Welcome: How to Read a Scientific Paper

πŸ‘‰ How to use this app

πŸš€ When you’re ready

What is a scientific paper?

1

So, what actually is a Paper?

A paper is a structured argument.

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2

If it’s in a Paper, it must be True!

Why publication isn’t a guarantee of correctness.

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3

How does Scientific Publishing Work?

Peer review, revisions, and journals.

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4

Different Types of Publication

Traditional journals, Preprints, and alternatives.

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5

Problems with Scientific Publishing

Incentives, paywalls, and inequalty.

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6

What is Open Science?

Sharing methods, data, code, and more.

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7

Good β‰  Perfect

No study, model, or paper is ever perfect, that doesn't mean it isn't good.

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The Anatomy of a Paper

Reading Strategies

πŸ“š Why are we reading this paper?

πŸ”¬ What should I focus on?

πŸ’¬ How to handle jargon

Reading Strategies

Strategies for Reading Papers

Intermittent breaking of isolation may ameliorate decrease in physical activity caused by isolation

Uchida, A., Nakagawa, K., Yoshimi, K., Nagasawa, Y., Yamaguchi, K., Uesaka, N., & Tohara, H.

PLOS ONE, 19(11), e0314262.

2024

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Title and Abstract Instructions

Unknown Concepts and Vocabulary
Introduction Instructions

Notes

Unknown Concepts and Vocabulary
Methods Instructions


πŸ“ Notes

❓ Questions

🚦 Flags
Results Instructions

πŸ“ Notes

❓ Questions

🚦 Flags
Pause
Background Understanding

What questions are they trying to answer?

Match the questions to the answers

Questions
Methods
Examine the Results
Summary of Findings
This study examined how
influences physical and physiological outcomes using a rat model. The authors were motivated by the idea that social isolation acts as a
, which may disrupt normal regulation of behaviour, metabolism, and muscle maintenance. To test this, they compared animals experiencing continuous isolation with animals in which isolation was
as a potential intervention. The researchers measured changes in
, including physical activity, body and muscle weight, and hormones. This approach allowed the authors to evaluate whether interruption of isolation could
associated with prolonged social isolation.
Discussion Instructions


πŸ“ Notes

❓ Questions

🚦 Flags
Understanding Instructions
Understanding
Reflection Instructions

❓ Open Questions

Methods
Discussion
My Rating and Review
How would you rate this paper?

If you missed a section, you can go back and rate it now.
AI Instructions
1

Let's ask ChatGPT

General LLM

Open ChatGPT Response
2

Let's ask Claude

General LLM

Open Claude Response
3

Let's Ask Anara

Science LLM

Open Anara Response
4

Consensus

Science LLM

Open Consensus Response
5

The Verdict

How did the LLMs do?

Open the Verdict

Brief overview of statistical tests

1

Summary Statistics and Data Types

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2

What is are statistical tests and why do we need them?

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3

What is a p-value?

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4

Why do we need to check assumptions of statistical tests?

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5

Type I and Type II Errors

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6

Confidence Intervals

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7

Why does sample size matter?

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8

What are effect sizes?

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9

Multiple testing corrections

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10

What is p-hacking?

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11

Which Test Should I Use?

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12

Common statistical mistakes in papers

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13

Resources

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Practice Games

Instructions

Microbiota alteration is associated with the development of stress-induced despair behavior

Marin, I. A., Goertz, J. E., Ren, T., Rich, S. S., Onengut-Gumuscu, S., Farber, E., Wu, M., Overall, C. C., Kipnis, J., & Gaultier, A.

Scientific Reports, 7(1), 43859.

2017

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Caffeine acts through neuronal adenosine A2A receptors to prevent mood and memory dysfunction triggered by chronic stress

Kaster, M. P., Machado, N. J., Silva, H. B., Nunes, A., Ardais, A. P., Santana, M., Baqi, Y., MΓΌller, C. E., Rodrigues, A. L. S., PorciΓΊncula, L. O., Chen, J. F., TomΓ©, Γ‚. R., Agostinho, P., Canas, P. M., & Cunha, R. A.

