Additional file 1 of Automation assisted anaerobic phenotyping for metabolic engineering
Bibliographic record
Abstract
Additional file 1: Table S1. Names and formulae of reaction abbreviations mentioned in Fig. 7 (main text). Metabolites in the reaction formulae are represented by their BiGG ID. Figure S1. Change in sterility with air-gap (data consolidated from main text Fig. 2d). Figure S2. Increase in pipetting error upon increasing pipetting speed by 300% for different volume ranges. Figure S3. Distribution of biomass yields (ratio of final to initial biomass) of wild type E. coli MG1655 grown in Rich Defined Media with different seals. Figure S4. Time-course showing cell density and instantaneous growth rate of different E. coli strains (described in Materials & methods) in RDM with and without a layer of oil in the presence of oxygen and with a layer of mineral oil inside an anaerobic chamber. Figure S5. Time-course showing cell density and instantaneous growth rate of E. coli strains (described in Materials & methods) with different pre-culturing strategies. Figure S6. Variance explained by each principal component for principal component analysis performed on metabolite yields and growth rates of E. coli strains (described in Materials & methods) grown in rich defined media in a bioreactor and microplates supplemented with reducing agents. Figure S7. Principal component analysis performed on the metabolite yields and growth rates of E. coli strains (described in Materials & methods) grown in rich defined media in a bioreactor and microplates supplemented with reducing agents. Figure S8. A comparison E. coli's metabolite yields and growth rates obtained from a bench-top 0.5 L bioreactor and 96-well microplates with different reducing agents for the strains: a. Wild Type MG1655, b. MG1655 Δ(adhE; pta)-D1, c. MG1655 Δ(adhE; pta)-D28, and d. MG1655 Δ(adhE; pta)-D59. Figure S9. Principal component analysis performed on the metabolite yields and growth rates of E. coli strains (described in Materials & methods) grown in rich defined media in a bioreactor and microplates supplemented with different substrate concentrations. Figure S10. A comparison E. coli's metabolite yields and growth rates obtained from a bench-top 0.5 L bioreactor and 96-well microplates with different initial glucose concentrations for the strains: a. Wild Type MG1655, b. MG1655 Δ(adhE; pta)-D1, c. MG1655 Δ(adhE; pta)-D28, and d. MG1655 Δ(adhE; pta)-D59.
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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 | 0.003 | 0.019 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.004 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.806 | 0.256 |
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".