Central tolerance in the thymus is where developing T-cells that strongly react to the body's own proteins are eliminated. The AIRE gene allows thymic cells to produce a wide range of these self-proteins, acting like a sample menu so the harmful T-cells can be weeded out. But I think we overstate its comprehensiveness, because my own grandfather's autoimmune thyroiditis developed late in life, proving some self-reactive cells still slip through this 'central' net. It's like my old code compiling clean but still having a hidden bug that crashes things years later.
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