📝 Step-by-Step Guide: Building a Manuscript

This guide will help you write a scientific manuscript from start to finish. Follow each section closely and always refer to the journal’s author guidelines.

1. Start with the Skeleton

• Before writing, choose your target journal and download its author instructions.

• Build a document template with these required sections:

  • Title page

  • Abstract (structured or unstructured, based on journal)

  • Main sections: Introduction, Methods, Results, Discussion, Conclusion

  • References

  • Acknowledgements

  • Tables and Figures (at the end)

2. Title Page (Follow Journal Format Exactly)

Begin by creating a skeleton of your manuscript based on the journal’s author guidelines. Pay close attention to formatting requirements. Start with the title page, which usually includes:

Title: Left ventricular dimensions at 36 weeks corrected age in extremely preterm newborns: a prospective 4D-echocardiography study
Short Title: [as per journal]
Authors: Full names with degrees and superscript affiliations (e.g., Silvia Nogara, MDa)
Affiliations: Use superscripts (a, b, c...) to link authors with institutions
Corresponding Author: Full contact details, email, phone, address
Funding & Support: List all funding bodies
Conflicts of Interest: Declare any
Data Sharing Statement: E.g., “Data available on request”
Prior Presentation: Indicate if findings were presented elsewhere
Contributors’ Statement: Describe what each author did
Confirm with: “All authors approved the final version and are accountable for all aspects of the work.”

Example with text:

• Title: Left ventricular dimensions at 36 weeks corrected age in extremely preterm newborns: a prospective 4D-echocardiography study

• Short title:

• Authors:
  Silvia Nogara, MDa; Carolina Michel Macias, MDa; Shiran S. Moore, MDa,b; Audrey Hebert, MD; Nina Nouraeyan, MD; Christine Drolet, MD; Anie Lapointe, MD; Andreanne Villeneuve, MD; Brahim Bensouda, MD; Daniela Villegas Martinez, MSca; Jessica Simoneau, DIT; Tiscar Cavalle-Garrido, MDc; Adrian Dancea, MDc; Guilherme Sant’Anna, MDa; Gabriel Altit, MDa

• Affiliations:
  a. Neonatology, McGill University Health Centre – Montreal Children’s Hospital; Department of Pediatrics, McGill University, Montreal, Quebec, Canada
  b. Neonatology, Dana Dwek Children’s Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
  c. Pediatric Cardiology, McGill University Health Centre – Montreal Children’s Hospital; Department of Pediatrics, McGill University, Montreal, Quebec, Canada

• Corresponding Author:
  Gabriel Altit, MDCM, MSc, FRCPC, FAAP
  Neonatology – Montreal Children’s Hospital – McGill University
  1001 Decarie Blvd, Montreal, QC, H4A 3J1, Canada
  Phone: (438) 497-7231
  Email: gabriel.altit@mcgill.ca

• Funding: Supported by the Department of Pediatrics at McGill University, the Just For Kids Foundation, the Foundation for Pediatric Research, and the Fonds de Recherche en Santé du Québec.

• Conflicts of Interest: None declared.

• Data Sharing Statement: Derived data will be shared upon reasonable request to the corresponding author.

• Prior Presentation: None.

• Contributors’ Statement Page:

  • Dr. Nogara: Data collection, analysis, interpretation, drafted manuscript

  • Drs. Michel Macias, Moore, Hebert, Nouraeyan, Drolet, Lapointe, Villeneuve, Bensouda, Cavalle-Garrido, Dancea, Sant’Anna: Critical manuscript review

  • Mrs. Villegas Martinez & Mrs. Simoneau: Data collection and critical review

  • Dr. Altit: Study design, data analysis, interpretation, critical manuscript review

  • All authors approved the final manuscript and are accountable for all aspects of the work.

3. Abstract

Follow the journal's abstract guidelines carefully—some require a structured abstract with a word limit (e.g., 125 or 250 words). Pay attention to the format (text vs. structured headings) as specified.

• Strictly follow journal format:

  • Word count (often 125 or 250 words)

  • Structure (unstructured, or headings like Background, Methods, Results, Conclusion)

• Be concise and stick to the main message.

• Do not add references or unexplained abbreviations.

4. Introduction (Max 1 Page)

Introduction should be a maximum of 2–3 paragraphs. It usually includes core principles about the topic, the knowledge gap, the research question, the study’s aims, and the hypothesis. It should be concise and no longer than one page. 

Structure:

1. Context: Brief background on the topic (2–3 sentences).

2. Knowledge Gap: What is missing or unknown.

3. Study Purpose: Research question, aims, and hypothesis.

Example:

Bronchopulmonary dysplasia (BPD) is known to affect RV development. However, longitudinal 4D-echocardiographic data on LV structure in extremely preterm infants are lacking.

5. Methods

This should include the inclusion and exclusion criteria for your study population, and the definitions you will use in the Results section to characterize the population (such as BPD, IVH, ROP, RV dysfunction, LV dysfunction, pulmonary hypertension, etc.), along with appropriate references. If Z-scores are used, indicate their source. The methodology must also describe the techniques employed. For echocardiography studies, this includes all steps: image acquisition, image storage, anonymization, file types, the analysis process, and data extraction. Clearly describe the metrics computed (e.g., EF, FAC, Z-scores). If data extraction was performed using a specific software, mention the software name, version, and city of origin (e.g., TomTec, version X.X, Munich, Germany). Indicate whether image analysis was performed blinded to patient status or involved a second reviewer. Then, describe the statistical analysis, including the tests used, software employed, and its version and location. Should mention you follow STROBE guidelines if observational. You need to finish with a statement on the REB approval (often provide the REB number and the board(s) that accepted the study), consenting of participants, ethics portion. 

