CosmoHammer: Cosmological parameter estimation with the MCMC Hammer

We study the benefits and limits of parallelised Markov chain Monte Carlo (MCMC) sampling in cosmology. MCMC methods are widely used for the estimation of cosmological parameters from a given set of observations and are typically based on the Metropolis-Hastings algorithm. Some of the required calculations can however be computationally intensive, meaning that a single long chain can take several hours or days to calculate. In practice, this can be limiting, since the MCMC process needs to be performed many times to test the impact of possible systematics and to understand the robustness of the measurements being made. To achieve greater speed through parallelisation, MCMC algorithms need to have short auto-correlation times and minimal overheads caused by tuning and burn-in. The resulting scalability is hence influenced by two factors, the MCMC overheads and the parallelisation costs. In order to efficiently distribute the MCMC sampling over thousands of cores on modern cloud computing infrastructure, we developed a Python framework called CosmoHammer which embeds emcee, an implementation by Foreman-Mackey et al. (2012) of the affine invariant ensemble sampler by Goodman and Weare (2010). We test the performance of CosmoHammer for cosmological parameter estimation from cosmic microwave background data. While Metropolis-Hastings is dominated by overheads, CosmoHammer is able to accelerate the sampling process from a wall time of 30 hours on a dual core notebook to 16 minutes by scaling out to 2048 cores. Such short wall times for complex data sets opens possibilities for extensive model testing and control of systematics.Comment: Published version. 17 pages, 6 figures. The code is available at http://www.astro.ethz.ch/refregier/research/Software/cosmohamme

Simulating the Large-Scale Structure of HI Intensity Maps

Intensity mapping of neutral hydrogen (HI) is a promising observational probe of cosmology and large-scale structure. We present wide field simulations of HI intensity maps based on N-body simulations of a $2.6\, {\rm Gpc / h}$ box with $2048^3$ particles (particle mass $1.6 \times 10^{11}\, {\rm M_\odot / h}$). Using a conditional mass function to populate the simulated dark matter density field with halos below the mass resolution of the simulation ($10^{8}\, {\rm M_\odot / h} < M_{\rm halo} < 10^{13}\, {\rm M_\odot / h}$), we assign HI to those halos according to a phenomenological halo to HI mass relation. The simulations span a redshift range of 0.35 < z < 0.9 in redshift bins of width $\Delta z \approx 0.05$ and cover a quarter of the sky at an angular resolution of about 7'. We use the simulated intensity maps to study the impact of non-linear effects and redshift space distortions on the angular clustering of HI. Focusing on the autocorrelations of the maps, we apply and compare several estimators for the angular power spectrum and its covariance. We verify that these estimators agree with analytic predictions on large scales and study the validity of approximations based on Gaussian random fields, particularly in the context of the covariance. We discuss how our results and the simulated maps can be useful for planning and interpreting future HI intensity mapping surveys.Comment: 35 pages, 19 Figures. Accepted for publication in JCA

