Structure determination of Split-soret Cytochrome from a Desulfovibrio species isolated from a human abdominal abcess

The determined structure of the split-soret cytochrome (SSC) isolated from Desulfovibrio desulfuricans ATCC 27774 (D.d.) revealed a new Heme arrangement, which suggests that this protein constitutes a new cytochrome class.. SSC is a 52.6kDa homodimer containing four hemes at one end of the molecule. In each monomer the two hemes have their edges overlapped within van der Waals contacts. The polypeptide chain of each monomer supplies the sixth ligand to the heme-iron of the other monomer. A similar protein was recently purified from a homologous Desulfovibrio clinical strain isolated from an abdominal wall abscess in human patient2. Crystals of this SSC were grown using vapour diffusion method in the presence of agarose gel. Diffraction data were collected using X-ray synchrotron radiation at the ESRF, beamline, ID 14-1. The structure will be solved by molecular replacement using the structure of the D.d. as a starting model

Behavior of a Model Dynamical System with Applications to Weak Turbulence

We experimentally explore solutions to a model Hamiltonian dynamical system derived in Colliander et al., 2012, to study frequency cascades in the cubic defocusing nonlinear Schr\"odinger equation on the torus. Our results include a statistical analysis of the evolution of data with localized amplitudes and random phases, which supports the conjecture that energy cascades are a generic phenomenon. We also identify stationary solutions, periodic solutions in an associated problem and find experimental evidence of hyperbolic behavior. Many of our results rely upon reframing the dynamical system using a hydrodynamic formulation.Comment: 22 pages, 14 figure

On the Nonlinear Stability of Asymptotically Anti-de Sitter Solutions

Despite the recent evidence that anti-de Sitter spacetime is nonlinearly unstable, we argue that many asymptotically anti-de Sitter solutions are nonlinearly stable. This includes geons, boson stars, and black holes. As part of our argument, we calculate the frequencies of long-lived gravitational quasinormal modes of AdS black holes in various dimensions. We also discuss a new class of asymptotically anti-de Sitter solutions describing noncoalescing black hole binaries.Comment: 26 pages. 5 figure

Effective numerical simulation of the Klein–Gordon–Zakharov system in the Zakharov limit

Solving the Klein-Gordon-Zakharov (KGZ) system in the high-plasma frequency regime $c\gg1$ is numerically severely challenging due to the highly oscillatory nature or the problem. To allow reliable approximations classical numerical schemes require severe step size restrictions depending on the small parameter $c^{−2}$ . This leads to large errors and huge computational costs. In the singular limit $c\to\infty$ the Zakharov system appears as the regular limit system for the KGZ system. It is the purpose of this paper to use this approximation in the construction of an effective numerical scheme for the KGZ system posed on the torus in the highly oscillatory regime $c\gg1$. The idea is to filter out the highly oscillatory phases explicitly in the solution. This allows us to play back the numerical task to solving the non-oscillatory Zakharov limit system. The latter can be solved very efficiently without any step size restrictions. The numerical approximation error is then estimated by showing that solutions of the KGZ system in this singular limit can be approximated via the solutions of the Zakharov system and by proving error estimates for the numerical approximation of the Zakharov system. We close the paper with numerical experiments which show that this method is more effective than other methods in the high-plasma frequency regime $c\gg1$

Non-ergodicity of Nose-Hoover dynamics

The numerical integration of the Nose-Hoover dynamics gives a deterministic method that is used to sample the canonical Gibbs measure. The Nose-Hoover dynamics extends the physical Hamiltonian dynamics by the addition of a "thermostat" variable, that is coupled nonlinearly with the physical variables. The accuracy of the method depends on the dynamics being ergodic. Numerical experiments have been published earlier that are consistent with non-ergodicity of the dynamics for some model problems. The authors recently proved the non-ergodicity of the Nose-Hoover dynamics for the one-dimensional harmonic oscillator. In this paper, this result is extended to non-harmonic one-dimensional systems. It is also shown for some multidimensional systems that the averaged dynamics for the limit of infinite thermostat "mass" have many invariants, thus giving theoretical support for either non-ergodicity or slow ergodization. Numerical experiments for a two-dimensional central force problem and the one-dimensional pendulum problem give evidence for non-ergodicity

BMJ Open

Objective To compare the effectiveness of the mobile e-Tabac Info Service (e-TIS) application (app) for helping adult smokers quit smoking with current practices. Design Pragmatic randomised controlled trial with a 1-year follow-up (2017–2018). Setting France, population-wide level. Participants 2806 adult smokers who wished to quit smoking were recruited via the website of the French National Mandatory Health Insurance fund. Of them, 1400 were randomised to the e-TIS app arm and 1406 were randomised to the current practices arm (control). Intervention The app involved personalised interactive contacts that included questionnaires, advice, activities and text messages. All contacts were individually tailored and based on each smoker’s progress. In the control group, recommended practices for quitting smoking were described on a non-interactive website. Primary and secondary outcomes measures The primary outcome was 7-day point prevalence abstinence (PPA) at 6 months. The secondary outcomes included continuous abstinence rates at 6 and 12 months, minimum 24-hour point abstinence at 3 months, minimum 30-day point abstinence at 12 months and number and duration of quit attempts. Results There was no difference between the e-TIS and control arms for the primary outcome (12.6% vs 13.7% for 7-day PPA at 6 months, p=0.3949, intention-to-treat analysis). However, e-TIS participants with high levels of exposure to the app, which was defined by the completion of at least eight activities or questionnaires, showed higher rates of smoking cessation than the control participants (17.6% vs 12.9% for 7-day PPA at 6 months, p=0.0169, per-protocol analysis). Conclusion Use of the e-TIS app was not associated with a higher rate of smoking cessation. However, high level of exposure to the e-TIS app may have been more effective than current practices

Longitudinal stroke recovery associated with dysregulation of complement system - A proteomics pathway analysis

Currently the longitudinal proteomic profile of post-ischemic stroke recovery is relativelyunknown with few well-accepted biomarkers or understanding of the biological systemsthat underpin recovery. We aimed to characterize plasma derived biological pathwaysassociated with recovery during the first year post event using a discovery proteomicsworkflow coupled with a topological pathway systems biology approach. Blood samples(n = 180, ethylenediaminetetraacetic acid plasma) were collected from a subgroup of60 first episode stroke survivors from the Australian START study at 3 timepoints: 3–7days (T1), 3-months (T2) and 12-months (T3) post-stroke. Samples were analyzed byliquid chromatography mass spectrometry using label-free quantification (data availableat ProteomeXchange with identifier PXD015006). Differential expression analysis revealedthat 29 proteins between T1 and T2, and 33 proteins between T1 and T3 weresignificantly different, with 18 proteins commonly differentially expressed across thetwo time periods. Pathway analysis was conducted using Gene Graph EnrichmentAnalysis on both the Kyoto Encyclopedia of Genes and Genomes and Reactomedatabases. Pathway analysis revealed that the significantly differentiated proteinsbetween T1 and T2 were consistently found to belong to the complement pathway.Further correlational analyses utilized to examine the changes in regulatory effects ofproteins over time identified significant inhibitory regulation of clusterin on complementcomponent 9. Longitudinal post-stroke blood proteomics profiles suggest that thealternative pathway of complement activation remains in a state of higher activation from3-7 days to 3 months post-stroke, while simultaneously being regulated by clusterin andvitronectin. These findings also suggest that post-stroke induced sterile inflammation andimmunosuppression could inhibit recovery within the 3-month window post-stroke