Research and evidence¶
Research pages trace what was measured, in which assay and population, and which model claims those observations can support. They do not turn a paper's reported signal or half-life into a default vaccine rate.
Use the rest of the documentation according to the question at hand:
| Section | Use it for |
|---|---|
| Getting started | Install mhctools, run a first prediction and read its result. |
| User guide | Choose a predictor or workflow, supply inputs and interpret its output. |
| Reference | Look up exact APIs, result fields, units, capabilities and limits. |
| Research | Inspect primary sources, measurement context, validation and what remains unidentifiable. |
Literature reviews already available¶
- mRNA vaccine antigen presentation compares direct APC expression, antigen transfer and cross-dressing. Its measurement extract retains the assay context of 23 macaque and human quantitative observations and a mouse pMHC time course.
- Dose-normalized lymph-node delivery collects primary SC and IM antigen, carrier and RNA measurements with their route, sampled time and denominator. It explains why whole-node percent of dose cannot directly calibrate core-bearing arrival inside APCs.
- Epitope position and peptide flanks asks whether a core near a protein or SLP end is presented more often. It separates controlled terminal-placement experiments from a universal position rule.
- Antigen processing and T-cell responses traces measured changes in processing, surface presentation and T-cell outcomes, which are related but distinct endpoints.
- Human serum peptidase calibration audits 12 studies and 27 reported hormone-stability measurements. It explains why those experiments do not calibrate enzyme hazards for a vaccine peptide.
The cleavage validation audit checks model conformance, source observations and missing independent validation. The protease candidate audit compares released assets and experimental recognition evidence. These are focused evidence and model audits rather than standalone reviews of all antigen processing. The assay-aware benchmark guide explains how to evaluate new measurements without conflating source reproduction with independent testing. The vaccine calibration audit gives physical bounds and shows why published RNA, label and pMHC time courses do not identify core-specific IM transport or intrinsic clearance rates.
Reviews needed for quantitative vaccine exposure¶
- IM SLP fragment transport: find time-resolved measurements of the intact parent and core-bearing fragments at the injection site, in afferent lymph, draining nodes and blood. Preserve route, formulation, species and whether a signal is peptide, label or carrier (exposure issue).
- APC uptake through presentation: seek matched measurements of internalization, productive localization, target-bearing fragments and surface peptide–MHC in the same antigen and APC system. Uptake or reporter fluorescence alone cannot establish an epitope dose fraction (endpoint issue).
- Surface pMHC persistence and transfer: separate newly loaded complexes from acquired preformed complexes, with allele, APC type, time course and loss mechanism recorded. The mRNA review establishes the route but does not supply a transferable lifetime (calibration issue).
- APC endolysosomal cleavage: extend the current source audit to quantitative, condition-matched CatS, CatL, CatB and AEP product maps that identify both epitope generation and destruction (coverage issue).
The SLP/mRNA calibration audit resolves the current identifiability question for the reviewed sources. Source-matched experiments remain necessary before fitted human IM rates can replace explicit scenarios.