Supplementary tables for the manuscript titled "DNA methylation haplotype block signatures responding to S. aureus subclinical mastitis and association with production and health traits".
Bibliographic record
Abstract
Supplemental Table S1 Detail information on cows selected for whole genome DNA methylation sequencing. Supplemental Table S2 General statistics on whole genome DNA methylation sequencing read statistics Supplemental Table S3 Comparisons of methylation level between cows with S. aureus subclinical mastitis and healthy control cows at a scope of the whole genome, chromosomes and gene features. Supplemental Table S4 List of differentially methylated cytosines in the context of CpG Supplemental Table S5 List of differentially methylated cytosines in the context of CHG and CHH Supplemental Table S6 Distribution of differentially methylated cytosines among chromosomes and genetic features Supplemental Table S7 Count of differentially methylated cytosines (DMCs) in the context of CpG, CHG and CHH in different gene features per gene Supplemental Table S8 Functional enrichment of differentially expressed genes harboring differentially methylated cytosines at different genomic functional regions Supplemental Table S9 Predicted methylation level for LINE-1 and tRNA-derived SINEs and comparisons between cows with S. aureus subclinical mastitis and healthy control cows Supplemental Table S10 Differential methylation haplotype blocks and their colocation with QTLs related to mastitis and immune capacity Supplemental Table S11 Differential genes with significant changes in general methylation level of regulatory regions and gene expression changes Supplemental Table S12 Functional enrichment for differential genes with significant changes in general methylation level of regulatory regions and gene expression changes Supplemental Table S13 Correlation between dMHBs located at regulatory regions and their overlapped differentially expressed genes Supplemental Table S14 Motif enrichment and identification in GE-dMHBs Supplemental Table S15 Functional enrichment for GE-dMHBs (dMHBs overlapped with genes and significantly correlated with the expression of corresponding genes) Supplemental Table S16 Candidate discriminate signatures selected from GE-dMHBs (pro-GE-dMHBs) and their overlapped genes Supplemental Table S17 Information about samples and primers used for TBAS and results of seven GE-dMHBs analyzed in 200 cows
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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 | 0.003 | 0.022 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.003 | 0.004 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.002 | 0.002 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.726 | 0.213 |
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".