Additional file 1 of Whole-genome sequencing analysis of two heat-evolved Escherichia coli strains
Bibliographic record
Abstract
Additional file 1: Supplementary Table S1. BM28 and BM28 ΔlysU NextSeq 2000 Illumina WGS data statistics. Supplementary Table S2. BM28 Oxford Nanopore WGS data statistics. Supplementary Table S3. Large deletions in BM28 and BM28 ΔlysU. Supplementary Table S4. BM28 and BM28 ΔlysU mutation details. Supplementary Table S5. High temperature growth scores of BM28-related cells with and without pOF39. Supplementary Table S6. Smaller BM28 and BM28 ΔlysU indels. Supplementary Table S7. PANTHER Overrepresentation Test of BM28 mutations using the Annotation Data Set GO cellular component complete. Supplementary Table S8. PANTHER Overrepresentation Test of BM28 ΔlysU mutations using the Annotation Data Set GO cellular component complete. Supplementary Table S9. Motility of DH10B, MG1655, BM28 and BM28 ΔlysU. Supplementary Figure S1. The 12 bp of homology between dinB and mhpE. Supplementary Figure S2. The O-antigen deletion in BM28 and BM28 ΔlysU. Supplementary Figure S3. BM28 and BM28 ΔlysU SNP mutation spectra. Supplementary Figure S4. Differences between BM28 and BM28 ΔlysU. Supplementary Figure S5. Growth of BM28 and BM28 ΔlysU on LB agar (left) and LB + Cb agar (right). Supplementary Figure S6. DH10B BM28 gDNA transformation plate. Supplementary Figure S7. PCR of BM28 gDNA using pOF39-specific primers. Supplementary Figure S8. Alignment of wildtype IS10R, wildtype IS10L and the IS10L/R hybrid from the BM28 Tn10. Supplementary Figure S9. Alignment of wildtype IS10R, wildtype IS10L and the IS10L/R hybrid from the BM28 ΔlysU Tn10. Supplementary Figure S10. Sequence logo of the IS10R target sequence, made using WebLogo (https://weblogo.berkeley.edu/logo.cgi). Supplementary Figure S11. Rho T96 is located on the surface of the protein and does not contact RNA polymerase nor other Rho monomers. Supplementary Figure S12. RpoC A595 is located on the surface of the protein and does not contact other RNA polymerase components, nor Rho. Supplementary Figure S13. RpoC T1135 is in close proximity to DksA, namely, DksA residue D90 (the closest distance, represented by a pink dotted line, is 7.1 Å). Supplementary Figure S14. RpoC T1135, DksA and a ppGpp molecule are fairly close to the active site magnesium ion of the RNA polymerase.
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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 | 0.007 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.003 | 0.005 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.003 | 0.001 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.648 | 0.144 |
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".