The anatomy of neuroepithelial tumours

Many neurological conditions conceal specific anatomical patterns. Their study contributes to the understanding of disease biology and to tailored diagnostics and therapy. Neuroepithelial tumours exhibit distinct anatomical phenotypes and spatiotemporal dynamics that differ from those of other brain tumours. Brain metastases display a preference for the cortico-subcortical boundaries of watershed areas and have a predominantly spherical growth. Primary CNS lymphomas localize to the white matter and generally invade along fibre tracts. In neuroepithelial tumours, topographic probability mapping and unsupervised topological clustering have identified an inherent radial anatomy and adherence to ventriculopial configurations of specific hierarchical orders. Spatiotemporal probability and multivariate survival analyses have identified a temporal and prognostic sequence underlying the anatomical phenotypes of neuroepithelial tumours. Gradual neuroepithelial de-differentiation and declining prognosis follow (i) an expansion into higher order radial units; (ii) a subventricular spread; and (iii) the presence of mesenchymal patterns (expansion along white matter tracts, leptomeningeal or perivascular invasion, CSF spread). While different pathophysiological hypotheses have been proposed, the cellular and molecular mechanisms dictating this anatomical behaviour remain largely unknown. Here we adopt an ontogenetic approach towards the understanding of neuroepithelial tumour anatomy. Contemporary perception of histo- and morphogenetic processes during neurodevelopment permit us to conceptualize the architecture of the brain into hierarchically organized radial units. The anatomical phenotypes in neuroepithelial tumours and their temporal and prognostic sequences share remarkable similarities with the ontogenetic organization of the brain and the anatomical specifications that occur during neurodevelopment. This macroscopic coherence is reinforced by cellular and molecular observations that the initiation of various neuroepithelial tumours, their intratumoural hierarchy and tumour progression are associated with the aberrant reactivation of surprisingly normal ontogenetic programs. Generalizable topological phenotypes could provide the basis for an anatomical refinement of the current classification of neuroepithelial tumours. In addition, we have proposed a staging system for adult-type diffuse gliomas that is based on the prognostically critical steps along the sequence of anatomical tumour progression. Considering the parallels in anatomical behaviour between different neuroepithelial tumours, analogous staging systems may be implemented for other neuroepithelial tumour types and subtypes. Both the anatomical stage of a neuroepithelial tumour and the spatial configuration of its hosting radial unit harbour the potential to stratify treatment decisions at diagnosis and during follow-up. More data on specific neuroepithelial tumour types and subtypes are needed to increase the anatomical granularity in their classification and to determine the clinical impact of stage-adapted and anatomically tailored therapy and surveillance

An Integrated System at the Bleien Observatory for Mapping the Galaxy

We describe the design and performance of the hardware system at the Bleien Observatory. The system is designed to deliver a map of the Galaxy for studying the foreground contamination of low-redshift (z=0.13--0.43) H$_{\rm I}$ intensity mapping experiments as well as other astronomical Galactic studies. This hardware system is composed of a 7m parabolic dish, a dual-polarization corrugated horn feed, a pseudo correlation receiver, a Fast Fourier Transform spectrometer, and an integrated control system that controls and monitors the progress of the data collection. The main innovative designs in the hardware are (1) the pseudo correlation receiver and the cold reference source within (2) the high dynamic range, high frequency resolution spectrometer and (3) the phase-switch implementation of the system. This is the first time these technologies are used together for a L-band radio telescope to achieve an electronically stable system, which is an essential first step for wide-field cosmological measurements. This work demonstrates the prospects and challenges for future H$_{\rm I}$ intensity mapping experiments.Comment: 11 pages, 12 figures, 1 table, Submitted to MNRA

HOPE: A Python Just-In-Time compiler for astrophysical computations

The Python programming language is becoming increasingly popular for scientific applications due to its simplicity, versatility, and the broad range of its libraries. A drawback of this dynamic language, however, is its low runtime performance which limits its applicability for large simulations and for the analysis of large data sets, as is common in astrophysics and cosmology. While various frameworks have been developed to address this limitation, most focus on covering the complete language set, and either force the user to alter the code or are not able to reach the full speed of an optimised native compiled language. In order to combine the ease of Python and the speed of C++, we developed HOPE, a specialised Python just-in-time (JIT) compiler designed for numerical astrophysical applications. HOPE focuses on a subset of the language and is able to translate Python code into C++ while performing numerical optimisation on mathematical expressions at runtime. To enable the JIT compilation, the user only needs to add a decorator to the function definition. We assess the performance of HOPE by performing a series of benchmarks and compare its execution speed with that of plain Python, C++ and the other existing frameworks. We find that HOPE improves the performance compared to plain Python by a factor of 2 to 120, achieves speeds comparable to that of C++, and often exceeds the speed of the existing solutions. We discuss the differences between HOPE and the other frameworks, as well as future extensions of its capabilities. The fully documented HOPE package is available at http://hope.phys.ethz.ch and is published under the GPLv3 license on PyPI and GitHub.Comment: Accepted for publication in Astronomy and Computing. 14 pages, 1 figure. The code is available at http://hope.phys.ethz.c

