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The desire to connect more and more devices and to make them more intelligent and more reliable, is driving the needs for the Internet of Things more than ever. Such IoT edge systems require sound security measures against cyber-attacks, since they are interconnected, spatially distributed, and operational for an extended period of time. One of the most important requirements for the security in many industrial IoT applications is the authentication of the devices. In this paper, we present a mutual authentication protocol based on Physical Unclonable Functions, where challenge-response pairs are used for both device and server authentication. Moreover, a session key can be derived by the protocol in order to secure the communication channel. We show that our protocol is secure against machine learning, replay, man-in-the-middle, cloning, and physical attacks. Moreover, it is shown that the protocol benefits from a smaller computational, communication, storage, and hardware overhead, compared to similar works.