Towards a comprehensive understanding of cellular metabolism
Bibliographic record
Abstract
Metabolism is the best mapped major biochemical network. Nevertheless, even in model organisms like baker's yeast, important pathways continue to be discovered. One strategy for pathway discovery is to analyze, by untargeted LC‐MS, the metabolic consequences of knocking out genes of unknown function. This approach recently identified a new route of converting glycolytic intermediates into ribose, which yeast cells activate when demand for ribose exceeds that for NADPH. With the aim of further elucidating pathways involving ribose and NADPH metabolism, we are now investigating several other poorly annotated enzymes. Multiple enzymes contribute to a ribose salvage pathway, which catabolizes ribosomal RNA to generate energy during nutrient starvation. Others contribute to NADPH homeostasis. The functional roles of these enzymes and pathways in the context of energy and cofactor metabolism will be described.
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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 | 0.002 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.003 | 0.001 |
| Bibliometrics | 0.003 | 0.001 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.005 | 0.010 |
| Open science | 0.002 | 0.002 |
| Research integrity | 0.002 | 0.008 |
| Insufficient payload (model declined to judge) | 0.003 | 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".