Least-biased correction of extended dynamical systems using observational data

We consider dynamical systems evolving near an equilibrium statistical state where the interest is in modelling long term behavior that is consistent with thermodynamic constraints. We adjust the distribution using an entropy-optimizing formulation that can be computed on-the- fly, making possible partial corrections using incomplete information, for example measured data or data computed from a different model (or the same model at a different scale). We employ a thermostatting technique to sample the target distribution with the aim of capturing relavant statistical features while introducing mild dynamical perturbation (thermostats). The method is tested for a point vortex fluid model on the sphere, and we demonstrate both convergence of equilibrium quantities and the ability of the formulation to balance stationary and transient- regime errors.Comment: 27 page

Entanglement of two qubits in a relativistic orbit

The creation and destruction of entanglement between a pair of interacting two-level detectors accelerating about diametrically opposite points of a circular path is investigated. It is found that any non-zero acceleration has the effect of suppressing the vacuum entanglement and enhancing the acceleration radiation thereby reducing the entangling capacity of the detectors. Given that for large accelerations the acceleration radiation is the dominant effect, we investigate the evolution of a two detector system initially prepared in a Bell state using a perturbative mater equation and treating the vacuum fluctuations as an unobserved environment. A general function for the concurrence is obtained for stationary and symmetric worldlines in flatspace. The entanglement sudden death time is computed.Comment: v2: Some typo's fixed, figures compressed to smaller filesize and added some references

Simplified Modelling of a Thermal Bath, with Application to a Fluid Vortex System

Based on the thermodynamic concept of a reservoir, we investigate a computational model for interaction with unresolved degrees of freedom (a thermal bath). We assume that a finite restricted system can be modelled by a generalized canonical ensemble, described by a density which is a smooth function of the energy of the restricted system. A thermostat is constructed to continuously perturb the resolved dynamics, while leaving the desired equilibrium distribution invariant. We build on a thermostatting framework developed and tested in the setting of molecular dynamics, using stochastic perturbations to control (and stabilize) the invariant measure. We also apply these techniques in the setting of a simplified point vortex flow on a disc, in which a modified Gibbs distribution (modelling a finite, rather than infinite, bath of weak vortices) provides a regularizing formulation for restricted system dynamics. Numerical experiments, effectively replacing many vortices by a few artificial degrees of freedom, are in excellent agreement with the two-scale simulations of Bühler. © 2010 Society for Industrial and Applied Mathematics

Lynch Syndrome Associated with Two MLH1 Promoter Variants and Allelic Imbalance of MLH1 Expression

© 2015 The Authors. **Human Mutation published by Wiley Periodicals, Inc. Lynch syndrome is a hereditary cancer syndrome caused by a constitutional mutation in one of the mismatch repair genes. The implementation of predictive testing and targeted preventative surveillance is hindered by the frequent finding of sequence variants of uncertain significance in these genes. We aimed to determine the pathogenicity of previously reported variants (c.-28A > G and c.-7C > T) within the MLH1 5â²untranslated region (UTR) in two individuals from unrelated suspected Lynch syndrome families. We investigated whether these variants were associated with other pathogenic alterations using targeted high-throughput sequencing of the MLH1 locus. We also determined their relationship to gene expr ession and epigenetic alterations at the promoter. Sequencing revealed that the c.-28A > G and c.-7C > T variants were the only potentially pathogenic alterations within the MLH1 gene. In both individuals, the levels of transcription from the variant allele were reduced to 50% compared with the wild-type allele. Partial loss of expression occurred in the absence of constitutional epigenetic alterations within the MLH1 promoter. We propose that these variants may be pathogenic due to constitutional partial loss of MLH1 expression, and that this may be associated with intermediate penetrance of a Lynch syndrome phenotype. Our findings provide further evidence of the potential importance of noncoding variants in the MLH1 5â²UTR in the pathogenesis of Lynch syndrome.Link_to_subscribed_fulltex

Adaptive Radiation Therapy (ART) Strategies and Technical Considerations: A State of the ART Review From NRG Oncology

The integration of adaptive radiation therapy (ART), or modifying the treatment plan during the treatment course, is becoming more widely available in clinical practice. ART offers strong potential for minimizing treatment-related toxicity while escalating or de-escalating target doses based on the dose to organs at risk. Yet, ART workflows add complexity into the radiation therapy planning and delivery process that may introduce additional uncertainties. This work sought to review presently available ART workflows and technological considerations such as image quality, deformable image registration, and dose accumulation. Quality assurance considerations for ART components and minimum recommendations are described. Personnel and workflow efficiency recommendations are provided, as is a summary of currently available clinical evidence supporting the implementation of ART. Finally, to guide future clinical trial protocols, an example ART physician directive and a physics template following standard NRG Oncology protocol is provided

