Developmentally Programmed <scp>DNA</scp> Rearrangements
Bibliographic record
Abstract
Abstract Developmentally programmed deoxyribonucleic acid (DNA) rearrangements are structural reorganisations of the genome that occur reproducibly during the development of a variety of organisms. In the majority of cases, programmed DNA rearrangements function to alter gene expression. V(D)J recombination is a DNA rearrangement that occurs during the development of the human immune system to assemble functional genes encoding antibodies. Some human pathogens use programmed DNA rearrangements to evade the immune system by varying the expression of their antigenic surface proteins. However, in some cases, the function of large‐scale developmentally programmed DNA rearrangements remains unknown. In the ciliate protozoan Tetrahymena thermophila , a wide variety of programmed rearrangements occur during the development of the somatic nucleus including chromosome fragmentation and deletion of specific DNA sequences. In a related ciliate Oxytricha trifallax , programmed genome rearrangements are needed to unscramble segments to assemble functional genes. Key Concepts Programmed DNA rearrangements utilise diverse recombination mechanisms. Human pathogens use programmed DNA rearrangements to vary expression of antigenic surface proteins to avoid the host immune system. V(D)J recombination in human development assembles functional genes encoding antibodies. Chromatin diminution in parasitic nematodes silences germ‐line‐specific gene expression in somatic cells. The ciliate protozoa undergo large‐scale programmed DNA rearrangements during nuclear development. The mechanism of programmed DNA deletion in the ciliate Tetrahymena thermophila involves small noncoding RNAs that direct formation of a specific chromatin structure. The ciliate Oxytricha trifallax unscrambles gene segments during the development of its somatic nucleus.
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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 | 0.000 |
| 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 | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.007 | 0.003 |
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".