Additional file 4 of Molecular characterization of Streptococcus suis isolates recovered from diseased pigs in Europe
Bibliographic record
Abstract
Additional file 4. Phylogenetic relationships based on core-genome single-nucleotide polymorphisms (SNPs) and genomic traits of the 251 Streptococcus suis isolates using a different reference genome. This figure presents a maximum-likelihood phylogenetic tree (left panel), constructed using 8,611 non-redundant core-genome SNP loci identified relative to the genome sequence of the ST16 serotype 9 reference strain GD-0088. This analysis confirms the findings depicted in Figure 3, using a different reference to provide comparative insights. The tree highlights several distinct clades, emphasizing the genetic diversity among the isolates. For reference, the serotype of each isolate, along with the genotypes determined by multilocus sequence typing (MLST), are annotated along the tree, showing their association with specific genomic clades. The right panel depicts the presence (in purple) or absence (in light blue) of antimicrobial resistance (AMR) genes and virulence-associated genes (VAGs), as determined from the whole-genome sequences of each isolate. “UT” denotes an untypable isolate.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.017 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.003 | 0.004 |
| 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) | 0.834 | 0.137 |
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".