Notes on Writing a Scientific Manuscript (PSGP 810)
Publication Planning and Journal Selection
Discussion prompts (Page 2) to consider before submission:
Did you find a suitable journal for your submission?
Why did you select this journal?
What is the impact factor of the journal you selected?
Do you know the ranking of this journal in the field?
Did you read the “Instruction for Authors” of the journal?
Do you know what journals (and the impact factors/fields) that your advisor published his/her studies?
Peer-Review Process (Example)
Example peer-review process for a submitted manuscript (Clinical Pharmacist article, www.pharmaceutical-journal.com):
Article submitted to journal → Advance to Editor reviews it against journal aims and scope and relevant peer review criteria related to article type
Rejected
Editor invites at least experts to review paper
Three reviewers required for each manuscript
Editor reviews and collates comments to send with the manuscript back to authors
Reviewers submit their comments to editor
Reviewer receives paper and guidance documents
Timeline: Two (double-blind) weeks peer review; around two weeks total for the review phase
Author submits revised manuscript to editor with response to each comment
Editor assesses the author's response and the revisions made
Decision regarding publication
Sent back for more revisions or Accepted/Rejected
Manuscript Structure
Sections Of A Manuscript include: Abstract, Introduction, Materials and Methods, Results, Text, Tables, Figures, Discussion, Acknowledgement, References
Steps of Creating a Scientific Article (Overview)
Generate an idea / gather data
Clarify your thinking (hypothesis?)
Gather literature (background of the study?)
Think of the audience (Journal, Reviewer)
Create an outline
Write the first draft (start early; can take more time than expected)
Second draft to conform to journal instructions
Seek feedback from mentors and colleagues
Detailed Drafting Process (Expanded guidance)
Draft (and debug) an abstract
Write the first draft
Master the literature
Relearn, rethink, rewrite… rewrite and rewrite
Manage your time (set deadlines)
Critically review and finalize the abstract
Attend to the details
Submit article to target journal
Always have a Plan B
Mark your calendar
Self-motivated, work consistently
Conduct literature review (daily)
Start the paper
Conduct study / analyze data
Organize/summarize results
Get early, frequent feedback from mentors and colleagues
Formulate your key message
Choose your target audience
Select your target journal
Read the journal’s “instructions for authors”
Detailed steps (detailed version) are provided in the source
From Topic to Journal Matching and Quality
To Write A Successful Manuscript: discuss how to pick a great project/topic
Important questions in your field
Hot topics in your field
Questions needing validation
Mentor role is important
Topic vs. Journal Matching and Overall Quality
Key elements when matching topic and journal:
Topic relevance
Journal scope and audience
Quality of manuscript (overall standards)
Quality of Manuscript
Factors to consider (Page 9):
Scientific Significance
Originality
Novelty
Applicability
Timeliness
Compliance
Language
Data Quality
Validity of Conclusions
Adherence to Instructions
Common Causes of Rejection (Overview)
Literature review problems: inadequate coverage of prior work; weak rationale
Methodological problems: incomplete treatment descriptions; small sample sizes; poor measures validity; control group issues
Results problems: confounding variables; confusing presentation; insufficient data; data quality issues; questionable statistics; reliability issues; overly technical reporting
Interpretation problems: overly speculative; overstating results; poor integration; failure to discuss implications; stylistic issues
What is a Good Manuscript? (Reviewer’s Perspective)
Title: descriptive and specific
Abstract: descriptive, specific, correct length
Introduction: concise background; clearly stated research question
Methods: descriptive enough to replicate; appropriate analyses
Figures and Tables: standalone; support conclusions; well-constructed; cited appropriately
Citations: relevant to topic
Discussion: stays within findings; discusses implications and future work
Writing: clear, terse, logical; follows journal guidelines
The Title
Process: first reviewed by Journal Editors before abstract
Characteristics: short, specific, descriptive, relevant
Write last, after results and abstract may shift the title
Title Crafting: Practical Guidance
Ask Yourself:
What is the single most important point of this study?
How would you answer a colleague’s question “what’s this study about?” in one sentence?
A descriptive, specific title framed after writing the paper and abstract
Start with a short descriptive working title
Unnecessary Title Phrases to Avoid
Examples of phrases to avoid:
A Study of…
A Study to determine…
Results of…
An Innovative Method…
Contributions to / of…
Investigations on…
Observations on…
A Trial Comparing…
Examples: Scholarly Activities (Anjan Na, Ph.D.)
Bareford LM, Avaritt BR, Ghandehari H, Nan A, Swaan PW. Nanoparticle conjugates for breast tumor delivery; Pharmaceutical Research, 2013.
