Statistical Analysis of Tritium Breeding Ratio Deviations in the DEMO Due to Nuclear Data Uncertainties

For the stable and self-sufficient functioning of the DEMO fusion reactor, one of the most important parameters that must be demonstrated is the Tritium Breeding Ratio (TBR). The reliable assessment of the TBR with safety margins is a matter of fusion reactor viability. The uncertainty of the TBR in the neutronic simulations includes many different aspects such as the uncertainty due to the simplification of the geometry models used, the uncertainty of the reactor layout and the uncertainty introduced due to neutronic calculations. The last one can be reduced by applying high fidelity Monte Carlo simulations for TBR estimations. Nevertheless, these calculations have inherent statistical errors controlled by the number of neutron histories, straightforward for a quantity such as that of TBR underlying errors due to nuclear data uncertainties. In fact, every evaluated nuclear data file involved in the MCNP calculations can be replaced with the set of the random data files representing the particular deviation of the nuclear model parameters, each of them being correct and valid for applications. To account for the uncertainty of the nuclear model parameters introduced in the evaluated data file, a total Monte Carlo (TMC) method can be used to analyze the uncertainty of TBR owing to the nuclear data used for calculations. To this end, two 3D fully heterogeneous geometry models of the helium cooled pebble bed (HCPB) and water cooled lithium lead (WCLL) European DEMOs were utilized for the calculations of the TBR. The TMC calculations were performed, making use of the TENDL-2017 nuclear data library random files with high enough statistics providing a well-resolved Gaussian distribution of the TBR value. The assessment was done for the estimation of the TBR uncertainty due to the nuclear data for entire material compositions and for separate materials: structural, breeder and neutron multipliers. The overall TBR uncertainty for the nuclear data was estimated to be 3~4% for the HCPB and WCLL DEMOs, respectivel

Atlas: analysis tools for low-depth and ancient samples

Summary: Post-mortem damage (PMD) obstructs the proper analysis of ancient DNA samples and can currently only be addressed by removing or down-weighting potentially damaged data. Here we present ATLAS, a suite of methods to accurately genotype and estimate genetic diversity from ancient samples, while accounting for PMD. It works directly from raw BAM files and enables the building of complete and customized pipelines for the analysis of ancient and other low-depth samples in a very user-friendly way. Based on simulations we show that, in the presence of PMD, a dedicated pipeline of ATLAS calls genotypes more accurately than the state-of-the-art pipeline of GATK combined with mapDamage 2.0. Availability: ATLAS is an open- source C++ program freely available at https://bitbucket.org/phaentu/atlas

Rebirth of X-ray Emission from the Born-Again Planetary Nebula A 30

The planetary nebula (PN) A30 is believed to have undergone a very late thermal pulse resulting in the ejection of knots of hydrogen-poor material. Using HST images we have detected the angular expansion of these knots and derived an age of 850+280-150 yr. To investigate the spectral and spatial properties of the soft X-ray emission detected by ROSAT, we have obtained Chandra and XMM-Newton observations of A30. The X-ray emission from A30 can be separated into two components: a point-source at the central star and diffuse emission associated with the hydrogen-poor knots and the cloverleaf structure inside the nebular shell. To help us assess the role of the current stellar wind in powering this X-ray emission, we have determined the stellar parameters of the central star of A 30 using a non-LTE model fit to its optical and UV spectrum. The spatial distribution and spectral properties of the diffuse X-ray emission is suggestive that it is generated by the post-born-again and present fast stellar winds interacting with the hydrogen-poor ejecta of the born-again event. This emission can be attributed to shock-heated plasma, as the hydrogen-poor knots are ablated by the stellar winds, under which circumstances the efficient mass-loading of the present fast stellar wind raises its density and damps its velocity to produce the observed diffuse soft X-rays. Charge transfer reactions between the ions of the stellar winds and material of the born-again ejecta has also been considered as a possible mechanism for the production of diffuse X-ray emission, and upper limits on the expected X-ray production by this mechanism have been derived. The origin of the X-ray emission from the central star of A 30 is puzzling: shocks in the present fast stellar wind and photospheric emission can be ruled out, while the development of a new, compact hot bubble confining the fast stellar wind seems implausible.Comment: 29 pages, 11 figures, 4 tables; accepted for publication by Ap

