Stateful protocol composition and typing

This is the final version. Available from the publisher via the link in this record.We provide in this AFP entry several relative soundness results for security protocols. In particular, we prove typing and compositionality results for stateful protocols (i.e., protocols with mutable state that may span several sessions), and that focuses on reachability properties. Such results are useful to simplify protocol verification by reducing it to a simpler problem: Typing results give conditions under which it is safe to verify a protocol in a typed model where only "well-typed" attacks can occur whereas compositionality results allow us to verify a composed protocol by only verifying the component protocols in isolation. The conditions on the protocols under which the results hold are furthermore syntactic in nature allowing for full automation. The foundation presented here is used in another entry to provide fully automated and formalized security proofs of stateful protocols

Stateful protocol composition

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this recordWe prove a parallel compositionality result for protocols with a shared mutable state, i.e., stateful protocols. For protocols satisfying certain compositionality conditions our result shows that verifying the component protocols in isolation is sufficient to prove security of their composition. Our main contribution is an extension of the compositionality paradigm to stateful protocols where participants maintain shared databases. Because of the generality of our result we also cover many forms of sequential composition as a special case of stateful parallel composition. Moreover, we support declassification of shared secrets. As a final contribution we prove the core of our result in Isabelle/HOL, providing a strong correctness guarantee of our proofs.Danish Council for Independent Research

Automated stateful protocol verification

This is the final version. Available from the publisher via the link in this record.In protocol verification we observe a wide spectrum from fully automated methods to interactive theorem proving with proof assistants like Isabelle/HOL. In this AFP entry, we present a fully-automated approach for verifying stateful security protocols, i.e., protocols with mutable state that may span several sessions. The approach supports reachability goals like secrecy and authentication. We also include a simple user-friendly transaction-based protocol specification language that is embedded into Isabelle

Bandit Models of Human Behavior: Reward Processing in Mental Disorders

Drawing an inspiration from behavioral studies of human decision making, we propose here a general parametric framework for multi-armed bandit problem, which extends the standard Thompson Sampling approach to incorporate reward processing biases associated with several neurological and psychiatric conditions, including Parkinson's and Alzheimer's diseases, attention-deficit/hyperactivity disorder (ADHD), addiction, and chronic pain. We demonstrate empirically that the proposed parametric approach can often outperform the baseline Thompson Sampling on a variety of datasets. Moreover, from the behavioral modeling perspective, our parametric framework can be viewed as a first step towards a unifying computational model capturing reward processing abnormalities across multiple mental conditions.Comment: Conference on Artificial General Intelligence, AGI-1

Performing Security Proofs of Stateful Protocols

This is the author accepted manuscript. The final version is available from IEEE via the DOI in this recordIn protocol verification we observe a wide spectrum from fully automated methods to interactive theorem proving with proof assistants like Isabelle/HOL. The latter provide overwhelmingly high assurance of the correctness, which automated methods often cannot: due to their complexity, bugs in such automated verification tools are likely and thus the risk of erroneously verifying a flawed protocol is non-negligible. There are a few works that try to combine advantages from both ends of the spectrum: a high degree of automation and assurance. We present here a first step towards achieving this for a more challenging class of protocols, namely those that work with a mutable long-term state. To our knowledge this is the first approach that achieves fully automated verification of stateful protocols in an LCF-style theorem prover. The approach also includes a simple user-friendly transaction-based protocol specification language embedded into Isabelle, and can also leverage a number of existing results such as soundness of a typed model.Danish Council for Independent ResearchEuropean Union Horizon 202

Order of Magnitude Smaller Limit on the Electric Dipole Moment of the Electron

The Standard Model of particle physics is known to be incomplete. Extensions to the Standard Model, such as weak-scale supersymmetry, posit the existence of new particles and interactions that are asymmetric under time reversal (T) and nearly always predict a small yet potentially measurable electron electric dipole moment (EDM), d_e, in the range of 10^(−27) to 10^(−30) e·cm. The EDM is an asymmetric charge distribution along the electron spin (S) that is also asymmetric under T. Using the polar molecule thorium monoxide, we measured d_e = (–2.1±3.7_(stat)±2.5_(syst)) × 10−29 e·cm. This corresponds to an upper limit of ❘d_e❘ < 8.7 × 10^(−29) e·cm with 90% confidence, an order of magnitude improvement in sensitivity relative to the previous best limit. Our result constrains T-violating physics at the TeV energy scale

