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We describe a C++ framework that uses graphical processing units (GPUs) to accelerate basic hierarchical Bayesian computation, and use it to compute the posterior distribution for the parameters of a galaxy luminosity function based on data with photometric noise and selection effects arising from a flux-limited detection threshold. In addition to estimating the population-level luminosity function parameters, the framework also provides estimates of the absolute magnitude of each object, which automatically correct for Eddington bias. To sample the posterior, we implement a Metropolis–Hastings-within-Gibbs algorithm that alternates between exploring the population-level and member-level parameters. The algorithm exploits conditional independence in hierarchical Bayesian models, which makes member-level exploration readily parallelizable on a GPU. The framework uses adaptive MCMC, automatically tuning Metropolis–Hastings proposal distributions on-the-fly. We present a simulation study demonstrating the accuracy and computational scaling of the algorithm. In addition, we compare hierarchical Bayesian estimation with maximum likelihood estimation (known to provide inconsistent estimates in this setting), providing a concrete demonstration of the benefits of using hierarchical models for luminosity function inference.

We present a flexible template-based photometric redshift estimation framework, implemented in C#, that can be seamlessly integrated into a SQL database (or DB) server and executed on-demand in SQL. The DB integration eliminates the need to move large photometric datasets outside a database for redshift estimation, and utilizes the computational capabilities of DB hardware. The code is able to perform both maximum likelihood and Bayesian estimation, and can handle inputs of variable photometric filter sets and corresponding broad-band magnitudes. It is possible to take into account the full covariance matrix between filters, and filter zero points can be empirically calibrated using measurements with given redshifts. The list of spectral templates and the prior can be specified flexibly, and the expensive synthetic magnitude computations are done via lazy evaluation, coupled with a caching of results. Parallel execution is fully supported. For large upcoming photometric surveys such as the LSST, the ability to perform in-place photo-z calculation would be a significant advantage. Also, the efficient handling of variable filter sets is a necessity for heterogeneous databases, for example the Hubble Source Catalog, and for cross-match services such as SkyQuery. We illustrate the performance of our code on two reference photo-z estimation testing datasets, and provide an analysis of execution time and scalability with respect to different configurations. The code is available for download at https://github.com/beckrob/Photo-z-SQL.

Loss-of-function mutations in the BRCA1 and BRCA2 genes increase the risk of cancer. Owing to their function in homologous recombination repair, much research has focused on the unstable genomic phenotype of BRCA1/2 mutant cells manifest mainly as large-scale rearrangements. We used whole-genome sequencing of multiple isogenic chicken DT40 cell clones to precisely determine the consequences of BRCA1/2 loss on all types of genomic mutagenesis. Spontaneous base substitution mutation rates increased sevenfold upon the disruption of either BRCA1 or BRCA2, and the arising mutation spectra showed strong and specific correlation with a mutation signature associated with BRCA1/2 mutant tumours. To model endogenous alkylating damage, we determined the mutation spectrum caused by methyl methanesulfonate (MMS), and showed that MMS also induces more base substitution mutations in BRCA1/2-deficient cells. Spontaneously arising and MMS-induced insertion/deletion mutations and large rearrangements were also more common in BRCA1/2 mutant cells compared with the wild-type control. A difference in the short deletion phenotypes of BRCA1 and BRCA2 suggested distinct roles for the two proteins in the processing of DNA lesions, as BRCA2 mutants contained more short deletions, with a wider size distribution, which frequently showed microhomology near the breakpoints resembling repair by non-homologous end joining. An increased and prolonged gamma-H2AX signal in MMS-treated BRCA1/2 cells suggested an aberrant processing of stalled replication forks as the cause of increased mutagenesis. The high rate of base substitution mutagenesis demonstrated by our experiments is likely to significantly contribute to the oncogenic effect of the inactivation of BRCA1 or BRCA2.

