Bibliographic record
Abstract
The reaction catalyzing direct demethylation of DNA involves the removal of a methyl group residue from the 5′ position on cytosine; the products of the reaction are nonmethylated cytosine in the dinucleotide CpG and methanol ( 1 ). The study of the proteins involved in demethylation requires an assay for measuring enzymatic DNA demethylation. A number of assays were previously described for determining the state of methylation of CpG sequences DNA. For example, certain restriction enzymes such as Hpa II or Hha I recognize subsets of CpG sequences only when the C is not methylated; thus, cleavage by this enzymes indicates demethylation of their recognition sequences ( 2 ) This assay is, however, obviously indirect and can only measure the state of methylation of a subset of CG sequences contained in the enzyme-specific recognition site. An additional problem is that this assay does not differentiate between DNA that is directly demethylated, and repair processes that remove methylated cytosines in DNA and replace them with other unmethylated cytosines found in the extracts. An additional assay is the bisulfite-mapping method, which can determine the state of methylation of cytosines at a single nucleotide resolution ( 3 ). This assay is based on the fact that nonmethylated cytosines are modified by bisulfite and converted to thymidine, whereas methylated cytosines are protected. This assay, similar to the restriction enzyme-based assays, is indirect; it does not measure demethylation but rather the conversion of cytosines.
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 | 0.002 | 0.002 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.003 |
| Insufficient payload (model declined to judge) | 0.003 | 0.004 |
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".