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Whilst he was engaged in travelling through the Bahr-el-Ghazel district, the revolt of the Mahdi occurred, and Emin Pasha was isolated from the outer world.

He entered the Sudan by Suakin on the Red Sea, and crossed the desert to Berber, reaching Khartum on November 1, 1868. He prolonged his stay for three years on the Bahr-el-Ghazel, solely absorbed in scientific studies, and, unlike his predecessors, he was unconcerned with reforms and attempts to suppress the slave-trade.

About the same time three English surveyors, Colonels Purdy, Colston, and Sidney Enser, made several topographical reports on much of the territory between the Bahr-el-Ghazel, the Shari, and the Nile. Later on, in 1876, General Gordon sent Romolo Gesei, an Italian in the service of the khédive, to navigate and to explore Lake Albert Nyanza.

In the sixties, Georg Schweinfurth, a native of Riga, in the Baltic provinces of Russia, set out to explore Nubia, Upper Egypt, and Abyssinia for botanical purposes. Subsequently the Royal Academy of Science in Berlin equipped him for an expedition to explore the region of the Bahr-el-Ghazel.

About the same time Slatin Bey surrendered in Darfur and embraced Muhammedan-ism, and Lupton Bey, following his example, also adopted the religion of Islam, and yielded in Bahr-el-Ghazel. Emin Pasha alone retained his authority, derived originally from Egypt, in the province of Equatoria. Sir H. M. Stanley afterwards made his famous journey "Through Darkest Africa" and rescued this famous pasha.

In 1868 Miss Tinné, nothing-daunted, started for Lake Chad from Tripoli, with the intention of closing in upon the Nile from the eastern sources of the affluents of the Bahr-el-Ghazel. On reaching Wadi-Aberjong, however, this brave-hearted woman was waylaid by the fierce Tuaregs, and was beheaded August 1, 1868.

During the years of 1859 and 1860, an adventurous Dutch lady of fortune, Miss Alexandrine Tinné, journeyed up the Nile as far as Gondokoro, and in 1861 she commenced to organise a daring expedition to find the source of the Bahr-el-Ghazel, and explore the territory between the Nile basin and Lake Chad. She started from Khartum, and ascended the Bahr-el-Ghazel as far as the affluent Bahr-el-Hamad.