Interpretation of Data Underlying the Link Between Colony Collapse Disorder (CCD) and an Invertebrate Iridescent Virus
Bibliographic record
Abstract
In a recent publication, Bromenshenk et al. claim that an iridovirus, Invertebrate Iridescent Virus-6 (IIV-6)1, is tightly linked to colony collapse disorder (CCD, the cause of many of the bee losses over the past four winters) based on proteomic analyses of bees from CCD-afflicted and unafflicted colonies (1). We believe that there are fundamental flaws in the interpretation of their data based on the following rationale. First, liquid chromatography-tandem MS (LC-MS/MS) tends to identify the most abundant proteins much more frequently and the major capsid protein of IIV-6 constitutes at least 17% of total virion protein (2) yet of the 792 IIV-6 peptides reported by the authors, only four (0.5%) are from protein 274L, the major capsid protein.
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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 | 0.007 | 0.016 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.003 | 0.002 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.002 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.004 | 0.001 |
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".