Additional file 1 of Ancestral reconstruction reveals catalytic inactivation of activation-induced cytidine deaminase concomitant with cold water adaption in the Gadiformes bony fish
Bibliographic record
Abstract
Additional file 1: Supplementary Figure 1. Comparison of the aicda genomic structure amongst vertebrates. Supplementary Figure 2. Comparison of the aicda synteny amongst vertebrates. Supplementary Figure 3. Atlantic cod AID purification and enzymatic characterization. Supplementary Figure 4. Expression and testing of Gm-AID produced in HEK293T cells. Supplementary Figure 5. Deciphering the basis of the absolute catalytic death of the polar cod AID. Supplementary Figure 6. Amino acid alignment of extant AIDs used for ASR analyses and predicted ancestral sequences. Supplementary Figure 7. Determination of the basic biochemical properties of resurrected ancestral AIDs to determine conditions for measurement of catalytic efficiency. Supplementary Table 1. Comparison of DNA interaction with substrate binding grooves on the surface of AID orthologs. Supplementary Table 2. Comparison of Gm-AIDH136 residue in interaction with -1 position nucleotide upstream of the target dC and total interactions with substrate to its equivalent residue in other AID orthologs. Supplementary Table 3. WRC/GYW enrichment in complementarity determining regions (CDRs) vs. frameworks (FRs) of IgVH genes of various Gadidae and vertebrate species. Supplementary Table 4. WGCW enrichment in complementarity determining regions (CDRs) vs. frameworks (FRs) of IgVH genes of various Gadidae and vertebrate species. Supplementary Table 5. AID hotspot abundance in the entire IgVH genes and GC content of annotated complete protein coding genes (CDSs) of various Gadidae and vertebrate species. Supplementary Table 6. The sequence of primers used in this study. Supplementary Table 7. GenBank accession number of the teleost aicda and Ig genes used in this study.
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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 | 0.009 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.003 | 0.004 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.002 | 0.003 |
| Open science | 0.003 | 0.001 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.766 | 0.160 |
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".