Categorical selection of the Ig CDR-H3 repertoire in splenic B cells (83.14)
Bibliographic record
Abstract
Abstract H chain CDR-H3 serves as the focus of the diveristy of the antibody repertoire. Repertoire development in the bone marrow is associated with a reduction of specific categories of CDR-H3, particularly those with excessive hydrophobic or polar (charged) amino acids and those with a length of eight or fewer amino acids. To test whether CDR-H3 selection continues within the spleen, we sorted B cells into transitional (T1), marginal zone (MZ) and follicular (FO) populations; cloned 364 unique, in-frame, open V7183DJCμ transcripts; and compared them to 509 previously obtained sequences from immature (IM) and mature, recirculating (MA) bone marrow B cells. The T1 CDR-H3 repertoire shared extensive similarity of length and loop amino acid hydrophobicity to that of IM CDR-H3s, whereas FO CDR-H3s most resembled that of MA B cells. MZ CDR-H3s averaged one half-codon shorter than IM and T1 CDR-H3s, and a full codon shorter than FO and MA CDR-H3s (p<0.05 and p<0.005, respectively). 13% (20/151) of MZ CDR-H3s contained 8 or fewer amino acids, versus only 4% (9/254) MB CDR-H3s [p<0.001]. MZ CDR-H3s were also enriched for highly charged CDR-H3s, representing 5.3% (8/151) of the transcripts versu only 0.4% (1/254)among MB CDR-H3s. Unlike the splenic F0 and bone marrow MA CDR-H3 repertoires, the MZ appears to be a reservoir for short and highly charged CDR-H3s amino acid motifs, including those with two or more arginines. The latter in particular has been associated with self-reactive specificities. Our findings suggest that specific categories of CDR-H3 sequence content may inhibit, permit, or even facilitate passage of the host B cell through critical checkpoints in central as well as peripheral development. Supported by HD043327, AI42732, and AI48115.
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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 | 0.000 | 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 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 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".