Population

• Inclusion/Exclusion criteria

• Study setting and recruitment period

Definitions

• Clearly define clinical conditions used in Results (e.g., BPD, PH, IVH), with references

Echocardiography (or Other Technique)

Describe in order:

• Image acquisition protocol (probe, views)

• Image storage & anonymization

• File formats used

• Image analysis: software (e.g., TomTec, version, city), metrics (e.g., EF, FAC, Z-scores), blinded review?

Statistical Analysis

• Variables compared, tests used

• Software name, version, location (e.g., R version 4.3.1, Boston, USA)

Ethics

6. Results

The Results section typically follows the order in which the tables are presented. Always begin with a statement on patient inclusion and exclusion and include a flow diagram outlining how the study population was selected, with corresponding numbers and reasons for exclusions. Then, describe the demographics and clinical characteristics of the population, which usually corresponds to Table 1. All tables should be placed at the end of the document in the order they are referenced. Some journals prefer sequential numbering (Table 1, Table 2, etc.), while others require differentiation between main and supplementary tables (e.g., Table 1, Supplementary Table 1). Ensure consistent formatting across all tables, with clearly defined abbreviations listed at the bottom, and make sure each table is well organized and easy to read. The next 2–3 paragraphs should present the core findings in a factual manner, closely aligned with the study aims and objectives. Figures must be referenced in the main text—every figure included must correspond to a specific mention. Do not include any figure that is not discussed in the text.

Start with a Population Flow Diagram (Figure)

• Show screening, inclusion, exclusion with numbers

• Mention in text: “Of 120 infants screened, 90 were included (Figure 1).”

Clinical Characteristics (Table 1)

• Describe your population demographics, diagnoses, and exposures

Main Findings

• 2–3 paragraphs following your objectives

• Each result must link to a Table or Figure

• Never include a figure or table that isn’t referenced in the text

7. Discussion

Discussion section, which should be focused and free of unnecessary elaboration. The first paragraph is typically a short summary of the main findings in relation to the aims and hypothesis. For example: "In this study, we analyzed 200 preterm infants and found that the right ventricle was smaller at 36 weeks in those with BPD. We also found..." The next 2–3 paragraphs should place your findings in the context of existing literature—what is new, what aligns with or differs from previous studies, and possible mechanisms explaining your results. All assertions must be supported by references—no statements should be left uncited. The final paragraph of the discussion addresses strengths and limitations. This can often be drafted early in the writing process, as most studies have known strengths (e.g., prospective design, large or multicenter cohorts, blinding, standardized protocols, trained personnel) and limitations (e.g., observational nature, small sample size, single center, variability in image acquisition, use of a single software platform, potential vendor-specific differences, missing data).

Structure:

1. Summary of Findings (aligned with aims/hypothesis)
   “We found that RV dimensions were significantly reduced in infants with BPD at 36 weeks...”

2. Interpretation in Context of Literature

   • Compare with prior studies (concordant or discordant)

   • Discuss potential mechanisms

   • All claims must have references

3. Strengths & Limitations

   • Strengths: prospective design, blinded assessment, standardized acquisition, etc.

   • Limitations: single center, small sample, missing data, operator variability

8. Conclustion

The conclusion should be a single paragraph of approximately five lines, summarizing the key message of the study and offering insights into potential future directions. One Paragraph.

3. • Highlight main conclusion and suggest future directions

9. References

Following the main text, include your References. Use EndNote—McGill offers free access. Not using a reference manager can quickly become unmanageable.

• Use EndNote (free via McGill)

• Ensure proper style (Vancouver, APA, etc. per journal)

• All cited in-text references must appear here

10. Acknowledgements

Finally, write the Acknowledgements section, where you thank families, funders, participants, nurses, the clinical team, the CNN (if applicable), or any other contributors deserving recognition. “We would like to thank the families, NICU staff, the Just for Kids Foundation, and the McGill Pediatrics Research Office.” Include CNN, data sources, or anyone not qualifying for authorship but who contributed meaningfully.

11. Tables and Figures

Then, create a separate section for Tables (e.g., Table 1, Table 2, Table 3) and one for Figures. Check the journal’s requirements carefully—some allow a maximum of five tables/figures total, while others also impose restrictions on supplementary materials. In the initial drafting stage, always keep everything consolidated in a single file. When you're ready to submit, you can split the document into individual files (manuscript, tables, figures) as required. This helps prevent confusion during revisions, especially for the corresponding author and co-authors. Add comments wherever you’re unsure or would like me to review and assist further.

• Place at the end of the document

• Number in order of appearance (Depends on Journal whether Supplementary Tables need to be re-numbered from start).

• Include clear titles and define all abbreviations

• Pay attention to:

  • Journal limits on number of tables/figures (some allow max 5 total)

  • Supplementary material format (Supplementary Table 1, etc.)

12. Final Steps Before Submission

• Keep everything in ONE consolidated file (manuscript + tables + figures)

• Comment on sections you’re unsure about for review

• Once approved for submission by all the authors (after rounds of review), split into journal-required files:

  • Main text

  • Figures

  • Tables

  • Supplementary files

✅ Quick Checklist

• Followed journal formatting?

• Title page complete?

• Abstract meets word count and structure?

• Introduction <1 page?

• Methods detailed and reproducible?

• Results in line with objectives, with all figures/tables referenced?

• Discussion well structured with clear limitations?

• EndNote used for references?

• Acknowledgements included?

• All figures and tables formatted and labeled?