The cold-induced lipokine 12,13-diHOME promotes fatty acid transport into brown adipose tissue
The main results reproduced: recomputed values matched the published ones within tolerance.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
- ✓Same input data as the authors
- ✓Reported values were directly comparable
- ✓The central claim held under reproduction
- 🔴A deviation arose in the data or preprocessing
- 🔴A deviation was attributed to the published material
- 🟡Reported values were not (fully) derivable from the shared data
- 🟡The deviation was non-trivial in magnitude
- 🟡Overall, the reproduction showed a material discrepancy
A 0–100 reproducibility-quality score from the per-question grades, shown as a z-score: standard deviations above (+) or below (−) the mean of comparable assessments.
▸Reproduction agent’s raw note
Described well enough for the SHIPPED data, and the result is mostly 1:1. PMID 28346411 (Lynes et al., Nat Med 2017) is a predominantly wet-lab paper with one computational layer: an 88-lipid LC-MS/MS screen + correlation analyses of the lead lipid 12,13-diHOME. There is NO authors' code and NO raw-data deposit (no GEO/SRA/MetaboLights/Metabolomics-Workbench; statistics were done in Excel/Prism/RStudio+limma). What IS shipped is figure source-data Excel (MOESM1-4). Using a third-party stack (scipy/statsmodels) on the paper's OWN Fig-1 source data on «our HPC», we reproduced the full Figure-1 statistical layer: the paired cold-induction of 12,13-diHOME (Fig 1b, P=0.002716 to the digit; increased in all 9 subjects) and every simple Spearman correlation in Fig 1d-i + Supp Fig 3b-i (n=55) - 14/21 graded sub-claims EXACT, 1 within-tol. Three honest gaps: (1) the Fig 1a 88-lipid volcano is NOT reproducible because only the lead lipid's values were deposited (the discovery matrix/raw MS is absent, so the data-availability statement over-promises); (2) the Fig 1g ALAT panel prints P=0.0011 which is statistically impossible for its own printed r=-0.348 at n=55 (correct ~0.0093, which we get) - a likely copy-typo, flagged not fabricated; (3) the BMI-adjusted covariate p-values (0.0463/0.0494/0.0274) are not reproduced by OLS, partial-Pearson, or partial-Spearman (we get larger values) and 'a linear model' is under-specified. NOT attempted (out of scope, wet-lab/manual): all mouse experiments (Fig 2-4 serum diHOME, qPCR of Ephx/Cyp, FA-uptake, FATP1/CD36 translocation, cold tolerance) and the raw LC-MS peak-picking (proprietary SCIEX, not deposited). Overall: the in-scope statistical results that have data reproduce essentially exactly; the discovery screen cannot be reproduced from the deposit.
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.
-
v1 current initial assessment Score 78assessed: 2026-06-18 ⛓ d5b9fc825840
✎ 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
-
🤖 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.
Deep full-text extraction
Model: sonnetBecause brown adipose tissue (BAT) takes up and burns lipids and is linked to systemic metabolic homeostasis, the authors hypothesized that there exist thermogenic lipokines that activate BAT in response to cold exposure.
- ★ 12,13-diHOME is a cold-induced lipokine that stimulates BAT activity finding
- ★ Circulating 12,13-diHOME levels are negatively correlated with BMI and insulin resistance in humans finding
- ★ The 12,13-diHOME-producing enzymes (sEH isoforms Ephx1/Ephx2) are induced in BAT by cold exposure finding
- ★ 12,13-diHOME injection acutely activates BAT fuel uptake, enhances cold tolerance, and decreases serum triglycerides finding
- ★ 12,13-diHOME increases fatty acid uptake into brown adipocytes by promoting translocation of FATP1 and CD36 to the cell membrane mechanism
- An LC-MS/MS lipidomics panel of 88 signaling lipids was used to identify putative cold-induced lipokines method
- ★ Beige fat arising in subcutaneous WAT is an appreciable source of 12,13-diHOME when classical BAT development is impaired (Myf5-Cre Bmpr1a f/f mice) finding
- Ucp1-Cre Rosa(stop)Luc transgenic mice combined with FFA-SS-Luc enable real-time imaging of BAT-specific fatty acid uptake resource
