Additional file 6 of A minimized symbiotic gene set from the 1.68 Mb pSymB chromid of Sinorhizobium meliloti reveals auxiliary symbiotic loci
Bibliographic record
Abstract
Additional file 6: Fig. S4. Symbiotic phenotype of key strains on the alternate S. meliloti host Melilotus officinalis (yellow sweet clover) and the consistent nodule morphology of exclusively Fix− SmB1.0 nodules. (A) The shoot dry weight of M. officinalis inoculated with SmB1.0 was consistently Fix− and indistinguishable from un-inoculated controls (red). This appears to be due to the simultaneous removal of the B301 and B307 regions as seen when M. officinalis is inoculated with SmB1.0+ pSymBΔB302ΔB307. The addition of pSymBΔB302 to SmB1.0 was able to restore the symbiosis wild-type levels as was seen with alfalfa (light blue). SmB2.0 was Fix+ with M. officinalis at a level below that seen with alfalfa (orange). Mean shoot height differences were assessed using one-way ANOVA followed by a Tukey multiple comparison test. (B-D) Wild-type-inoculated nodules of M. officinalis 5 weeks post-inoculation displayed typical development with highly elongated bacteroids. (E-J) SmB1.0-inoculated nodules of M. officinalis 5 weeks post-inoculation exhibited consistent early arrest of nodule development (E-F, further magnified in G) with poorly elongated bacteria (H). Proximal part of the nodule was often devoid of infected cells and possessed numerous infection threads (I-J). Nodules were fixed and stained with the DNA-binding dye SYTO13. Images are representative of a minimum of five independent nodules examined. Scale bars: (B, E-G) 100 μm; (C-D, H-J) 25 μm. Arrowheads point to examples of bacteria in infection threads.
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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 | 0.011 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.003 | 0.002 |
| Bibliometrics | 0.002 | 0.003 |
| 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) | 0.819 | 0.194 |
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".