The Hha and YdgT proteins are suggested to modulate the expression of horizontally acquired genes by interacting with H-NS and StpA, which play central roles in the transcriptional silencing of such genes. However, it is also possible that Hha/YdgT repress gene expression independently of H-NS/StpA, as we have not fully understood the molecular mechanism through which Hha/YdgT modulate H-NS/Stp...

Although recent work has developed systematic procedures and formal methods to help identify unsafe control actions for Systems-Theoretic Process Analysis (STPA) Step 1, the identification of causal factors in STPA Step 2 has received less attention. This research develops additional guidance and procedures that can be used to identify causal factors and build scenarios in STPA Step 2.

Proteins with RNA chaperone activity are able to promote folding of RNA molecules by loosening their structure. This RNA unfolding activity is beneficial when resolving misfolded RNA conformations, but could be detrimental to RNAs with low thermodynamic stability. In order to test this idea, we constructed various RNAs with different structural stabilities derived from the thymidylate synthase ...

Nucleoid-associated proteins are bacterial proteins that are responsible for chromosomal DNA compaction and global gene regulation. One such protein is Escherichia coli Histone-like nucleoid structuring protein (H-NS) which functions as a global gene silencer. Whereas the DNA-binding mechanism of H-NS is well-characterized, its paralogue, StpA which is also able to silence genes is less underst...

Safety becomes a critical aspect for software-intensive systems in different applications areas. Many hazard analysis techniques are proposed and used to investigate system design models to elicit hazards and design flaws. STPA (SystemTheoretic Process Analysis) is a modern hazard analysis technique, which is based on a new systems-theoretic model of accidents for large and complex systems. Wit...

The E. coli protein StpA has RNA annealing and strand displacement activities and it promotes folding of RNAs by loosening their structures. To understand the mode of action of StpA, we analysed the relationship of its RNA chaperone activity to its RNA-binding properties. For acceleration of annealing of two short RNAs, StpA binds both molecules simultaneously, showing that annealing is promote...

 The implementation of autonomous vehicles involves an increase in the number and depth of system interactions in comparison to user-driven cars. There is a corresponding need to address the system safety implications of autonomy. Traditional hazard analysis techniques are not designed to identify hazardous states caused by system interactions. An emerging technique based on systems theory, Sy...

PURPOSE Both humans and software are notoriously challenging to account for in traditional hazard analysis models. The purpose of this work is to investigate and demonstrate the application of a new, extended accident causality model, called systems theoretic accident model and processes (STAMP), to radiation oncology. Specifically, a hazard analysis technique based on STAMP, system-theoretic p...

Security analysis is an essential activity in security engineering to identify potential system vulnerabilities and specify requirements the early design phases. Due increasing complexity of modern systems, traditional approaches lack power insecure incidents caused by complex interactions among physical human social entities. By contrast, System-Theoretic Process Analysis for (STPA-Sec) approa...