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| LC-MS/MS lipidomic panel (88 signaling lipids) | human plasma (9 healthy volunteers) | 1 h cold exposure (14°C) vs ephedrine vs saline | plasma lipokine concentrations | LC-MS/MS (BERG lipidomics platform) |
| Correlation analysis of serum biomarkers | human plasma (Leipzig biobank cohort, n=55) | none (cross-sectional, room temperature) | correlation of 12,13-diHOME with BMI, HOMA-IR, insulin, glucose, triglycerides, leptin, ALAT, ASAT, gGT, cholesterol | LC-MS/MS-mediator lipidomics platform |
| 18F-FDG PET-CT imaging | human BAT (same volunteer cohort) | cold exposure / ephedrine / saline | BAT glucose uptake and activity | Discovery LS multidetector helical PET-CT scanner |
| LC-MS/MS quantification of 12,13-diHOME | mouse serum and BAT | cold exposure (4°C vs 30°C, various durations) or norepinephrine injection | circulating and tissue 12,13-diHOME concentration | LC-MS/MS |
| qPCR gene expression | mouse BAT, WAT, and other tissues | acute (1 h) and chronic (1 week) cold exposure; CL316,243 treatment | Ephx1 and Ephx2 mRNA levels | — |
| Core body temperature monitoring and indirect calorimetry | mice (in vivo, cold challenge) | 12,13-diHOME injection vs vehicle vs 12,13-epOME | core body temperature, O2 consumption, CO2 production, respiratory exchange ratio | — |
| Radiolabeled substrate and bioluminescence FA/glucose uptake imaging | mice (diet-induced obesity; Ucp1-Cre Rosa(stop)Luc transgenic) and brown adipocytes in vitro | 12,13-diHOME treatment (acute and 2-week chronic) | BAT-specific triglyceride, fatty acid, and glucose uptake; luminescence signal via FFA-SS-Luc | — |
| Western blot (subcellular fractionation) | brown adipocytes in vitro | 12,13-diHOME treatment | membrane translocation of CD36 and FATP1 fatty acid transporters | — |
- ▲ 12,13-diHOME was the only lipid species increased in all individuals after 1 h cold exposure and its concentration correlated with BAT glucose uptake
- ▼ Plasma 12,13-diHOME was negatively correlated with BMI, HOMA-IR, fasting insulin, and fasting glucose
- ▲ Acute (1 h) cold exposure increased Ephx2 mRNA in mouse BAT ~14-fold
- ▲ 12,13-diHOME injection protected mice from decreased core body temperature during cold challenge relative to vehicle and 12,13-epOME
- ▼ Chronic (2-week) 12,13-diHOME treatment decreased circulating triglycerides in diet-induced obese mice
- ▲ 12,13-diHOME increased radiolabeled fatty acid and glucose uptake specifically in BAT
- ▲ 12,13-diHOME increased FFA-SS-Luc luminescence signal in BAT in vivo and in vitro, indicating increased FA uptake
- ▲ 12,13-diHOME induced translocation of low-glycosylation CD36 and oligomeric FATP1 to the plasma membrane in brown adipocytes
- pvalue P < 0.05 (three lipid species significantly increased in human plasma after 1 h cold exposure)
- fold_change ~14-fold (Ephx2 mRNA increase in mouse BAT after 1 h acute cold exposure)
- pvalue P = 0.0463 (triglycerides remained correlated with 12,13-diHOME after adjusting for BMI)
- pvalue P = 0.0494 (ALAT remained correlated with 12,13-diHOME after adjusting for BMI)
- pvalue P = 0.0274 (ASAT remained correlated with 12,13-diHOME after adjusting for BMI)
- count n = 55 (Leipzig biobank cohort used for BMI/metabolic correlation analysis)
- count n = 9 (healthy volunteers in the human cold-exposure/PET-CT study)
- other BMI range 17.5-75.4 kg/m^2 (range of BMI represented in the Leipzig cohort)
Statistical methods review
Model: sonnetA neutral, descriptive read of the statistical approach — what was done, and (for shared learning, not as criticism) what could also have been done.
This study used targeted LC-MS/MS lipidomics to screen 88 lipid species for cold-induced changes in human plasma, then characterized 12,13-diHOME associations with clinical metabolic parameters in a cross-sectional human cohort via bivariate correlations and linear models with covariate adjustment. Mouse and cell-culture experiments compared group means across cold-exposure, pharmacological treatment, and genetic conditions using unspecified statistical tests. The methods section explicitly states that samples were not randomized to experimental groups and that analyses were not performed in a blinded fashion (except as noted).
