Homozygosity for a partial deletion of apoprotein A-V signal peptide results in intracellular missorting of the protein and chylomicronemia in a breast-fed infant
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). PMID 24529129 (Albers, Schlein et al., Atherosclerosis 2014) is a single-patient clinical/molecular case report of an infant homozygous for an APOA5 signal-peptide deletion. Described well enough, but it contains NO pipeline-derived computational result: methods are entirely wet-lab/clinical (Sanger sequencing of APOA5 exon 2, Western blot, immunofluorescence, primary-hepatocyte expression assays, clinical chemistry). There is no deposited data accession (Europe PMC hasData:N / hasTMAccessionNumbers:N; no GEO/SRA/ENA/figshare/zenodo/dbGaP/EGA/PRIDE) and no code repository, so the P16 'third-party tool on the paper's data' route does not apply either. Nothing was forced or fabricated. I did run ONE honest, deterministic in-silico cross-check (no «our HPC», no data download): the variant nomenclature c.16_39del / p.Ala6_Ala13del is internally consistent with the public APOA5 RefSeq (24 nt, in-frame, 8 aa lost) -- exact. NOT ATTEMPTED (out of scope / impossible to reproduce computationally): plasma apoA-V level, LPL activity, subcellular localization, triglyceride course -- all wet-lab/clinical measurements with no deposited artifact.
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 initial assessmentassessed: 2026-06-18 ⛓ d394afaf8397
✎ 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
- 2026-06-18
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-18no 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 24529129
Title: Homozygosity for a partial deletion of apoprotein A-V signal peptide results in intracellular missorting of the protein and chylomicronemia in a breast-fed infant Authors: Albers K, Schlein C, Wenner K, Lohse P, Bartelt A, Heeren J, Santer R, Merkel M. Venue: Atherosclerosis 2014;233(1):97-103. DOI 10.1016/j.atherosclerosis.2013.12.009 Type: Single-patient clinical/molecular case report.
What kind of study is this?
An 11-month-old boy with severe hypertriglyceridemia. A homozygous 24-nt deletion in APOA5 exon 2 (c.16_39del; p.Ala6_Ala13del) was identified by Sanger sequencing. Functional consequences were studied with cell- and molecular-biology assays. Triglycerides were elevated only during breastfeeding and normalized after weaning. Plasma apoA-V was undetectable despite normal LPL activity.
Methods reported (from abstract + indexed methods; full text is paywalled, 403)
| Method | Class | In scope (pipeline)? |
|---|---|---|
| Sanger sequencing of APOA5 exon 2 (variant detection) | wet-lab + manual variant calling | No — single-amplicon Sanger, manual HGVS annotation, no high-throughput pipeline |
| Western blot (apoA-V) | wet-lab | No |
| Immunofluorescence microscopy (subcellular localization) | wet-lab / imaging, manual interpretation | No |
| Expression studies in apoA-V–deficient primary hepatocytes | wet-lab cell biology | No |
| Clinical chemistry (triglycerides, LPL activity, apoA-V level) | clinical assay | No |
In-scope pipeline-derived results
None. There is no bioinformatic pipeline in this paper:
- No high-throughput sequencing (no WGS/WES/RNA-seq/microarray).
- No deposited data accession (Europe PMC
hasData:N,hasTMAccessionNumbers:N; no GEO/SRA/ENA/figshare/zenodo/dbGaP/EGA/PRIDE accession exists for this paper). - No code repository (none cited; none discoverable).
- Reported numeric results (TG mg/dL, LPL activity, apoA-V western signal) are wet-lab/clinical measurements, not pipeline outputs — not reproducible by re-running software.
The "third-party tool on the paper's own data" route (brief P16) does not apply: there is no public dataset to run a tool on.
Outcome
DROP — drop_reason non_pipeline (per «path»):
"not actually a computational-pipeline reproduction." Honest, not forced.
One honest auditability cross-check performed (not a pipeline reproduction)
The single in-silico-checkable assertion is the variant nomenclature. I verified
it deterministically against the public APOA5 RefSeq CDS (NM_052968.5 /
NP_443200.2) with reproduction/verify_hgvs.py (no «our HPC», no data download):
- c.16_39del = 24 nt ✓ (paper: "24 nucleotide deletion")
- deletion is in-frame / codon-aligned to codons 6–13 ✓
- removes 8 amino acids ✓ (paper: "eight amino acid loss")
- protein change derives to p.Ala6_Ala13del ✓ (exact match to paper) Result: the variant annotation is internally consistent — exact. This audits the manual nomenclature; it does not constitute reproduction of a computational result the paper produced (there is none).
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.
PMID 24529129 is a single-patient clinical/molecular case report (Albers, Schlein et al., Atherosclerosis 2014) with no computational pipeline, no deposited data, and no code — correctly dropped as non_pipeline. The reported endpoints (undetectable plasma apoA-V, normal LPL, lipid-droplet missorting, TG course) are wet-lab measurements that cannot be put against any output (q1/q2 red on data/endpoint availability, not an authors' defect). The one honest, deterministic in-silico cross-check — variant nomenclature c.16_39del / p.Ala6_Ala13del against public RefSeq — was exact, and there is no fabrication signal; overall yellow reflects a sound study that simply has nothing computationally reproducible.
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.