Author response: Endangered wild salmon infected by newly discovered viruses
Bibliographic record
Abstract
Keystone species are animals and plants that play a pivotal role in supporting the ecosystems they live in, making their conservation a high priority. Chinook and sockeye salmon are two such species. These fish play a central role in the coastal ecosystems of the Northeast Pacific, where they have supported Indigenous populations for thousands of years. The last three decades have seen large declines in populations of Chinook and sockeye salmon. One factor that may be involved in these declines is viral infection. In the last ten years, advances in DNA sequencing technologies have led to the discovery of many new viruses, and Mordecai et al. used these technologies to look for new viruses in Pacific salmon. First, Mordecai et al. looked for viruses in dead and dying salmon from farms and discovered three previously unknown viruses. Next, they screened for these viruses in farmed salmon, hatchery salmon and wild salmon to determine their distribution. Two of the viruses were present in fish from the three sources, while one of the viruses was only found in farmed fish. The fact that the three viruses are distributed differently raises questions about how the viruses are transmitted within and between farmed, hatchery and wild salmon populations. These findings will aid salmon-conservation efforts by informing the extent to which these viruses are present in wild salmon populations. Future work will focus on determining the risks these viruses pose to salmon health and investigating the potential for exchange between hatchery, farmed and wild salmon populations. While farmed Pacific salmon may pose some transmission risk to their wild counterparts, they also offer the opportunity to study disease processes that are not readily observable in wild salmon. In turn, such data can be used to develop policies to minimize the impact of these infectious agents and improve the survival of wild salmon populations.
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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 | 0.003 | 0.012 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.001 | 0.003 |
| Research integrity | 0.004 | 0.003 |
| Insufficient payload (model declined to judge) | 0.377 | 0.179 |
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".