Additional file 1 of Compositional analysis of the tonsil microbiota in relationship to Streptococcus suis disease in nursery pigs in Ontario
Bibliographic record
Abstract
Additional file 1. Figure S1: Relative abundance of tonsillar microbiota of the diagnosis groups (20 confirmed, 20 healthy, and 23 probable cases) on 9 swine farms. A: Boxplots of the top 5 phyla show that Firmicutes had the highest relative abundance across the samples. Firmicutes outliers included two confirmed cases on two different farms and one healthy pig on another farm. B: Boxplots of the relative abundance of top 5 genera show that Streptococcus had the highest relative abundance across the three diagnosis groups. Streptococcus outliers include two confirmed cases from two different farms and one healthy pig on another farm. C: Model coefficients of the PERMANOVA analysis. Only the top 15 taxa that contribute most to the tonsillar community differences are shown. The genus Streptococcus had the largest positive coefficient, indicating that it was important to the model for disguising microbiomes in the diagnosis groups.
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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 | 0.019 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.799 | 0.071 |
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".