AlphaPIX associates with calpain 4, the small subunit of calpain, and has a dual role in integrin-mediated cell spreading.
The main results reproduced, with only marginal, non-material deviations.
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
- ✓Reported values are derivable from the shared data
- ✓Any deviation was negligible
- ✓The central claim held under reproduction
- ✓Overall, the reproduction was clean
- 🔴Could not use the authors’ exact input data
- 🔴Reported values were only indirectly comparable
▸Reproduction agent’s raw note
DROP (non_pipeline) — re-verified clean re-run. 'AlphaPIX associates with calpain 4, the small subunit of calpain, and has a dual role in integrin-mediated cell spreading' (Rosenberger G, Gal A, Kutsche K; J Biol Chem 2005;280(8):6879-6889; DOI 10.1074/jbc.M412119200; no PMCID) is a wholly wet-lab molecular/cell-biology study. Its results derive from a CytoTrap yeast-two-hybrid screen, co-immunoprecipitation, GST pull-down assays, integrin-dependent cell-spreading assays in CHO-K1 cells, immunofluorescence/colocalization microscopy, and pharmacological inhibition (calpeptin, calpain inhibitor IV). There is NO high-throughput sequencing, NO microarray, NO bioinformatic pipeline, NO deposited dataset accession (none in PubMed, Europe PMC core record, or the JBC article), and NO analysis-code repository. Hence there is no pipeline-derived result to reproduce and nothing for a «our HPC» compute job to run. The paper is clearly written and well-described, but it is out of scope for computational reproduction. Determination re-confirmed independently on 2026-06-22 from the PubMed abstract+methods and the JBC DOI record, in agreement with the prior run that was routinely requeued. Not attempted: any wet-lab experiment (out of scope by design). This is an honest, well-founded drop, not an infrastructure failure.
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 ⛓ 93be65e31f41
✎ 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
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🤖 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-15611136
Title: AlphaPIX associates with calpain 4, the small subunit of calpain, and has a dual role in integrin-mediated cell spreading. Authors: Rosenberger G, Gal A, Kutsche K. Journal: Journal of Biological Chemistry, 2005; 280(8):6879–6889. PMID: 15611136 · PMCID: none · DOI: 10.1074/jbc.M412119200 Code: none · Data accession: none
Determination: OUT OF SCOPE — no pipeline-derived computational results
This is a wholly wet-lab molecular / cell-biology study of a protein–protein interaction and its functional consequence. Every reported result is generated by bench experiments, manual microscopy, or biochemical assays. There is no bioinformatic pipeline, no high-throughput sequencing, no microarray, no deposited dataset, and no analysis code to reproduce.
Methods reported (all wet-lab / manual)
| Method | What it produces | Pipeline-derived? |
|---|---|---|
| CytoTrap yeast two-hybrid screen | Identification of calpain 4 as alphaPIX binding partner | No (genetic interaction screen, manual) |
| Co-immunoprecipitation | In-vivo interaction confirmation (blots) | No (wet-lab) |
| GST pull-down assays | Direct/domain-mapped interaction (blots) | No (wet-lab) |
| Cell spreading assays | Spread-cell counts / morphology over time | No (manual microscopy assay) |
| Immunofluorescence / colocalization | Subcellular localization images | No (manual microscopy) |
Data / code availability
- No data-availability or code-availability statement (typical for a 2005 JBC biochemistry paper).
- No GEO/SRA/ENA/ArrayExpress/PRIDE/figshare/zenodo accession (confirmed: PubMed record + Europe PMC core record carry none; enriched scaffold found none).
- No software repository (no GitHub/GitLab/Zenodo code DOI).
Consequence
There is nothing for a «our HPC» SLURM compute job to run — no input data exists,
no pipeline is described, and no reported value is derived from a computational
analysis. Per BRIEF Hard Rule 6 and the SCREENING.md taxonomy, this is a
controlled drop with drop_reason = non_pipeline (the publication is not a
computational-pipeline reproduction target). This is an HONEST, well-founded
drop — not a failure of our infrastructure.
Evidence trail
- PubMed abstract + method list: https://pubmed.ncbi.nlm.nih.gov/15611136/ → methods listed: CytoTrap, coimmunoprecipitation, GST pull-down, cell spreading assays, immunofluorescence. No HTS / microarray / accessions.
- Enriched scaffold metadata: no DOI, no PMCID, no code_url, no data_accession.
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.
Correct non-pipeline drop. PMID 15611136 (Rosenberger, Gal & Kutsche, J Biol Chem 2005) is a wholly wet-lab molecular/cell-biology paper: its results come from a CytoTrap yeast two-hybrid screen, co-IP, GST pull-down, cell-spreading assays and immunofluorescence — there is no high-throughput data, no deposited accession, and no analysis code. claims.tsv is empty by observation. q1/q2 are red because there is no input data or pipeline-derived value to compare 1:1, while q3-q8 are green because nothing was computed, nothing deviates, and there is no fabrication or discrepancy. The drop was determined at scoping with zero compute — the resource-respecting, honest handling of a harvest false positive.
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.