Verjährungsfristverkürzung und Haftungsbeschränkung

Zwischen Art. 210 Abs. 4 OR und Art. 199 OR besteht ein Wertungswiderspruch. Es wäre nämlich wertungsmässig widersprüchlich, wenn gemäss Art. 210 Abs. 4 OR im Konsumentenkaufrecht die Verjährung für neue Kaufsachen nicht unter zwei Jahre und bei gebrauchten Sachen nicht unter ein Jahr verkürzt werden darf, demgegenüber aber die Sachgewährleistungsansprüche des Käufers im Konsumentenkaufrecht über Art. 199 OR wegbedungen werden könnten. Deshalb wird in dieser Dissertation der zwischen Art. 210 Abs. 4 OR und Art. 199 OR bestehende Wertungswiderspruch im Rahmen der juristischen Methodenlehre ausgelegt. Es kann vorweggenommen werden, dass aufgrund der Auslegung dieses Wertungswiderspruchs den Sachgewährleistungsansprüchen im Konsumentenkaufrecht von Gesetzes wegen zwingende Natur zukommt. Dieses Auslegungsresultat führt zu von der Lehre und Rechtsprechung noch nicht abgehandelten Fragestellungen und eröffnet die Möglichkeit, verschiedene Rechtsfragen im Konsumentenkaufrecht anhand einer neuen Auslegungsoptik zu interpretieren

Investigation of metal flow in bridge die extrusion of Alloy 6063 and subsequent effect on surface quality and weld seam integrity

This paper describes a detailed study of tube extrusion by simulation using finite element method (FEM). The finite element model used one-sixth of symmetry. The extrusion load, emperature evolution and metal flow were predicted. Innovative methods, combining both grid and surface tools, were used to define in detail the flow of material. These showed clearly the inner and outer surface formation mechanisms of the tube extrusion. The seam weld, an important quality indicator, was also evaluated by selecting an appropriate criterion

Accelerated Modeling of Near and Far-Field Diffraction for Coronagraphic Optical Systems

Accurately predicting the performance of coronagraphs and tolerancing optical surfaces for high-contrast imaging requires a detailed accounting of diffraction effects. Unlike simple Fraunhofer diffraction modeling, near and far-field diffraction effects, such as the Talbot effect, are captured by plane-to-plane propagation using Fresnel and angular spectrum propagation. This approach requires a sequence of computationally intensive Fourier transforms and quadratic phase functions, which limit the design and aberration sensitivity parameter space which can be explored at high-fidelity in the course of coronagraph design. This study presents the results of optimizing the multi-surface propagation module of the open source Physical Optics Propagation in PYthon (POPPY) package. This optimization was performed by implementing and benchmarking Fourier transforms and array operations on graphics processing units, as well as optimizing multithreaded numerical calculations using the NumExpr python library where appropriate, to speed the end-to-end simulation of observatory and coronagraph optical systems. Using realistic systems, this study demonstrates a greater than five-fold decrease in wall-clock runtime over POPPY's previous implementation and describes opportunities for further improvements in diffraction modeling performance.Comment: Presented at SPIE ASTI 2018, Austin Texas. 11 pages, 6 figure

Mortality in Patients with Brainstem Cavernous Malformations

OBJECTIVE Brainstem cavernous malformations (BSCM)-associated mortality has been reported up to 20% in patients managed conservatively, whereas postoperative mortality rates range from 0 to 1.9%. Our aim was to analyze the actual risk and causes of BSCM-associated mortality in patients managed conservatively and surgically based on our own patient cohort and a systematic literature review. METHODS Observational, retrospective single-center study encompassing all patients with BSCM that presented to our institution between 2006 and 2018. In addition, a systematic review was performed on all studies encompassing patients with BSCM managed conservatively and surgically. RESULTS Of 118 patients, 54 were treated conservatively (961.0 person years follow-up in total). No BSCM-associated mortality was observed in our conservatively as well as surgically managed patient cohort. Our systematic literature review and analysis revealed an overall BSCM-associated mortality rate of 2.3% (95% CI: 1.6-3.3) in 22 studies comprising 1,251 patients managed conservatively and of 1.3% (95% CI: 0.9-1.7) in 99 studies comprising 3,275 patients with BSCM treated surgically. CONCLUSION The BSCM-associated mortality rate in patients managed conservatively is almost as low as in patients treated surgically and much lower than in frequently cited reports, most probably due to the good selection nowadays in regard to surgery