Detection of joining points for genomic DNA circularization in cell culture
Bibliographic record
Abstract
We previously reported on extrachromosomal circular DNA extracted from mouse brain. We attempted to reconfirm the formation of circular DNA from this region in a culture system. From a circular DNA-enriched fraction of a mouse embryonic tumor-derived cell line capable of inducing neuronal differentiation, circular DNA in the same region was isolated by nested inverse polymerase chain reaction as performed previously. We attempted to amplify and identify some junctions that were evidence of circularization. In this analysis, we captured several junctions that indicated circularization in cultured cells induced to differentiate into neurons. We observed that some of the sequences shared the same point of attachment, indicating that there exist genomic sequences that are amenable to binding toward circularization. Cells were X-ray-irradiated to determine whether any transformation occurred in DNA circularization. Consequently, circularization junctions occurred after differentiation-induced stimulation and before and after X-ray irradiation. This finding indicated that circularization junctions can be formed from this region without being inhibited by X-ray irradiation and irrespective of cell differentiation stage. Furthermore, the presence of circular DNA was confirmed in which genomic fragments from different chromosomes were replaced. These findings suggest that extrachromosomal circular DNA contributes to the interchromosomal translocation of genomic fragments.
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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 | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 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 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
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".