I have no financial interests or relationship to disclose with regard to the subject matter of this presentation.

Disclaimers

1. I am an "open" scientist. I have a bias toward the
     core tenets of Open Science as better practices.

2. "Quality" is a fairly subjective idea. 

3. It's easy to take the higher moral ground - don't.
      We are not here to chastise, we are here to
      discuss a way to improve our science.

4. For this reason, I am going to assume all issues come
      in good faith.

5. I also assume that there is far more subjectivity in
      the scientific method than we want to admit.

This is a new chapter

This is a new chapter

Take home #0

This is a take home message

What use do we have for papers

  1. Formulate hypotheses
     
  2. Formulate methods
     
  3. "Validate" results
     
  4. Start or continue an offline (field-wide) discussion

1. Metadata heuristics

The "good old heuristics"

  • Journal (Impact Factor)
     
  • Amount of citations

(Self-)Citations

  • Google Scholar: 57 citations
  • Semantic Scholar: 40 citations
  • Non self-citations: 20 citations

Journals and impact factors

Title Journal Year Citations
Pluripotency of mesenchymal stem cells derived from adult Nature 2002 4512
Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial International Journal of Antimicrobial Agents 2020 3189
6-month consequences of COVID-19 in patients discharged from hospital: a cohort study Lancet 2021 3029
Primary Prevention of Cardiovascular Disease with a Mediterranean Diet New England Journal of Medicine 2013 2671
A specific amyloid-β protein assembly in the brain impairs memory Nature 2008 2384
Predictive Validity of a Medication Adherence Measure in an Outpatient Setting The Journal of Clinical Hypertension 2008 2145
MicroRNA signatures of tumor-derived exosomes as diagnostic biomarkers of ovarian cancer Gynecologic Oncology 2008 1940
Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children Lancet 1998 1741
Recent progress in processing and properties of ZnO Progress in Materials Science 2004 1636
Visfatin: A protein secreted by visceral fat that mimics the effects of insulin Science 2005 1564

https://retractionwatch.com/the-retraction-watch-leaderboard/top-10-most-highly-cited-retracted-papers/

Take home #1

Heuristics might be easy to implement,
but they hold biases

Any observed statistical regularity will tend to collapse
once pressure is placed upon it for control purposes¹

1. Goodhart, 1975

When a measure becomes a target,
it ceases to be a good measure

Goodhart's Law:

2. An "Open Science" definition of "quality"

What can "good quality manuscript" mean?

  • Can I validate it?
  • How easily can I implement it?
  • Is the methodology solid?
  • Can I reproduce it by just reading it?
  • Can I reproduce it through its available deliverables?
  • How much time will I have to invest to implement it?

Trustable and/or implementable,
as in easily reproducible/replicable

Good quality manuscript

\approx

3. Reproducibility and replicability

The reproducibility issue

2010s:

  • Failed attempts to reproduce core concepts of social psychology and biomedical research
  • Studies on systematic biases

2016: Survey by Nature¹: 70% of researchers failed to reproduce other's results, 50%+ failed to reproduce their own

1. Baker 2016 (Nature)

Systematic bias

Lakens et al., 2024 (EBT)

Really reproducible?

Same hardware, two Freesurfer builds (different glibc version)
Difference in estimated cortical tickness.¹

Same hardware, same FSL version, two glibc versions
Difference in estimated tissue segmentation.²

Same hardware, two Freesurfer builds (two glibc versions)

Difference in estimated parcellation.²

1. Glatard, et al., 2015 (Front. Neuroinform.)   2. Ali, et al., 2021 (Gigascience)

Reproducibility checklists

https://fairerdata.github.io/FAIRER-Aware-REPRODUCIBILITY-Assessment/

What to look for for replicability and reproducibility

  • Extremely well documented methods
  • Open Standard Operative Procedures
  • Open code
  • Open running environment (e.g. containers)
  • Open data (at least first derivatives)

Standard Operating Procedures

https://github.com/TheAxonLab/hcph-sops

Take home #2

Do not give reproducibility for granted,
even more so replicability.

 

Instead, look for the possibilities to reproduce a study yourself (or gain insight in their "success").

(caveat: it will take time)

3. Another "good quality" indicator: Registered Reports

Registered Reports

Images courtesy of Oscar Esteban (CC-BY-4.0)

Ethics committee,
internal project assessment, ...

Re-learn scientific process

Currently not adapted to short projects

Guarantees a publication!

Registered Reports

Registered Reports Quality

Soderberg et al. 2021 (Nat. Hum. Behav,)

Registered reports are scored as better quality
against equivalent papers
in a  blinded test

(29 RRs, 86 papers, 353 reviewers)

Take home #3

Look for registered reports in your field, chances are their quality will be superior to non-registered reports.

 

The next time you start a (long) project, consider registered reports.

Shout Out: Registered abstracts session today @ 15h00
(Auditorium 900)

Any question [/opinions/objections/...]?

smoia
@SteMoia
s.moia.research@gmail.com
Stefano Moia, 2025

Find the presentation at:

slides.com/smoia/esmrmb2025/scroll