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 distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.250 | 0.000 |
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 teacher head, 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".