Additional file 1 of A longitudinal census of the bacterial community in raw milk correlated with Staphylococcus aureus clinical mastitis infections in dairy cattle
Bibliographic record
Abstract
Additional file 1: Fig. S1. Holstein cows with S. aureus clinical mastitis. This diagram illustrates 10 dairy cows diagnosed with S. aureus clinical mastitis from five dairy herds in Quebec, Canada. All mastitis occurred via natural infections. Milk samples (n = 599) were collected from all four quarters bi-weekly. Identifiers of each cow name are ‘H’ for the herd and ‘C’ for the assigned cow number. The red and the blue square boxes represent clinical mastitis with visible symptoms infected by S. aureus and other mastitis pathogens, respectively. The black square boxes represent non-mastitic milk. The open square boxes regardless of colors indicate milk samples where no 16S rRNA data is available due to missing milk samples (n = 16), low bacterial DNA (n = 6), and low library read size (n = 10). Fig. S2 Groups of dairy cows. A total of ten dairy cows (11 quarters) affected by S. aureus clinical mastitis were grouped based on the relative abundance of Staphylococcus at Week 0. Two quarters, a healthy and a CM quarter, were selected and indicated under the name of each cow. At Week 0, Staphylococcus was solely the predominant genus in mastitic milk samples in Group I while it was barely detectable in Group II with relative abundance of less than 10%. Fig. S3 Relative abundance of 11 OTUs and OTU0001 (Staphylococcus) over the lactation in healthy and mastitic quarters. The line graphs depict the changes of the relative abundance of 11 OTUs and OTU0001 in two quarters (healthy vs. mastitic quarters) from each cow over the study period. The vertical dotted lines indicate either beginning or ending of S. aureus CM.
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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 | 0.012 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.004 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.625 | 0.047 |
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".