Reconstructing DNA replication kinetics from small DNA fragments
Bibliographic record
Abstract
In higher organisms, DNA replicates simultaneously from many origins. Recent in vitro experiments have yielded large amounts of data on the state of replication of DNA fragments. From measurements of the time dependence of the average size of replicated and nonreplicated domains, one can estimate the rate of initiation of DNA replication origins, as well as the average rate at which DNA bases are copied. One problem in making such estimates is that, in the experiments, the DNA is broken up into small fragments, whose finite size can bias downward the measured averages. Here, we present a systematic way of accounting for this bias by deriving theoretical relationships between the original domain-length distributions and fragment-domain length distributions. We also derive unbiased average-domain-length estimators that yield accurate results, even in cases where the replicated (or nonreplicated) domains are larger than the average DNA fragment. Then we apply these estimators to previously obtained experimental data to extract improved estimates of replication kinetics parameters.
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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 | 0.000 |
| 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) | 0.000 | 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".