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A method of operating a fuel cell system includes providing a fuel inlet stream into a fuel cell stack, operating the fuel cell stack to generate electricity and a hydrogen containing fuel exhaust stream, separating at least a portion of hydrogen contained in the fuel exhaust stream using a cascaded

A method of operating a fuel cell system includes providing a fuel inlet stream into a fuel cell stack, operating the fuel cell stack to generate electricity and a hydrogen containing fuel exhaust stream, separating at least a portion of hydrogen contained in the fuel exhaust stream using a cascaded electrochemical hydrogen pump, such as a high temperature, low hydration ion exchange membrane cell stack having at least two membrane cells arranged in process fluid flow series, and providing the hydrogen separated from the fuel exhaust stream into the fuel inlet stream.

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What is claimed is: 1. A method of operating a fuel cell system, comprising: providing a fuel inlet stream into a fuel cell stack; operating the fuel cell stack to generate electricity and a hydrogen containing fuel exhaust stream; separating at least 95% of hydrogen contained in the fuel exhaust s

What is claimed is: 1. A method of operating a fuel cell system, comprising: providing a fuel inlet stream into a fuel cell stack; operating the fuel cell stack to generate electricity and a hydrogen containing fuel exhaust stream; separating at least 95% of hydrogen contained in the fuel exhaust stream using a cascaded electrochemical hydrogen pump; and providing the hydrogen separated from the fuel exhaust stream into the fuel inlet stream. 2. The method of claim 1, wherein the step of separating comprises separating at least 99% of hydrogen contained in the fuel exhaust stream using the cascaded electrochemical hydrogen pump and wherein the fuel cell stack comprises a SOFC stack and wherein the fuel inlet stream comprises a hydrocarbon fuel inlet stream. 3. The method of claim 2, wherein the step of separating comprises separating about 100% of hydrogen contained in the fuel exhaust stream using the cascaded electrochemical hydrogen pump. 4. The method of claim 1, wherein: the cascaded electrochemical hydrogen pump comprises a high temperature, low hydration ion exchange membrane cell stack; and the membrane cell stack comprises at least one membrane cell arranged in process fluid flow series with at least one other membrane cell. 5. The method of claim 4, wherein the high temperature, low hydration ion exchange membrane cell stack comprises a stack of acid doped non-fluorinated ion exchange ionomer membrane cells. 6. The method of claim 5, wherein each membrane of the membrane cells comprises a polybenzimidazole (PBI) membrane doped with at least one of sulfuric or phosphoric acid. 7. The method of claim 1, further comprising providing a remaining fuel exhaust stream consisting essentially of water and carbon dioxide from the cascaded electrochemical hydrogen pump to a dryer, separating the water from the carbon dioxide in the dryer and sequestering the separated carbon dioxide. 8. The method of claim 7, wherein an entire output of the system comprises the sequestered carbon dioxide, water and oxygen depleted air from a fuel cell stack air exhaust stream. 9. A fuel cell system, comprising: a fuel cell stack; a cascaded electrochemical hydrogen pump; a first conduit which operatively connects a fuel exhaust outlet of the fuel cell stack to a first inlet of the cascaded electrochemical hydrogen pump; and a second conduit which operatively connects a first outlet of the cascaded electrochemical hydrogen pump to a fuel inlet of the fuel cell stack. 10. The system of claim 9, wherein the cascaded electrochemical hydrogen pump is adapted to separate at least 95% of hydrogen contained in a fuel exhaust stream in the first conduit and wherein the fuel cell stack comprises a SOFC stack. 11. The system of claim 10, wherein the cascaded electrochemical hydrogen pump is adapted to separate at least 99% of hydrogen contained in the fuel exhaust stream in the first conduit. 12. The system of claim 11, wherein the cascaded electrochemical hydrogen pump is adapted to separate about 100% of hydrogen contained in the fuel exhaust stream in the first conduit. 13. The system of claim 9, wherein: the cascaded electrochemical hydrogen pump comprises a high temperature, low hydration ion exchange membrane cell stack; and the membrane cell stack comprises at least one membrane cell arranged in process fluid flow series with at least one other membrane cell. 14. The method of claim 13, wherein the high temperature, low hydration ion exchange membrane cell stack comprises a stack of acid doped non-fluorinated ion exchange ionomer membrane cells. 15. The method of claim 14, wherein each membrane of the membrane cells comprises a polybenzimidazole (PBI) membrane doped with at least one of sulfuric or phosphoric acid. 16. The system of claim 9, further comprising at least one of: a first heat exchanger which is adapted to provide heat from a stack fuel exhaust stream to a stack fuel inlet stream; a second heat exchanger which is adapted to provide heat from the stack fuel exhaust stream to an air inlet stream; or a third heat exchanger which is adapted to remove heat from a hydrogen stream after the hydrogen stream is separated from the fuel exhaust stream by the cascaded electrochemical hydrogen pump. 17. The system of claim 9, further comprising a dryer which is connected to an exhaust output of the cascaded electrochemical hydrogen pump, and which in use separates water from carbon dioxide in an exhaust stream of the cascaded electrochemical hydrogen pump. 18. The system of claim 17, further comprising a carbon dioxide storage tank connected to an output of the dryer. 19. The system of claim 9, further comprising a water gas shift reactor and a humidifier. 20. A fuel cell system, comprising: a fuel cell stack; and a first means for separating at least 95% of hydrogen contained in a stack fuel exhaust stream and for providing the hydrogen separated from the fuel exhaust stream into a stack fuel inlet stream.