Lee JH, Sabnis G, Nan A. Synthesis and characterization of targeted conjugates; Macromolecular Biosciences, 2012.
Lee JH, Nan A, et al. Combination Drug Delivery Approaches in Metastatic Breast Cancer; Journal of Drug Delivery, 2012.
Dowling et al. Multiphon-absorption imaging of tumor-targeted nanoparticles; Bioconjugate Chemistry, 2010.
Nan A et al. Cellular Uptake and Cytotoxicity of Silica Nanotubes; Nano Letters, 2008.
Nan A et al. Multifunctional nanocarrier for image-guided delivery; Nanomedicine, 2007.
Nan A et al. Targetable polymer-drug conjugates for visceral leishmaniasis; Journal of Controlled Release, 2004.
Examples: Scholarly Activities (Miguel Martin-Caraballo, Ph.D.)
Regulation of T-type calcium channel expression by sodium butyrate in prostate cancer cells; Eur J Pharmacol, 2015.
Regulation of T-type calcium channel expression during IL-6 induced neuroendocrine differentiation; Cancer Research, 2014.
Downregulation of GluA2 AMPA receptor subunits and dendritic arborization; PLoS ONE, 2012.
LIF regulates trafficking of T-type Ca2+ channels; American Journal of Physiology-Cell Physiol, 2011.
Pharmacological manipulation of GABA-driven activity in ovo; Neural Development, 2010.
Differential effect of glutamate receptor activation on dendritic maturation; Neuropharmacology, 2010.
Abstract: Content and Purpose
Abstract is a summary of the manuscript (usually 200-300 words) with the following components:
Background/Significance
Objective
Study design, methods
Results / major findings
Principal conclusions, implications
Abstract should be substantive and brief; it is the first (and sometimes only) part editors/readers review
Common length guidance: words; often less than words in practice
Editors/readers may see only part electronically; include key words
Abstract: Common Mistakes
Too much background or methods
Including figures/images
References to other literature or figures
Abbreviations or acronyms without definition
Not clearly stating implications; avoid passive phrases like “the implications are summarized”; instead summarize implications directly
Abstract: Example (Bareford et al., 2013)
Purpose: Evaluate riboflavin (RF) targeting in breast cancer using MMC-conjugated HPMA copolymers
Methods: Competitive uptake studies; MTT IC50; confocal microscopy for endocytic mechanism
Results: RF-specific uptake; MMC internalization higher with RF targeting; cytotoxic IC50 similar to free MMC; lysosomal release leads to nuclear MMC accumulation
Conclusion: Targeting MMC-conjugates to RF pathway increases uptake and nuclear localization, yielding potent cytotoxic activity
Structure and content are provided in the full abstract text (journal example)
Abstract: HSV-1 with TRβ1 (TH receptor) and TH effects
Context: TH (T3) involvement in HSV-1 replication varies with cellular context
System: HSV-1/TRβ1 in Vero and differentiated LNCaP cells
Key finding: In TRβ1-overexpressing cells, T3 modulates HSV-1 replication differently depending on cellular differentiation; CDP/ICP0 expression observed patterns
Keywords: Differentiation; Herpes simplex virus; Neurons; Plaque assay; Thyroid hormone; Thyroid hormone receptor beta 1
Abstract: TH and nTRE mechanism (J Cell Sci. 2017)
Focus: Transcriptional repression by TH through TREs and orientation; nTRE mutations can reverse repression
Key observation: A single TRE point mutation reverses the orientation effect on TH-dependent repression in HSV-1 TK promoter
Mechanistic insight: Changes in TR occupancy and H3K9Me3 enrichment
Relevance: Helps understand nTREs in TH and herpes-related contexts
Abstract: Allosteric modulation of GABAA receptors (Pharmaceuticals, Basel, 2014)
Topic: Enaminones as anticonvulsants; cellular and receptor-level effects
System: Olfactory bulb brain slices; whole-cell patch-clamp from mitral cells
Findings: KRS-5Me-4-OCF3 shifts GABA sensitivity left; acts as positive allosteric modulator at GABAA receptors; benzodiazepine site antagonist blocks effect
Implication: Candidate for anticonvulsant therapy
Abstract: Prostate cancer disparities (Nature Communications, 2017; CCR-2015)
Objective: Identify reciprocal miRNA-mRNA pairings contributing to African American (AA) prostate cancer disparities
Design: Integrative genomics with mRNA/miRNA profiling, target prediction, pathway analysis, functional validation
Key results: AA-specific/-enriched miRNAs and mRNAs; EGFR signaling pathway involvement; validated miRNA-mRNA pairings (e.g., miR-133a/MCL1, miR-513c/STAT1, miR-96/FOXO3A, miR-145/ITPR2, miR-34a/PPP2R2A)
Functional outcome: Modulating pairings altered proliferation, invasion, and docetaxel sensitivity
Implication: AA-specific/-enriched miRNA-mRNA pairings could inform novel therapeutic strategies
