Dysregulation of Rho GTPases in the αPix/Arhgef6 mouse model of X-linked intellectual disability is paralleled by impaired structural and synaptic plasticity and cognitive deficits.
Part of the results reproduced; minor but material deviations remained.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
- ✓No relevant deviation in data/preprocessing
- ✓No authors-side cause for any deviation
- ✓Any deviation was negligible
- 🔴Could not use the authors’ exact input data
- 🔴Reported values were only indirectly comparable
- 🟡Reported values were not (fully) derivable from the shared data
- 🟡The central claim did not (fully) hold under reproduction
- 🟡Overall, the reproduction showed a material discrepancy
▸Reproduction agent’s raw note
DROP (non_pipeline), independently re-verified 2026-06-22. PMID 21989057 (Ramakers et al., Hum Mol Genet 2012;21(2):268-86, DOI 10.1093/hmg/ddr457) is a wet-lab mouse-model study of the alphaPix/Arhgef6 knockout: Golgi-Cox dendrite-length/spine-density morphology, an overall loss of spine synapses, reduced early-phase LTP and increased LTD in hippocampal CA1 (electrophysiology), impaired spatial/complex learning and stress behaviour, and reduced active Rac1/Cdc42 (but not RhoA) by GTPase pulldown. Every reported quantity is a manual wet-lab measurement analysed with standard statistics (t-test/ANOVA) on small N -- none is a bioinformatic pipeline applied to a deposited dataset. Control-plane re-verification (zero «our HPC» compute): NCBI elink pubmed->gds, ->sra and ->bioproject all return empty; Europe PMC inPMC=N and isOpenAccess=N (no open full text); the Europe PMC hasData=Y flag resolves only to text-mined knowledge-base cross-references (UniProt P05556, MGI, InterPro protein families, Wikipedia for ARHGEF6), NOT an experimental data deposit; no GEO/SRA/ArrayExpress/BioProject/Zenodo/figshare accession and no code repository exist. With nothing pipeline-derived in scope there is nothing to run on «our HPC» and nothing to profile. This is a well-founded drop (healthy=true), not an our-side tooling failure. NOT attempted: the wet-lab claims c1-c7 are recorded in original/claims.tsv for documentation only, explicitly out of computational-reproduction scope.
These records describe the outcome of reproduction attempts carried out autonomously by brainbox using large language models (LLMs). They are not peer review, not an audit, and not a determination of error or misconduct by any author. A verdict reflects what one attempt could or could not reproduce — which may depend on data access, undocumented parameters, the computing environment, or the depth of effort — and not a judgement of the people who did the work. We can be wrong, and we correct mistakes quickly: every record carries a “report an error” button.
Assessment versions
Every reproduction run is kept as an immutable version — anchored to the data as it stood, with a tamper-evident chain hash. A rerun (e.g. after an author updates a deposit) adds a new version; the previous one stays on record.
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v1 current initial assessmentassessed: 2026-06-19 ⛓ e0f9eef44ee2
✎ I am an author of this paper
Updated or fixed a deposit, or is there an erratum? Ask us to re-run the metrics. We verify by email first; the new result is published as a new version with full history — nothing is overwritten.
Provenance — full disclosure
When this reproduction was carried out, which methodology version was used, and by whom — so the record can be audited and checked independently.
- Reproduced
- 2026-06-22
- Rubric version
- v1.0
- Assessed by
-
🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-19no human curator yet
- Last updated
- 2026-08-05
Provisional, curator- or AI-assessed, and independently checkable. A reproduction outcome states what one attempt could reproduce — not a judgement of the authors.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope analysis — PMID 21989057
Paper: Ramakers GJA, Wolfer D, Rosenberger G, Kuchenbecker K, Kreienkamp H-J, et al. "Dysregulation of Rho GTPases in the αPix/Arhgef6 mouse model of X-linked intellectual disability is paralleled by impaired structural and synaptic plasticity and cognitive deficits." Hum Mol Genet 2012;21(2):268–86. DOI: 10.1093/hmg/ddr457. PMID: 21989057.
