Additional file 1 of Respiratory syncytial virus (RSV) enhances translation of virus-resembling AU-rich host transcripts
Bibliographic record
Abstract
Supplementary Material 1: Supplementary Fig. S1. Related to Fig. 1. RSV infection does not induce stress granule formation in HEp2 and A549 cells. Western blot demonstrating PKR upregulation during RSV infection. GAPDH serves as a loading control. RSV infection only induces low levels of eIF2α phosphorylation. Western blot demonstrating lack of strong eIF2α phosphorylation during RSV infection by comparing eIF2α-P and total eIF2α levels between mock- and RSV-infectedand untreated and NaAsO2-treatedin A549 cells. RSV infection was confirmed by immunoblotting with a polyclonal anti-RSV antibody. β-actin serves as a loading control. Relative quantification against control samples. P values were calculated with one-way ANOVA with Sidak’s multiple comparisons test.Western blot comparing eIF2α-P and total eIF2α levels between mock- and RSV-infectedat different time points. Viral proteins were detected using a polyclonal anti-RSV antibody. P values were calculated with one-way ANOVA with Sidak’s multiple comparisons test.RSV infection does not induce stress granule formation seen by indirect immunofluorescent staining of mock- and RSV-infected cellsvia stress granule markers PABPand G3BP. RSV proteins were detected using a polyclonal anti-RSV antibodyand nuclei were stained using DAPI. The white box corresponds to 10 μm and is enlarged in the zoom panel to visualize viral inclusion bodies where nascent viral transcripts are transcribed. Inclusion bodies are known to contain PABP.Stress granule formation seen by indirect immunofluorescent staining of arsenite-treated cellsdetecting stress granule markers PABP and G3BP. Nuclei were stained using DAPI.Polysome profiles of sucrose gradient fractionated mock- and RSV-infected A549 cells. AUC quantification between polysomes and monosomesare plotted to estimate translation levels. AUC quantification between free RNA fractionand 40S, 60S and 80S are plotted to determine changes in free monosomes and 80S subunits. P values were calculated with an unpaired t-test for polysome vs monosome comparisons and a two-way ANOVA with Sidak’s multiple comparisons test. AUC: area under the curve.
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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) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.890 | 0.248 |
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".