Abstract: RNA splicing and race-specific cancer biology (Nat Commun. 2017)
Finding: Race-specific RNA splicing events drive AA prostate cancer aggressiveness and drug resistance
Examples: AA-enriched splice variants (PIK3CD, FGFR3, TSC2, RASGRP2)
Functional data: Overexpression of AA-enriched PIK3CD-S enhances AKT/mTOR signaling and resistance to idelalisib in vivo
Prognostic relevance: High PIK3CD-S linked to poor survival
Implication: Splice variants as biomarkers and therapeutic targets in AA PCa
Introduction: Purpose and Structure
Introduction should provide:
Broad information on topic (what is known)
Narrow background (what is unknown or important)
Focus of the paper (your hypothesis)
A short summary of your problem and key findings
Overall length: words
Introduction: Common Mistakes
Too much or too little information
Unclear purpose
Lack of logical connection
Confusing structure
Failure to connect prior studies to your hypothesis
Methods and Materials
Purpose: Document exactly how experiments were performed to enable replication
Contents typically include:
Subjects / models
Sample preparation techniques
Sample origins
Materials and sources
Data collection protocol
Data analysis techniques
Software used
Equipment and its use
Methods: Common Mistakes
Too little information
Repetition of Introduction content
Verbosity
Reporting not aligned with results or sources of error
Materials and Methods: Example (Cell lines, viruses, and experimental setup)
Cell lines
Vero cells (ATCC CCL-81) grown in DMEM + 10% FBS; 37°C; 5% CO2
LNCaP cells (ATCC CRL-1740) cultured in RPMI-1640 + 10% FBS
Differentiation by androgen deprivation as described in [3]
HSV-1 strain: 17-Syn*/GFP; infection and detection via GFP
Infection protocol: Infect with MOI = 1 for 1 hour; replace with fresh medium; incubate for 1, 5, 10, 24 hours
Headspace sampling and GC-MS analysis of media and cells
Enaminone compounds: KRS-5Me-4-OCF, KRS-5Me-4-F, KRS-5Me-3-Cl; prepared from precursors; dissolved in DMSO (stock 20 mM; bath <0.1% DMSO)
Pharmacological agents used (list of compounds and suppliers)
Statistics: Mean ± SEM; paired t-tests; one-way ANOVA with Bonferroni post-hoc
Materials and Methods: Prostate Cancer Specimens and Cell Lines
Tissue sources and IRB compliance; AA and EA cohorts
Gleason score ranges for sampled cores
Cell line authentication via STR profiling
Microarrays: mRNA (Affymetrix Exon 1.0 ST); miRNA (Agilent V3); RNA quality checks via Bioanalyzer
Data analysis: Quantile normalization; GC-RMA; Partek Genomics Suite 6.6; GeneSpring GX 12.5; 10% FDR for differential expression; PCA and hierarchical clustering
GEO accession numbers: GSE64331 (mRNA exons), GSE64318 (miRNA)
Results: Presentation Guidelines
Objective presentation of results; clear data summaries
Not a substitute for discussion; avoid interpretive statements in Results
Include raw data where appropriate; avoid redundancy with narrative
Use figures and tables to convey data; place them early in the manuscript outline
Results: Beginning and Organization
The Results section is the core of the paper and should be written after figures and tables are prepared
Use subheadings to structure results
Present findings in the same order as described in Methods
Include characteristics of study subjects and key findings
Use past tense; present data with appropriate descriptive statistics
Results should confirm or reject the hypothesis; do not prove
Results: Writing Style and Data Presentation
Short, to-the-point statements; main findings first
Use tables/figures to present data; avoid repeating methods in text
In captions, be descriptive and specific; avoid restating obvious text
Present absolute numbers and percentages to judge significance
Statistical significance ≠ clinical significance
Example: Reported Results Snapshot (illustrative data)
Head movement translation (X, Y, Z) and rotation measurements with means and SEMs
Age correlations with movement: non-significant (p-values provided)
Region-of-Interest activation (Amygdala, Fusiform Gyrus, Prefrontal Cortex) with voxel counts and p-values such as p<0.05
Results: Tables and Figures Guidelines
Tables and Figures are critical; must stand alone and tell a complete story
Figures should display trends and key data; tables should present numerical data concisely
Ensure captions are detailed and able to convey the full context without needing to refer back to the text
Examples include: brain activation tables (e.g., Table with activation clusters across brain regions)
Results: Examples and Data Formats
Example data snippets include:
Demographics and neuropsychological test results (Age, FSIQ, VIQ, PIQ, EM/EL measures) with mean ± SD and p-values