Memory for medication side effects in younger and older adults: the role of subjective and objective importance

Older adults often experience memory impairments, but can sometimes use selective processing and schematic support to remember important information. The current experiments investigate to what degree younger and healthy older adults remember medication side effects that were subjectively or objectively important to remember. Participants studied a list of common side effects, and rated how negative these effects were if they were to experience them, and were then given a free recall test. In Experiment 1, the severity of the side effects ranged from mild (e.g., itching) to severe (e.g., stroke), and in Experiment 2, certain side effects were indicated as critical to remember (i.e., “contact your doctor if you experience this”). There were no age differences in terms of free recall of the side effects, and older adults remembered more severe side effects relative to mild effects. However, older adults were less likely to recognize critical side effects on a later recognition test, relative to younger adults. The findings suggest that older adults can selectively remember medication side effects, but have difficulty identifying familiar but potentially critical side effects, and this has implications for monitoring medication use in older age

Complete chloroplast genome sequence of Holoparasite Cistanche Deserticola (Orobanchaceae) reveals gene loss and horizontal gene transfer from Its host Haloxylon Ammodendron (Chenopodiaceae)

The central function of chloroplasts is to carry out photosynthesis, and its gene content and structure are highly conserved across land plants. Parasitic plants, which have reduced photosynthetic ability, suffer gene losses from the chloroplast (cp) genome accompanied by the relaxation of selective constraints. Compared with the rapid rise in the number of cp genome sequences of photosynthetic organisms, there are limited data sets from parasitic plants. The authors report the complete sequence of the cp genome of Cistanche deserticola, a holoparasitic desert species belonging to the family Orobanchaceae

Identification of Key Residues for pH Dependent Activation of Violaxanthin De-Epoxidase from Arabidopsis thaliana

Plants are often exposed to saturating light conditions, which can lead to oxidative stress. The carotenoid zeaxanthin, synthesized from violaxanthin by Violaxanthin De-Epoxidase (VDE) plays a major role in the protection from excess illumination. VDE activation is triggered by a pH reduction in the thylakoids lumen occurring under saturating light. In this work the mechanism of the VDE activation was investigated on a molecular level using multi conformer continuum electrostatic calculations, site directed mutagenesis and molecular dynamics. The pKa values of residues of the inactive VDE were determined to identify target residues that could be implicated in the activation. Five such target residues were investigated closer by site directed mutagenesis, whereas variants in four residues (D98, D117, H168 and D206) caused a reduction in enzymatic activity indicating a role in the activation of VDE while D86 mutants did not show any alteration. The analysis of the VDE sequence showed that the four putative activation residues are all conserved in plants but not in diatoms, explaining why VDE in these algae is already activated at higher pH. Molecular dynamics showed that the VDE structure was coherent at pH 7 with a low amount of water penetrating the hydrophobic barrel. Simulations carried out with the candidate residues locked into their protonated state showed instead an increased amount of water penetrating the barrel and the rupture of the H121–Y214 hydrogen bond at the end of the barrel, which is essential for VDE activation. These results suggest that VDE activation relies on a robust and redundant network, in which the four residues identified in this study play a major role

Bright ligand-activatable fluorescent protein for high-quality multicolor live-cell super-resolution microscopy

We introduce UnaG as a green-to-dark photoswitching fluorescent protein capable of high-quality super-resolution imaging with photon numbers equivalent to the brightest photoswitchable red protein. UnaG only fluoresces upon binding of a fluorogenic metabolite, bilirubin, enabling UV-free reversible photoswitching with easily controllable kinetics and low background under Epi illumination. The on- and off-switching rates are controlled by the concentration of the ligand and the excitation light intensity, respectively, where the dissolved oxygen also promotes the off-switching. The photo-oxidation reaction mechanism of bilirubin in UnaG suggests that the lack of ligand-protein covalent bond allows the oxidized ligand to detach from the protein, emptying the binding cavity for rebinding to a fresh ligand molecule. We demonstrate super-resolution single-molecule localization imaging of various subcellular structures genetically encoded with UnaG, which enables facile labeling and simultaneous multicolor imaging of live cells. UnaG has the promise of becoming a default protein for high-performance super-resolution imaging. Photoconvertible proteins occupy two color channels thereby limiting multicolour localisation microscopy applications. Here the authors present UnaG, a new green-to-dark photoswitching fluorescent protein for super-resolution imaging, whose activation is based on a noncovalent binding with bilirubin