Dynamic behaviour of the B<sub>12</sub>riboswitch
Bibliographic record
Abstract
Riboswitches are RNA segments that serve as ligand-responsive genetic control elements. They modulate the expression of certain genes in response to changing concentrations of metabolites. In this paper, we study the dynamic behaviour of the B12 riboswitch in E. coli--perhaps the most widely studied and best known of all riboswitches--through a mathematical model of its regulatory pathway. To carry this out, we simulate dynamic experiments in which the bacterial B12 uptake capacity is measured after being depleted of this vitamin for a long time. The results of these simulations compare favourably with reported experimental data. The model also predicts that an overshoot of intracellular B12 should be observed if the replenishment experiments were to be carried out for longer times. This behaviour is discussed in terms of a possible evolutionary advantage for E. coli, together with the fact that regulation at the transcriptional and translational levels is almost equivalent dynamically.
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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 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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 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".