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The term is confusingly used for both atoms and cells, and are only alike in their locations.

In atomic structure, the word was applied in the modern sense in 1912 by Ernest Rutherford, from his experiment that showed a very small solid mass within each atom. The word was used as early as 1844 by Michael Faraday to mean the center of an atom. The word nucleus means 'kernel' which was another term used to describe the central mass, and which was still used for several years after Rutherford's experiments.

In cytology, the term 'lumen' for a cell nucleus was used by Antonie van Leeuwenhoek around 1676. In 1831, Scottish botanist Robert Brown used the terms 'aerola' and 'nucleus' to describe the darker spots he saw within orchid cells.

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