The IL-17 receptor IL-17RE mediates polyIC-induced exacerbation of experimental allergic asthma

Background: The interleukin 17 receptor E (IL-17RE) is specific for the epithelial cytokine interleukin-17C (IL-17C). Asthma exacerbations are frequently caused by viral infections. Polyinosinic:polycytidylic acid (pIC) mimics viral infections through binding to pattern recognition receptors (e.g. TLR-3). We and others have shown that pIC induces the expression of IL-17C in airway epithelial cells. Using different mouse models, we aimed to investigate the function of IL-17RE in the development of experimental allergic asthma and acute exacerbation thereof. Methods: Wild-type (WT) and IL-17RE deficient (Il-17re−/− ) mice were sensitized and challenged with OVA to induce allergic airway inflammation. pIC or PBS were applied intranasally when allergic airway inflammation had been established. Pulmonary expression of inflammatory mediators, numbers of inflammatory cells, and airway hyperresponsiveness (AHR) were analyzed. Results: Ablation of IL-17RE did not affect the development of OVA-induced allergic airway inflammation and AHR. pIC induced inflammation independent of IL-17RE in the absence of allergic airway inflammation. Treatment of mice with pIC exacerbated pulmonary inflammation in sensitized and OVA-challenged mice in an IL-17REdependent manner. The pIC-induced expression of cytokines (e.g. keratinocyte-derived chemokine (KC), granulocyte-colony stimulating factor (G-CSF)) and recruitment of neutrophils were decreased in Il-17re−/− mice. pIC-exacerbated AHR was partially decreased in Il-17re−/− mice. Conclusions: Our results indicate that IL-17RE mediates virus-triggered exacerbations but does not have a function in the development of allergic lung disease

An Automated, Language-Based Approach to the Creation of Component Libraries

A major promise of component-based software engineering is the reduction of application development time and costs by reusing software components. The existence of and access to component libraries, as well as the ability to build such libraries in the first place, is therefore key in a component-based development infrastructure to facilitate the envisioned reuse. We believe that the future demand for component libraries will increase substantially because many companies are about to adopt the software product line ideas. Due to the lack of a general standard for component libraries and because of the restrictions of existing ones, it is very often the case that new reuse libraries are written from scratch to fit a user's specific requirements. An additional problem is the size and the focus of (existing) component libraries or component repositories. With an increasing size and a broadening focus of the library it becomes harder to retrieve the "right" components due to more complex classification structures, which hinders effective reuse. This will lead to a large number of specific libraries, rather than to the global all-encompassing single one. This work introduces a component library description language, which allows for the definition of a component library, its provided functionality, and its associated semantics on a high level of abstraction. The language compiler uses those definitions made in the (XML-based) language to automatically generate a component library, which is a user-defined, customized application, including a web-based user interface and a persistent storage facility to store the components handled by the library. The language approach allows for the rapid development of domain specific component libraries in a time and cost efficient manner and therefore supports the need for fast creation of reuse libraries with minimal up-front investment

Simultaneous Swift X-ray and UV views of comet C/2007 N3 (Lulin)

