Additional file 1 of Engineering Escherichia coli for the utilization of ethylene glycol
Bibliographic record
Abstract
Additional file 1: Figure S1. The effect of microaerobic (oxygen-limiting) conditions on glycolate production, as predicted by modeling at different substrate uptake rates (SUR) and non-growth associated ATP maintenance (NGA ATPM) values. (A) SUR of 5 mmol/gDW·h and default NGA ATPM value (8.39 mmol/gDW·h.). (B) SUR of 0.7 mmol/gDW·h and NGA ATPM value of 4.8 mmol/gDW·h. (C) SUR of 0.7 mmol/gDW·h and NGA ATPM value of 3.2 mmol/gDW·h. (D) SUR of 0.7 mmol/gDW·h and NGA ATPM value of 1.6 mmol/gDW·h. In each case, flux balance analysis (FBA) was used to predict the glycolate yield (mol glycolate/mol EG), cell growth rate (gDW/gDW·h), respiratory quotient (RQ, mol CO2/mol O2) and the substrate specific productivity (SSP, g glycolate/g EG·h) over a range of oxygen uptake rates (OURs, mmol O2/gDW·h). All values other than the SSP are shown on the primary vertical axis. An RQ value of 0.4 (shown by the dotted black line) was selected for the RQ-based strategy employed in the final bioreactor experiment. The molar yield (mol glycolate/mol EG) predicted at this RQ value is indicated for each case.
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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 | 0.011 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.001 | 0.003 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.782 | 0.142 |
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".