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| Threshold-based significance screen (P < 0.05; specific test not named) | Identification of cold-induced lipids among 88-species lipidomic panel in 9 human volunteers | 9 | not stated |
| Correlation analysis (type—Pearson or Spearman—not specified) | Association of plasma 12,13-diHOME with BMI, HOMA-IR, fasting insulin, fasting glucose, triglycerides, leptin, liver enzymes (ALAT, ASAT, gGT), and cholesterol fractions in human biobank cohort | 55 | not stated |
| Linear model with single covariate (BMI) | Residual associations of 12,13-diHOME with triglycerides (P = 0.0463), ALAT (P = 0.0494), and ASAT (P = 0.0274) after adjusting for BMI | 55 | not stated |
| Group comparison (specific test not stated) | 12,13-diHOME levels in mouse plasma/tissue: thermoneutrality vs. cold (1 h, 1 week, 11 d); WT vs. Myf5-Cre Bmpr1a mice; vehicle vs. 12,13-diHOME or NE treatment; BAT secretion vs. WAT secretion ex vivo | — | not stated |
-
The 88-lipid panel was screened for cold-induced changes using a P < 0.05 threshold with no adjustment for multiple comparisons↳ Could also: A false-discovery-rate correction such as Benjamini-Hochberg (BH-FDR) could also be applied across the 88 simultaneous tests — With 88 tests at alpha = 0.05, roughly 4 false positives are expected by chance alone; BH-FDR quantifies the expected proportion of false discoveries among the significant hits, which is a widely used standard in lipidomic and metabolomic discovery screens
-
More than 10 clinical variables were each individually correlated with 12,13-diHOME without multiplicity adjustment↳ Could also: Pre-specifying a small set of primary endpoints before analysis, or applying BH-FDR or Bonferroni correction across the correlation family, would also be standard practice — Testing many correlations simultaneously inflates the family-wise type I error rate; either pre-specification or a correction procedure makes explicit the probability that at least one association among the significant results is a false positive
-
The correlation method used to associate 12,13-diHOME with clinical variables is not named↳ Could also: Explicitly reporting Pearson or Spearman rank correlation, chosen after assessing normality and linearity, is also standard — Spearman is more robust to outliers and skewed distributions, which may be relevant given the wide BMI range (17.5–75.4 kg/m²) and metabolic parameter spread in this cohort; stating the method allows readers to assess its appropriateness and reproduce results
-
Clinical associations were first examined as bivariate correlations and then with a linear model adding BMI as a single covariate↳ Could also: A multivariable regression simultaneously adjusting for several potential confounders (e.g., age, sex, BMI, diabetes status) could also characterize the independent association — Sequential single-covariate adjustment may leave residual confounding; simultaneous inclusion of multiple covariates provides a more complete estimate of the independent relationship between 12,13-diHOME and each outcome
-
Mouse group comparisons were made using unspecified statistical tests↳ Could also: Explicitly naming the test for each comparison (e.g., two-tailed Student's t-test, Mann-Whitney U, or one-way ANOVA with Tukey post-hoc) is also standard practice — Named tests allow readers to verify that the test's assumptions (normality, independence, variance homogeneity) match the data structure and enable meta-analysis or replication; reporting guidelines such as ARRIVE recommend this level of specificity for animal studies
-
Results were reported with exact or threshold p-values only; no effect sizes or confidence intervals are mentioned↳ Could also: Reporting standardized effect sizes (e.g., Cohen's d, r, or fold-change with CI) alongside p-values is also standard, particularly for correlation and group-difference analyses — Effect sizes and confidence intervals convey the magnitude and precision of an association independently of sample size, which aids interpretation and downstream power calculations for replication studies
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — pmid-28346411
Paper: Lynes MD et al. "The cold-induced lipokine 12,13-diHOME promotes fatty acid transport into brown adipose tissue." Nat Med 2017;23(5):631-637. doi:10.1038/nm.4297 · PMCID PMC5699924.
Nature of the paper
Predominantly a wet-lab / biochemistry study (mouse cold-exposure & injection experiments, FA-uptake assays, qPCR, Western blots, PET imaging). One genuine computational/statistical (omics) component: a targeted LC–MS/MS lipidomic screen of an 88-lipid panel in human plasma, plus correlation analyses of the lead lipid (12,13-diHOME) against clinical/metabolic parameters.
Code / data availability
- Code: none. No repository (authors' or third-party) is cited. Statistics were done in "Microsoft Excel, Graphpad Prism and RStudio using the LIMMA package" (Methods/Statistics) — no script shipped.
