Additional file 1 of Ancestral reconstruction reveals catalytic inactivation of activation-induced cytidine deaminase concomitant with cold water adaption in the Gadiformes bony fish
Why this work is in the frame
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
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.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.000 |
| 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 | 0.001 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.100 | 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 it