Bibliographic record
Abstract
Each day a cell must face a constant onslaught of DNA lesions. Although we tend to worry most about environmental sources of DNA damage (e.g., chemical agents, UV radiation, ionizing radiation), a human cell must repair over 10,000 DNA lesions per day to counteract endogenous sources of DNA damage (Lindahl 1993). DNA itself has a measurable half-life—spontaneous depurination can generate abasic sites in DNA strands at an estimated rate of 2,000–10,000 lesions per human cell per day (Lindahl 1993). Indeed, it has been proposed that much of the DNA repair machinery has evolved to contend with DNA damage generated by the byproducts of cellular metabolism—reactive oxygen species, endogenous alkylating agents, and DNA singleand doublestrand breaks resulting from collapsed DNA replication forks or from oxidative destruction of deoxyribose residues (Lindahl and Wood 1999; Lindahl 2000). Failure to repair such lesions can lead to a deleterious mutation rate, genomic instability, or cell death. In higher eukaryotes, the damage that occurs in genes responsible for DNA repair and/or cell cycle regulation can lead to threatening diseases such as cancer. The timely and efficient repair of eukaryotic DNA damage is further complicated by the realization that DNA lesions must be detected and repaired in the context of highly condensed, 100–400-nm-thick chromatin fibers (Belmont and Bruce 1994). The nucleosome is the first level of DNA compaction in the nucleus and is formed by the wrapping of 147 bp of DNA around a histone octamer composed of two H2A–H2B dimers and a H3–H4 tetramer. Linear arrays of nucleosomes are then folded into more compact structures, stabilized by linker histones such as histone H1. These compact structures are well known to hinder nuclear processes like transcription, and several in vitro studies have demonstrated that the assembly of DNA lesions into chromatin greatly hinders their detection and subsequent repair (see below). Within cells, of course, the repair machinery has created the means to contend with chromosomal structures, and an enormous number of DNA lesions are faithfully repaired each cell cycle. Here we review recent studies that have begun to elucidate this cellular machinery that facilitates DNA repair within the context of chromatin.
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.002 | 0.002 |
| Scholarly communication | 0.003 | 0.004 |
| Open science | 0.001 | 0.002 |
| Research integrity | 0.003 | 0.002 |
| Insufficient payload (model declined to judge) | 0.006 | 0.007 |
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".