Additional file 1 of Epigenetic silencing and genome dynamics determine the fate of giant virus endogenizations in Acanthamoeba
Bibliographic record
Abstract
Additional file 1. Figures S1–S8. Word document. Fig. S1 Synteny between Neff and C3 chromosomes. Fig. S2 Phylogeny of serine/threonine kinase endogenized into the Neff genome. Fig. S3 Distance from chromosome ends of genomic features in Neff and C3. Fig. S4 Detailed characterization of representative viral insertions in Acanthamoeba str. Neff. Fig. S5 Mobile element diversity based on genomic context in Neff and C3. Fig. S6 Methylation level of genes, mobile elements, and intergenic regions in Acanthamoeba strains Neff and C3. Fig. S7 Methylation level of viral genes and regions in Acanthamoeba strains Neff and C3. Fig. S8 Comparison of Nanopolish and Enzymatic Methyl-seq analyses.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.009 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.003 | 0.005 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.003 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.805 | 0.192 |
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".