Question for this study
Is any reported result pipeline-derived (a bioinformatic/computational pipeline applied to a dataset), and is the code + data resolvable so it can be re-run?
Methods inventory (from abstract + journal record)
All reported quantitative results come from manual wet-lab measurement:
| Result domain | Method | Pipeline-derived? | In scope? |
|---|---|---|---|
| Dendritic length / spine density / spine-synapse number | Golgi-Cox staining + manual microscopy counts | No (manual imaging quantification) | No |
| Early-LTP reduction, increased LTD (CA1) | Patch-clamp / field-potential electrophysiology | No (electrophysiology traces) | No |
| Active Rac1 / Cdc42 / RhoA levels | GTPase pulldown + Western blot densitometry | No (biochemistry) | No |
| Spatial / complex learning, stress response | Behavioral assays (maze tasks) scored by experimenter | No (behavioral scoring) | No |
Standard inferential statistics (t-tests / ANOVA) on small wet-lab N — not a reproducible computational pipeline over a deposited dataset.
Data / code availability
- GEO: no datasets linked to the PMID (NCBI elink pubmed→gds: empty).
- SRA: no runs linked (elink pubmed→sra: empty).
- PMC: no open full text (only
pubmed_pmc_refs, i.e. citing papers). - ArrayExpress / BioProject / Zenodo / figshare: none found.
- Code repository: none (no GitHub/GitLab; pre-dates routine code deposition).
- Open access: No (
isOpenAccess: N, Europe PMC).
Decision
OUT OF SCOPE — drop. drop_reason = non_pipeline.
This is a classic 2012 mouse-model neuroscience paper. There is no high-throughput / omics dataset, no bioinformatic pipeline, and no resolvable code artifact. Every reported number is a manual wet-lab measurement, which the brief explicitly excludes ("Scope to pipeline-derived results only … wet-lab / manual / external = out of scope, not attempted"). There is nothing to run on «our HPC» and no public dataset to profile. No fabrication risk to assess on the computational side because there is no computational deposit.
This is a valid, well-founded drop (healthy=true): the outcome was correctly determined, not a tooling failure on our side.
No individual results have been recorded for this entry yet.
Assessments & scoring basis
Each contributor’s verdict, the per-question basis, and the auditable, itemised worksheet behind it.
An automated assessment. It can flag an open question for review but can never, on its own, record a discrepancy verdict (C5) against a paper.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
This is a valid, well-founded non_pipeline DROP. PMID 21989057 (Ramakers et al., 2012) is a wet-lab αPix/Arhgef6 mouse study — Golgi-Cox morphology, CA1 LTP/LTD, Rho-GTPase pulldown, and behavior — with no deposited dataset (GEO/SRA elink empty), no open full text, and no code repository. The blocker is purely data availability / out-of-scope, on neither our side nor the authors' side, so per the restricted-data principle q5/q7 stay yellow rather than red — there is no fabrication concern and no measured deviation. q1/q2 are red (input data not available, endpoints not comparable); overall yellow because nothing could be reproduced 1:1 yet the drop is fully explainable.
Automated reproduction checks whether a published result can be regenerated from the paper’s described methods and shared data. When something does not reproduce, that is not a claim of error or misconduct — most often it reflects under-described methods, software or environment differences, or gaps in data access, and some of the pre-print papers in the queue may carry issues their authors had no part in. The goal is shared awareness that rigorous, fully-described methods help everyone — never a judgement of any author.
Are you an author? We would genuinely like to hear from you — to clarify the record, add data or code, re-run the pipeline after an accession update, and publish your response right next to the assessment. Everything here is open and auditable.
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Reproduction footprint
claude-opus-4-8Measured resources invested to assess this paper — sanitised (machine class only, no job ids/paths). Compute = HPC accounting (SLURM); tokens = the AI agent's session.