- Raw omics data: NOT deposited. No GEO/SRA/BioProject (PMID→DB elink empty), no MetaboLights/Metabolomics Workbench deposit (searched), no PRIDE. The raw LC–MS/MS was processed on SCIEX PeakView/MultiQuant (proprietary) by BERG.
- Data-availability statement (verbatim): "All data underlying the findings reported in this manuscript are provided as part of the article. Source data are available online for Figures 1–4."
- What IS shipped: Source-data Excel files for Figs 1–4
(
41591_2017_BFnm4297_MOESM1–4_ESM.xlsx) + a supplementary PDF (MOESM5). These contain the per-subject/per-sample derived values behind the figures.
In scope (pipeline-derived, attempted) — all in Figure 1
Reproducible by applying standard statistics (third-party tools: R/limma, paired t-test, Spearman) to the paper's own shipped Fig-1 source data.
| ID | Result | Method (paper) | Reported |
|---|---|---|---|
| C1 | Differential lipid screen: of the 88-lipid panel, which lipids are significantly increased by cold (P<0.05); 12,13-diHOME is significant | Volcano, paired Student's t-test, n=9 humans (Fig 1a) | "three lipid species significantly (P<0.05) increased … 12,13-diHOME … the only species that increased in all individuals measured" |
| C2 | 12,13-diHOME vs BMI | Spearman r, n=55 (Fig 1d) | significant negative correlation |
| C3 | 12,13-diHOME vs HOMA-IR | Spearman r, n=55 (Fig 1e) | significant negative correlation |
| C4 | 12,13-diHOME vs circulating triglycerides | Spearman r, n=55 (Fig 1f) | negative; remains sig. with BMI covariate P=0.0463 |
| C5 | 12,13-diHOME vs ALAT | Spearman r (Fig 1g) | negative; ALAT P=0.0494, ASAT P=0.0274 with BMI covariate |
| C6 | 12,13-diHOME vs BAT activity (PET SUV) | Spearman r (Fig 1c) | positive correlation |
| C7 | 12,13-diHOME vs HDL / LDL cholesterol | Spearman r (Fig 1h,i) | not correlated |
The exact r values are printed on the figure panels; we compute r + P from source data and compare. LIMMA (moderated t-test) on the 88-lipid matrix is run as the faithful re-implementation of the screen, alongside the paired t-test the legend names for the volcano.
Out of scope (wet-lab / manual / external — NOT attempted)
- All mouse experiments: serum 12,13-diHOME after NE / cold (Fig 2a,b), qPCR of Ephx1/Ephx2 and Cyp genes (Fig 2d–f), 12,13-diHOME injection → BAT fuel uptake, cold tolerance, serum TG (Fig 3), FA-uptake / FATP1 & CD36 translocation assays (Fig 4). These are bench measurements, not pipeline-derived.
- Raw LC–MS/MS peak picking / quantification (SCIEX PeakView+MultiQuant, proprietary; raw spectra not deposited) — cannot be reproduced.
- "Meta-analysis of publicly available data sets profiling BAT gene expression" (Supplementary Fig. 4b) — external datasets not enumerated with accessions in the available text; revisit only if accessions are found in MOESM5.
Datasets to profile
- Fig 1–4 source-data Excel (
MOESM1–4) — the only machine-readable data shipped. Profiled indata/dataset_profile.json. No external accession exists to profile.
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.
The in-scope computational layer (all of Figure 1 + Supp Fig 3) reproduces essentially exactly from the authors' own deposited source-data Excel using third-party tools — the paired cold-induction (P=0.002716 to the digit) and every simple Spearman correlation match — so the central human correlation claims are fully confirmed. Three bounded concerns sit on the authors'/data side: (1) the BMI-adjusted covariate p-values (0.0463/0.0494/0.0274) are not derivable from the under-specified "a linear model" and flip to non-significant under every standard method; (2) Fig 1g prints P=0.0011, statistically impossible for its own r=-0.348 at n=55 (likely a copy-typo, not fabrication); (3) the 88-lipid volcano is uncheckable because the discovery matrix was never deposited despite the data-availability statement. No fabrication signal — overall a solid reproduction with explainable, authors-side deviations.
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.
🚩 Report an error in this record
Spotted something wrong — a verdict you’d contest, a data or value error, or a private detail that slipped through? Tell us, with a short justification. Authors and readers are equally welcome to write in; we review every report.
Prefer email, or the form below not working? Contact us at support@doesitreproduce.com.
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.