Additional file 2 of Host miRNAs regulate Escherichia coli O157 mucosal colonization through host-mucosa-attached microbiota interactions in calves
Bibliographic record
Abstract
Supplementary Material 2: Mucosa-attached microbes divergent in abundance contribute to altered niche occupancy and altered bacterial functions. A. The Beeswarm plot showing absolute niche breadth value for abundant (left panel), intermediate (middle panel), and rare (right panel) microbes (P > 0.01 ***,0.01 ≤ P ≤ 0.05 **, 0.05 ≤ P < 0.1 *). B. The stack plot showing relative niche occupancy for mucosa-attached microbes from calves without challenge or post challenge at T2 or T5 for both WT and RE. The relative niche occupancy is defined as the sum of absolute niche breadth value for abundant-specific microbes/the sum of niche breadth value for all microbes for each group. C. The stack plot showing the contributions of abundant/intermediate/rare microbes to the most enriched bacterial functions post challenge. D. The Venn plot showing shared and specific intermediate microbes contributing the most enriched bacterial function at WT-T2 and WT-T5. E. The Venn plot showing shared and specific intermediate microbes contributing the most enriched bacterial function at RE-T2 and RE-T5.
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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) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.001 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.833 | 0.133 |
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".