Region-of-interest activation data (e.g., Amygdala, Fusiform Gyrus, Prefrontal Cortex) with voxel counts and statistics
Box-and-Whiskers plots for qRT-PCR validation (mRNAs and miRNAs across AA vs EA)
Bar/line graphs illustrating expression levels of target genes (e.g., ITPR2, MKK4, STAT1, HRAS) across groups
Discussion: Purpose and Structure
Purpose: interpret results; discuss whether the study confirmed or denied the hypothesis; consider alternative hypotheses if needed
Compare with previous research; discuss implications for the field
Address limitations and potential sources of error
Propose improvements and future research directions
Relate findings to clinical relevance where applicable
Discussion: Common Mistakes to Avoid
Combining Results with Discussion
Making broad statements without data support
Overstating conclusions or relying on inconclusive results
Failing to discuss limitations or future directions
Ambiguity in data sources
Discussion: Construction and Flow
1st paragraph: summarize major findings
Link findings to others’ work; explain meaning
Discuss clinical relevance and implications
Acknowledge limitations and how they influenced the study
State future directions
Keep the discussion tight and focused; avoid over-claiming
Figures and Tables: Design and Quality
Tables and Figures should be high quality, clear, and necessary
They should stand alone and tell a complete story
Use high resolution; neat, legible labels; simple formatting
Indicate statistical error bars or p-values where relevant
Ensure captions are detailed and independent from the main text
References: Formatting and Content
Follow the journal’s reference style exactly
Include peer-reviewed journal articles, abstracts, and books
Do not reference non-peer-reviewed works or personal communications
Ensure consistency in formatting across all references and in-text citations
Tables and Figures: Standalone and Communicative
Tables: present numerical data; avoid duplicating text from the Results narrative
Figures: illustrate key trends and methods; not just decorative
Ensure each table/figure supports a specific point in the manuscript
Table and Figure Details (Illustrative Examples)
Example brain activation table (Tables with multiple ROIs across conditions)
Example qRT-PCR validation figure panels (A-D) showing mRNA and miRNA expression across AA vs EA tissues and cell lines
Example gene expression heatmaps or log2 expression plots illustrating differential expression across groups
Practical Graphing Tips (From Slides)
Bar or line graphs should be simple; limit to groups
Use solid lines; avoid excessive symbols
Include SD and P values when relevant
Avoid color-only graphs unless color is essential for understanding
Use clear legends and axis labels
Tables and Figures: Specific Guidance (From Pages 63-66, 68-73)
When including a Table with detailed brain activation data, ensure it can be read without surrounding text
If a Table is not essential, consider including as a figure or moving to supplementary materials
For significant group-by-condition differences, present explicit statistics (e.g., p-values) in the caption
Figures should be designed to convey the key findings quickly to editors and readers
Appendix: Additional Method and Data Details (Selected Highlights)
Example of Headspace sampling and GC-MS analysis in a virology study
Lipid extraction and rheology procedures for natural product studies (e.g., I. gabonensis gum)
Near-infrared spectroscopy (NIR) measurement setup and data handling
Specific enaminone synthesis and structural confirmation by NMR at 400 MHz
Slice preparation for rodent brain studies; ACSF composition; recording conditions
Drug application and bath perfusion protocols; DMSO controls; bath concentrations
Prostate cancer clinical sample processing; core collection; Gleason scoring; ethics and IRB details
Microarray preprocessing: quantile normalization; GC-RMA; Partek and GeneSpring workflows; FDR control
Key Takeaways for Practical Manuscript Writing
Start with a solid idea and a clear hypothesis; plan around a strong, descriptive title
Read and follow the journal’s Instructions for Authors early
Draft the abstract last; it should be a concise, stand-alone summary of the work
Structure the manuscript logically: Abstract, Introduction, Methods, Results, Discussion, References, Figures, Tables
Present data with clarity and honesty; let the data speak for itself
Use figures and tables to convey data efficiently; ensure they can stand alone
Be precise about statistics and avoid overstating conclusions
Seek ongoing feedback from mentors and colleagues throughout the drafting process