Additional file 1 of Transcriptomic evidence for visual adaptation during the aquatic to terrestrial metamorphosis in leopard frogs
Bibliographic record
Abstract
Additional file 1: Figure S1. Principal components analysis (PCA) plot of rlog transformed counts from the A) transcriptome-wide and B) vision gene coding sequence analyses illustrating the outlier juvenile, dark exposed sample. Figure S2. Enrichment of Gene ontology (GO) terms. Figure S3. Principal components analysis plot of rlog transformed counts of visual gene coding sequences. Figure S4. Spectral sensitivity of photoreceptors detected through microspectrophotometry in (A) one tadpole and (B) one adult Lithobates sphenocephalus. Figure S5. Examples of raw microspectrophotometry data and raw Gaussian fits (coloured and transparent) and Govardovskii et al. [55] template fits (black and non-transparent) for each cell and pigment type found in the tadpole (A–C) and adult (D–G) Lithobates sphenocephalus. Figure S6. Examples of raw microspectrophotometry data and raw Gaussian fits (cyan) and Govardovskii et al. [55] template fits (black) for RH1 ‘red’ rods in Lithobates sphenocephalus adults where the A2 template (solid) was a better fit than the A1 template (dashed). Figure S7. Expression profiles of significantly differentially expressed cone and rod phototransduction genes between tadpoles and juveniles. Figure S8. Comparison of averaged cross-normalized expression levels (TMM) for each major crystallin type. Figure S9. Expression profiles of taxon-specific lens crystallin genes that have not specifically been identified in frogs and that differ substantially between tadpole and adults (adjusted P-value < 0.05; Additional file 6). Figure S10. Comparison of averaged refractive increment index (dn/dc) for each major crystallin type. Table S1. Sample information and read counts for the frogs used in the RNA-seq analyses. Table S2. Summary data from fits of individual photoreceptor scans from one Lithobates sphenocephalus tadpole (n = 41) and one adult (n = 33) to visual pigment templates from Govardovskii et al. [55]. Table S3. Cross-normalized expression values (TMM) and computationally estimated refractive index increment (dn/dc) values for the ubiquitous and known frog taxon-specific specific crystallins.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.986 | 0.000 |
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 teacher head, 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".