It is known that the soft tail of the gamma-ray bursts' spectra show excesses from the exact power-law dependence. In this article we show that this departure can be detected in the peak flux ratios of different BATSE DISCSC energy channels. This effect allows to estimate the redshift of the bright long gamma-ray bursts in the BATSE Catalog. A verification of these redshifts is obtained for the 8 GRB which have both BATSE DISCSC data and measured optical spectroscopic redshifts. There is good correlation between the measured and estimated redshifts, and the average error is $\Delta z \approx 0.33$. The method is similar to the photometric redshift estimation of galaxies in the optical range, hence it can be called as “gamma photometric redshift estimation”. The estimated redshifts for the long bright gamma-ray bursts are up to $z \simeq 4$. For the the faint long bursts – which should be up to $z \simeq 20$– the redshifts cannot be determined unambiguously with this method.

The last decade has seen a dramatic change in the way astronomy is carried out. The dawn of the the new microelectronic devices, like CCDs has dramatically extended the amount of observed data. Large, in some cases all sky surveys emerged in almost all the wavelength ranges of the observable spectrum of electromagnetic waves. This large amount of data has to be organized, published electronically and a new style of data retrieval is essential to exploit all the hidden information in the multiwavelength data. Many statistical algorithms required for these tasks run reasonably fast when using small sets of in-memory data, but take noticeable performance hits when operating on large databases that do not fit into memory. We utilize new software technologies to develop and evaluate fast multidimensional indexing schemes that inherently follow the underlying, highly non-uniform distribution of the data: they are layered uniform indices, hierarchical binary space partitioning, and sampled flat Voronoi tessellation of the data. These techniques can dramatically speed up operations such as finding similar objects by example, classifying objects or comparing extensive simulation sets with observations. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

This paper describes spectra of quasar candidates acquired during the commissioning phase of the Low-Resolution Spectrograph of the Hobby-Eberly Telescope. The objects were identified as possible quasars from multicolor image data from the Sloan Digital Sky Survey. The 10 sources had typical r'magnitudes of 19-20, except for one extremely red object with r'? 23. The data, obtained with exposure times between 10 and 25 minutes, reveal that the spectra of four candidates are essentially featureless and are not quasars, five are quasars with redshifts between 2.92 and 4.15 (including one broad absorption line quasar), and the red source is a very late M star or early L dwarf.

Correction to: Oncogene (2017) 36, 746–755; doi:10.1038/onc.2016.243; published online 25 July 2016 In Figure 2c, the label above the middle panel in this paper was published incorrectly. The correct label should read BRCA1−/− instead of BRCA2−/−. The corrected figure 2 is below. The publishers wishto apologise for any inconvenience caused.

We present the multi-GPU realization of the StePS(Stereographically Projected Cosmological Simulations) algorithm with MPI–OpenMP–CUDA hybrid parallelization and nearly ideal scale-out to multiple compute nodes. Our new zoom-in cosmological direct N-body simulation method simulates the infinite universe with unprecedented dynamic range for a given amount of memory and, in contrast to traditional periodic simulations, its fundamental geometry and topology match observations. By using a spherical geometry instead of periodic boundary conditions, and gradually decreasing the mass resolution with radius, our code is capable of running simulations with a few gigaparsecs in diameter and with a mass resolution of ∼109M⊙in the center in four days on three compute nodes with four GTX 1080 Ti GPUs in each. The code can also be used to run extremely fast simulations with reasonable resolution for fitting cosmological parameters. These simulations are useful for prediction needs of large surveys. The StePScode is publicly available for the research community.

The accuracy of distinguishing amino-terminal signal peptides from cytosolic proteins has been improved to 95% by combining a neural network classifier with von Heijne's statistical prediction, the latter is itself 85–90% reliable. The network processed not the cleavage site, but amino-terminal 20-residue segments by the ‘tiling’ algorithm. Concordant positive predictions of both methods led to the safe identification of 496 novel signal peptides from the Protein Identification Resources.