TRX: A Formally Verified Parser Interpreter

Parsing is an important problem in computer science and yet surprisingly little attention has been devoted to its formal verification. In this paper, we present TRX: a parser interpreter formally developed in the proof assistant Coq, capable of producing formally correct parsers. We are using parsing expression grammars (PEGs), a formalism essentially representing recursive descent parsing, which we consider an attractive alternative to context-free grammars (CFGs). From this formalization we can extract a parser for an arbitrary PEG grammar with the warranty of total correctness, i.e., the resulting parser is terminating and correct with respect to its grammar and the semantics of PEGs; both properties formally proven in Coq.Comment: 26 pages, LMC

Evolving localizations in reaction-diffusion cellular automata

We consider hexagonal cellular automata with immediate cell neighbourhood and three cell-states. Every cell calculates its next state depending on the integral representation of states in its neighbourhood, i.e. how many neighbours are in each one state. We employ evolutionary algorithms to breed local transition functions that support mobile localizations (gliders), and characterize sets of the functions selected in terms of quasi-chemical systems. Analysis of the set of functions evolved allows to speculate that mobile localizations are likely to emerge in the quasi-chemical systems with limited diffusion of one reagent, a small number of molecules is required for amplification of travelling localizations, and reactions leading to stationary localizations involve relatively equal amount of quasi-chemical species. Techniques developed can be applied in cascading signals in nature-inspired spatially extended computing devices, and phenomenological studies and classification of non-linear discrete systems.Comment: Accepted for publication in Int. J. Modern Physics

The Effects of Haptic Feedback on Postural Sway

Purpose: Effectiveness of haptic feedback on reducing postural sway Hypothesis: Haptic input improves static standing stability. Individuals with increased variability in sway may have an increased risk for falls. Therefore, our haptic feedback device may have the ability to reduce risk of falling. Postural control is a dynamic system involving vision, vestibular system, proprioception, and musculoskeletal system. Postural control enables people to maintain their balance, reduce their sway, and keep an upright posture. Haptic feedback is tactile or vibratory cues that assist a subject in determining where they are in space

Antibody persistence and booster responses to split-virion H5N1 avian influenza vaccine in young and elderly adults

Avian influenza continues to circulate and remains a global health threat not least because of the associated high mortality. In this study antibody persistence, booster vaccine response and cross-clade immune response between two influenza A(H5N1) vaccines were compared. Participants aged over 18-years who had previously been immunized with a clade 1, A/Vietnam vaccine were re-immunized at 6-months with 7.5 mu g of the homologous strain or at 22-months with a clade 2, alum-adjuvanted, A/Indonesia vaccine. Blood sampled at 6, 15 and 22-months after the primary course was used to assess antibody persistence. Antibody concentrations 6-months after primary immunisation with either A/Vietnam vaccine 30 mu g alum-adjuvanted vaccine or 7.5 mu g dose vaccine were lower than 21days after the primary course and waned further with time. Re-immunization with the clade 2, 30 mu g alum-adjuvanted vaccine confirmed cross-clade reactogenicity. Antibody crossreactivity between A(H5N1) clades suggests that in principle a prime-boost vaccination strategy may provide both early protection at the start of a pandemic and improved antibody responses to specific vaccination once available

Resolving the Stellar Populations in a z=4 Lensed Galaxy

We present deep near-infrared Keck/NIRC imaging of a recently-discovered z=4.04 galaxy (Frye & Broadhurst 1998). This is lensed by the rich foreground cluster Abell~2390 (z~0.23) into highly-magnified arcs 3-5arcsec in length. Our H- and K'-band NIRC imaging allows us to map the Balmer+4000Ang break amplitude. In combination with high-quality archival HST/WFPC2 data, we can spatially resolve stellar populations along the arcs. The WFPC2 images clearly reveal several bright knots, which correspond to sites of active star formation. However, there are considerable portions of the arcs are significantly redder, consistent with being observed >100Myr after star formation has ceased. Keck/LRIS long-slit spectroscopy along the arcs reveals that the Ly-alpha emission is spatially offset by ~1arcsec from the rest-UV continuum regions. We show that this line emission is most probably powered by star formation in neighboring HII regions, and that the z=4 system is unlikely to be an AGN.Comment: Accepted for publication in the Astrophysical Journal. Uses emulateapj.sty and graphics.sty (included). 34 pages - has 5 tables and 21 encapsulated postscript figures, 4 in colour mail (B&W versions also provided

Molecular basis for functional switching of GFP by two disparate non-native post-translational modifications of a phenyl azide reaction handle

Through the genetic incorporation of a single phenyl azide group into superfolder GFP (sfGFP) at residue 148 we provide a molecular description of how this highly versatile chemical handle can be used to positively switch protein function in vitro and in vivo via either photochemistry or bioconjugation. Replacement of H148 with p-azido-L-phenylalanine (azF) blue shifts the major excitation peak ∼90 nm by disrupting the H-bond and proton transfer network that defines the chromophore charged state. Bioorthogonal click modification with a simple dibenzylcyclooctyne or UV irradiation shifts the neutral-anionic chromophore equilibrium, switching fluorescence to the optimal ∼490 nm excitation. Click modification also improved quantum yield over both the unmodified and original protein. Crystal structures of both the click modified and photochemically converted forms show that functional switching is due to local conformational changes that optimise the interaction networks surrounding the chromophore. Crystal structure and mass spectrometry studies of the irradiated protein suggest that the phenyl azide converts to a dehydroazepine and/or an azepinone. Thus, protein embedded phenyl azides can be used beyond simple photocrosslinkers and passive conjugation handles, and mimic many natural post-translational modifications: modulation though changes in interaction networks