We present an analysis of simultaneous X-Ray and UV observations ofcomet C/2007 N3 (Lulin) taken on three days between January 2009 and March 2009 using the Swift observatory. For our X-ray observations, we used basic transforms to account for the movement of the comet to allow the combination of all available data to produce an exposure-corrected image. We fit a simple model to the extracted spectrum and measured an X-ray flux of 4.3+/-1.3 * 10^-13 ergs cm-2 s-1 in the 0.3 to 1.0 keV band. In the UV, we acquired large-aperture photometry and used a coma model to derive water production rates given assumptions regarding the distribution of water and its dissociation into OH molecules about the comet's nucleus. We compare and discuss the X-ray and UV morphology of the comet. We show that the peak of the cometary X-ray emission is offset sunward of the UV peak emission, assumed to be the nucleus, by approximately 35,000 km. The offset observed, the shape of X-ray emission and the decrease of the X-ray emission comet-side of the peak, suggested that the comet was indeed collisionally thick to charge exchange, as expected from our measurements of the comet's water production rate (6--8 10^28 mol. s-1). The X-ray spectrum is consistent with solar wind charge exchange emission, and the comet most likely interacted with a solar wind depleted of very highly ionised oxygen. We show that the measured X-ray lightcurve can be very well explained by variations in the comet's gas production rates, the observing geometry and variations in the solar wind flux.Comment: Paper accepted for publication in Astronomy and Astrophysics, 6 March 2012, 12 pages, 8 colour figures, one tabl

Spectral Analysis of the Chandra Comet Survey

We present results of the analysis of cometary X-ray spectra with an extended version of our charge exchange emission model (Bodewits et al. 2006). We have applied this model to the sample of 8 comets thus far observed with the Chandra X-ray observatory and ACIS spectrometer in the 300-1000 eV range. The surveyed comets are C/1999 S4 (LINEAR), C/1999 T1 (McNaught-Hartley), C/2000 WM1 (LINEAR), 153P/2002 (Ikeya-Zhang), 2P/2003 (Encke), C/2001 Q4 (NEAT), 9P/2005 (Tempel 1) and 73P/2006-B (Schwassmann-Wachmann 3) and the observations include a broad variety of comets, solar wind environments and observational conditions. The interaction model is based on state selective, velocity dependent charge exchange cross sections and is used to explore how cometary X-ray emission depend on cometary, observational and solar wind characteristics. It is further demonstrated that cometary X-ray spectra mainly reflect the state of the local solar wind. The current sample of Chandra observations was fit using the constrains of the charge exchange model, and relative solar wind abundances were derived from the X-ray spectra. Our analysis showed that spectral differences can be ascribed to different solar wind states, as such identifying comets interacting with (I) fast, cold wind, (II), slow, warm wind and (III) disturbed, fast, hot winds associated with interplanetary coronal mass ejections. We furthermore predict the existence of a fourth spectral class, associated with the cool, fast high latitude wind.Comment: 16 pages, 16 figures, and 7 Tables; accepted A&A (Due to space limits, this version has lower resolution jpeg images.

Inferring heterozygosity from ancient and low coverage genomes

While genetic diversity can be quantified accurately from high coverage sequencing data, it is often desirable to obtain such estimates from data with low coverage, either to save costs or because of low DNA quality, as is observed for ancient samples. Here, we introduce a method to accurately infer heterozygosity probabilistically from sequences with average coverage Embedded Image of a single individual. The method relaxes the infinite sites assumption of previous methods, does not require a reference sequence, except for the initial alignment of the sequencing data, and takes into account both variable sequencing errors and potential postmortem damage. It is thus also applicable to nonmodel organisms and ancient genomes. Since error rates as reported by sequencing machines are generally distorted and require recalibration, we also introduce a method to accurately infer recalibration parameters in the presence of postmortem damage. This method does not require knowledge about the underlying genome sequence, but instead works with haploid data (e.g., from the X-chromosome from mammalian males) and integrates over the unknown genotypes. Using extensive simulations we show that a few megabasepairs of haploid data are sufficient for accurate recalibration, even at average coverages as low as Embedded Image At similar coverages, our method also produces very accurate estimates of heterozygosity down to Embedded Image within windows of about 1 Mbp. We further illustrate the usefulness of our approach by inferring genome-wide patterns of diversity for several ancient human samples, and we found that 3000–5000-year-old samples showed diversity patterns comparable to those of modern humans. In contrast, two European hunter-gatherer samples exhibited not only considerably lower levels of diversity than modern samples, but also highly distinct distributions of diversity along their genomes. Interestingly, these distributions were also very different between the two samples, supporting earlier conclusions of a highly diverse and structured population in Europe prior to the arrival of farming