment-bound

contaminants was highlighted by a metals budget developed for the main

channel length. This confirmed that channel bank erosion of contaminated

floodplains is now the major source of metals to the fluvial system.

ExampleExample

Evaluating abstracts: Abstract 5- Engineering/CommunicationsEvaluating abstracts: Abstract 5- Engineering/Communications

High frequency digital power line transmission for terrestrial and marine networks

The aim of this work was to investigate a feasibility study based on an appropriate method of propagation results, analysing suitability of communication through power line transmission channels. With this as the main aim the emphasis of the work has been placed on: initially the design of simulators resulted from the modelling of the channel, followed by low complexity protocols and modulation schemes, and the real time performance evaluation of point to point multimedia kit designed and tested for application on a QinetiQ project.

This thesis describes the work carried out in the areas of propagation, modulation design, duplex protocol, modelling and simulation and real time channel evaluation. Also presented herein is the design and implementation of conditioning units “Coupling Devices” together with implementation of remote/local control mechanism to aid the project requirement” remote control of the vessel via power line.

The effectiveness of these devices, and various measurements and real time trials of the simulators, and the multi media kit, is the prim importance throughout this thesis. Simulation results, while assessing the effectiveness of an OFDM COSSAP model, mainly are tried over an AWGN channel, and later on over a Rayliegh fading channel and subsequently over AWCN, with appropriate for power line channel, are used to illustrate and support this work. The most important results are the successful outcome of the multi media multiplexed kit trials on board RV TRITON a QinetiQ vessel, and similarly at the power line laboratory, where real time text, audio and video, as well as duplex conferencing were demonstrated with modems connecting at 33.6 kbits/s.

Finally, investigation of the three-phase 440V power line channel resulted in lodging a patent that uses the STD/STC techniques. These techniques, whilst in their field are not new, however with the diversity gain achieved when using smart power line modem design will enhance data throughputs in multiples of the presently achievable rate.

ExampleExample

Bone mineral density and bone turnover markers in children with chronic renal failure

•Bone mineral density (BMD) at lumbar spine (L2-L4) was measured by dual energy X-ray absorptiometry (DEXA) in 21 children with predialysis chronic renal failure (CRF) and 44 children with end stage renal failure (ESRF) on regular hemodialysis. BMD results were expressed as Z-scores. Osteopenia was documented in 13 predialysis patients (61.9%) and 26 patients (59.1%) of children with ESRF. No significant correlation was observed between Z-scores and the duration of CRF or estimated creatinine clearance. In osteopenic children there was a negative correlation between Z-scores and serum phosphorus (r= -0.61, p= 0.004), intact parathyroid hormone (r=- 0.47, p= 0.03), bone specific alkaline phosphatase (r= -0.52, p= 0.02) and positive correlation with total calcium (r= 0.41, p= 0.07) and 25 hydroxy cholicalciferol (r= 0.53, p= 0.02). Osteopenic children who had iPTH values 200 pg/ml were more osteopenic than those who had lower iPTH levels (p=0.006). In conclusion osteopenia, assessed by DEXA, is frequent in children with CRF. It occurs early irrespective of the duration or the severity of CRF. In children with ESRF the degree of osteopenia is correlated to the laboratory markers of renal osteodystrophy and patients with biochemical findings of secondary hyperparathyroidism are more osteopenic than the others.

ExampleExample


TitleTitle

AbstractAbstract


MethodsMethods

ResultsResults

AnalysisAnalysis



• Purposes

• Frame

• Tips

• Mistakes

• Examples

PurposesPurposes

• What is the nature of the

proposed research topic?

• Why is it important?

FrameFrame

• Brief description of your problem domain: – Understand its basic terminology

and issues– Formulate a research question.– Provide the motivation for the

proposed project.

Frame…Frame…

• Explanation of the problem

boundaries:

– Elucidate what aspects of the

problem domain are to be included

and what aspects would be

excluded from the thesis project.

Frame…Frame…

• Formulation of research question (hypothesis): – Easily understood – Guide and inform the research project.– Focus on a single aspect of the problem

domain.– Can be refined into more specific

project objectives, satisfaction of which would lead directly to answering the research question.

• For exploratory or phenomenological research, you may not have any hypotheses.

Frame…Frame…

• Highlighting the significance of

your research in practical and

theoretical terms.

Tips……

• Try to place your research question in the context of either a current "hot" area, or an older area that remains viable.

• Provide a brief but appropriate historical backdrop.

• Provide the contemporary context in which your proposed research question occupies the central stage.

Tips……

• Identify "key players" and refer to the most relevant and representative publications.

• Try to paint your research question in broad brushes and at the same time bring out its significance.

Word Choice• Examine vs. Analyze

– Activity to gain knowledge vs. Describing the analysis of that knowledge

• Bloom’s Taxonomy– Knowledge– Comprehension– Application– Analysis– Synthesis– Evaluation

Tips……

• Bloom’s Taxonomy– Knowledge: Recitation of fact

• Found, identified, labeled

– Comprehension: State a problem or interpret fact• Discuss, predict, compare

– Application: Apply old information to solve new problems

• Solve, show, examine, classify

– Analysis: Used to explain patterns or meaning• Analyze, investigate, compare, contrast

– Synthesis: Making predictions or discussing possibilities

• Predict, plan, devise, propose

– Evaluation: Drawing conclusions, making recommendations

• Justify, verify, argue, recommend, determine

Tips……

High quality introduction

• The reader’s interest should be engaged.

• He should understand why the general topic is worth pursuing and what your research question is.

MistakesMistakes

• If the research problem is framed in the context of a general, rambling literature review, then the research question may appear trivial and uninteresting.

• No hard and fast rules on how to frame your research question.

• No prescription on how to write an interesting and informative opening paragraph.

MistakesMistakes

• A lot depends on your creativity,

your ability to think clearly and the

depth of your understanding of

problem areas.

ExamplesExamples

• Writing and thinking are closely linked

enterprises “fuzzy writing reflects fuzz, thinking”.

• People have difficulty translating their ideas into words, they generally do not know the material well as they think.

Documents

Dr. Ashraf Abdel Basset Prof. of Pediatrics Mansoura Faculty of Medicine Writing a Scientific Manuscript