Additional file 1 of Profound DNA methylomic differences between single- and multi-fraction alpha irradiations of lung fibroblasts
Bibliographic record
Abstract
Additional file 1. Figure S1: Minus-Average plots illustrating the number of differentially methylated regions (DMRs) identified using various filters for statistical significance in α-irradiated fibroblasts. A DMRs detected in fibroblasts irradiated to single-fraction doses of α-particles. B DMRs detected in fibroblasts irradiated to multi-fraction doses of α-particles. Red, green, and gold dots indicate enriched regions with adjusted p value < 0.05, adjusted p value < 0.1, and raw p value <0.05, respectively. P values were adjusted for multiple testing using the false discovery rate method. Table S1: Parameters of the single-fraction α-irradiation using americium-241 sources in lung fibroblast cells. Table S2: Parameters of the 14-day multi-fraction α-irradiation equally delivered every 24 hours using americium-241 sources in lung fibroblast cells. Table S3: Number of differentially methylated regions (DMRs) in α-irradiated fibroblasts. The dose was delivered either as a singlefraction or equally distributed in 14 fractions (multi-fraction) with one fraction per day every 24 hours. The DMRs were generated using the MEDIPS package. The adjusted p values were computed using the false discovery rate (FDR) method. Table S4: Genes harboring the aging-associated differentially methylated regions (DMRs) in the α-irradiated lung fibroblasts. The total dose was delivered either as a single-fraction (SF) or 14-d multi-fraction (MF) every 24 hours. These events are based on the epigenetic chronological DNAm clock from Horvath [33] and the biological DNAm clock from Levine, et al. [34]. HypoDMRs, hypomethylated DMRs; hyperDMRs, hypermethylated DMRs; chr, chromosome. Table S5: The list of all differentially methylated regions (DMRs) located within the promoter site of the genome and their associated genes identified in the lung fibroblasts irradiated to single-fraction (SF) doses of α-particles. HypoDMRs, hypomethylated DMRs; HyperDMRs, hypermethylated DMRs; chr, chromosome. Table S6: The list of all differentially methylated regions (DMRs) located within the promoter site of the genome and their associated genes identified in the lung fibroblasts irradiated to multi-fraction (MF) doses of α-particles. Each fraction was equally delivered every 24 hours for 14 days. HypoDMRs, hypomethylated DMRs; HyperDMRs, hypermethylated DMRs; chr, chromosome.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.013 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.833 | 0.118 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".