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Emerging thorium-based reactor designs and fuel cycles present challenges to traditional non-destructive assay techniques used in international safeguards. Specifically, assaying the masses of 233U and 235U when they are present together in samples with high gamma ray backgrounds is difficult because of similar passive neutron signatures and relatively weak gamma-ray emissions of 233U. The Pacific Northwest National Laboratory (PNNL) and the Massachusetts Institute of Technology (MIT) are developing a portable neutron resonance transmission analysis (pNRTA) system as one potential solution to these challenges. This method provides isotopic concentration data for a sample via neutron time-of-flight (TOF) measurements that exploit epithermal neutron resonance cross-sections. A recently developed pNRTA system uses a commercially available, pulsed deuterium-tritium neutron generator with a ∼2 m flight path and a GS20 lithium glass scintillator detector. This paper describes the prototype pNRTA system design, a refined radiation transport model of the system, preliminary measurements with thorium and uranium sources, and demonstration of a quantitative isotopic estimation algorithm. [ABSTRACT FROM AUTHOR]