Precise Doppler Monitoring of Barnard's Star

We present 248 precise Doppler measurements of Barnard's Star (Gl 699), the second nearest star system to Earth, obtained from Lick and Keck Observatories during 25 years between 1987 and 2012. The early precision was 20 \ms{} but was 2 \ms{} during the last 8 years, constituting the most extensive and sensitive search for Doppler signatures of planets around this stellar neighbor. We carefully analyze the 136 Keck radial velocities spanning 8 years by first applying a periodogram analysis to search for nearly circular orbits. We find no significant periodic Doppler signals with amplitudes above $\sim$2 \ms{}, setting firm upper limits on the minimum mass (\msini) of any planets with orbital periods from 0.1 to 1000 days. Using a Monte Carlo analysis for circular orbits, we determine that planetary companions to Barnard's Star with masses above 2 \mearth{} and periods below 10 days would have been detected. Planets with periods up to 2 years and masses above 10 \mearth{} (0.03 \mjup) are also ruled out. A similar analysis allowing for eccentric orbits yields comparable mass limits. The habitable zone of Barnard's Star appears to be devoid of roughly Earth-mass planets or larger, save for face-on orbits. Previous claims of planets around the star by van de Kamp are strongly refuted. The radial velocity of Barnard's Star increases with time at $4.515\pm0.002$ \msy{}, consistent with the predicted geometrical effect, secular acceleration, that exchanges transverse for radial components of velocity.Comment: 21 pages & 11 figures; accepted to ApJ for publication; revision comments: the conclusions and results remain unchanged, removed the last paragraph in section 4.2, a few minor changes to the text, replaced figure 7 with figures 7 and 8, corrected typos in the rv data tables (tables 2 and 3, data downloadable from ApJ

A rocky planet transiting a nearby low-mass star

M-dwarf stars -- hydrogen-burning stars that are smaller than 60 per cent of the size of the Sun -- are the most common class of star in our Galaxy and outnumber Sun-like stars by a ratio of 12:1. Recent results have shown that M dwarfs host Earth-sized planets in great numbers: the average number of M-dwarf planets that are between 0.5 to 1.5 times the size of Earth is at least 1.4 per star. The nearest such planets known to transit their star are 39 parsecs away, too distant for detailed follow-up observations to measure the planetary masses or to study their atmospheres. Here we report observations of GJ 1132b, a planet with a size of 1.2 Earth radii that is transiting a small star 12 parsecs away. Our Doppler mass measurement of GJ 1132b yields a density consistent with an Earth-like bulk composition, similar to the compositions of the six known exoplanets with masses less than six times that of the Earth and precisely measured densities. Receiving 19 times more stellar radiation than the Earth, the planet is too hot to be habitable but is cool enough to support a substantial atmosphere, one that has probably been considerably depleted of hydrogen. Because the host star is nearby and only 21 per cent the radius of the Sun, existing and upcoming telescopes will be able to observe the composition and dynamics of the planetary atmosphere.Comment: Published in Nature on 12 November 2015, available at http://dx.doi.org/10.1038/nature15762. This is the authors' version of the manuscrip

Brevi spunti sul d.lgs. n. 150/2009 e sulla sua applicabilità agli Enti locali

© 2014 Taylor & Francis Group, LLC. Gene silencing in cancer frequently involves hypermethylation and dense nucleosome occupancy across promoter regions. How a promoter transitions to this silent state is unclear. Using colorectal adenomas, we investigated nucleosome positioning, DNA methylation, and gene expression in the early stages of gene silencing. Genome-wide gene expression correlated with highly positioned nucleosomes upstream and downstream of a nucleosome-depleted transcription start site (TSS). Hypermethylated promoters displayed increased nucleosome occupancy, specifically at the TSS. We investigated 2 genes, CDH1 and CDKN2B, which were silenced in adenomas but lacked promoter hypermethylation. Instead, silencing correlated with loss of nucleosomes from the -2 position upstream of the TSS relative to normal mucosa. In contrast, permanent CDH1 silencing in carcinoma cells was characterized by promoter hypermethylation and dense nucleosome occupancy. Our findings suggest that silenced genes transition through an intermediary stage involving altered promoter nucleosome positioning, before permanent silencing by hypermethylation and dense nucleosome occupancy.Link_to_subscribed_fulltex