Proceedings of the National Academy of Sciences of the United States of America, 112(25), 7833–7838.

2015

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Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression

Wray, N. R., Ripke, S., Mattheisen, M., Trzaskowski, M., Byrne, E. M., Abdellaoui, A., Adams, M. J., Agerbo, E., Air, T. M., Andlauer, T. M. F., Bacanu, S.-A., Bækvad-Hansen, M., Beekman, A. F. T., Bigdeli, T. B., Binder, E. B., Blackwood, D. R. H., Bryois, J., Buttenschøn, H. N., Bybjerg-Grauholm, J., ... Sullivan, P. F.

Nature Genetics, 50(5), 668–681.

2018

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Instructions
Discussion 1
Discussion 2
Discussion 3
Instructions

Drag from here

Describe the specific research question or hypothesis.
Describe the participants or subjects involved in the study.
Describe the study design and procedures.
Suggest the next steps for future research.
Describe the gap in knowledge that this study aims to fill.
Describe the overarching need for this study.
Give an overview of relevant literature to provide context.
Present the results obtained from the research.
Describe the limitations of the study and how they were addressed.
Contextualise the findings and with existing literature.
Explain the data collection methods used.

Intro

Methods

Results

Discussion

Instructions
Instructions

Sample size was determined a priori using a power analysis (Ξ± = 0.05, power = 0.8) based on effect sizes reported in previous studies.

Animals were randomly assigned to experimental groups using a computer-generated sequence, and investigators were blinded during data collection and analysis.

Statistical significance was assessed using p-values, as indicated in the figures.

Group sizes were chosen based on feasibility and consistency with previous studies.

All statistical analyses were performed using standard parametric tests.

Treatment increased response amplitude compared with controls (mean difference = 1.8 units, t(28) = 2.45, p = 0.02).

Several secondary analyses showed similar trends.

Results for outcomes showing no group differences are not shown.

A strong trend toward an increase was observed, although this did not reach statistical significance.

Although the observed effects are consistent with a direct action of the intervention, indirect effects mediated by changes in overall activity or physiology cannot be excluded.

Your Turn!

1

Effect of Caffeine on Heart Rate and Blood Pressure

Geethavani et al. (2014)

Read this paper
2

Forced treadmill exercise in the male rat: Effect on food intake and c-Fos expression

Eccles et al. (2025)

Read this paper
3

Coming Soon

4

Coming Soon

How to Start Searching for Scientific Papers

1

Start with a clear question

2

Turn your question into key terms

3

Use Boolean operators (AND, OR, NOT)

4

Use quotation marks for exact phrases

5

Use parentheses to control meaning

6

Expect to refine your search (this is normal)

7

Common beginner mistakes to avoid

8

Example search

9

Read titles first, abstracts second

How to Cite Scientific Sources

1

Know what needs a citation

2

Capture the essential details

3

In-text vs reference list

4

Choose a style and stick to it

5

Use DOIs and stable links

6

Do I need to cite X?

7

Avoid common citation mistakes

8

Use a reference manager

Useful Resources for Reading, Writing, and Managing Papers

Reference management & citing

Save papers, organise PDFs, and generate citations.

Zotero

Bibliography manager

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Find papers

Search engines, discovery tools, and alerts.

Google Scholar

Search engine for academic literature

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Europe PMC

Academic literature search (Europe PMC)

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OpenAlex

Catalogue of scientific papers

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PubCrawler

Automated literature search tool

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Writing & publishing

Draft manuscripts and share the research process.

Overleaf

Online LaTeX editor

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Research Equals

Publish your unique research process

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Annotation, review & community

Annotate papers, review them, and find community resources.

Paperstars

Rate and review scientific papers

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Hypothes.is

Social annotation for papers

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Center for Open Science

Open science tools and resources

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Open Research Calendar

Free events around open science

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Stats & analysis

Data Analysis & Statistics

G*Power

Power analysis (free software)

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R

Statistical computing and graphics

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University of Edinburgh

Experimental Design & Data Analysis

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StatsTutor

Tutors’ Quick Guide to Statistics (PDF)

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National University

Statistics resources hub

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Statistics by Jim

Clear, practical statistics tutorials

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