Assessing stationary distributions derived from chromatin contact maps.

BACKGROUND:The spatial configuration of chromosomes is essential to various cellular processes, notably gene regulation, while architecture related alterations, such as translocations and gene fusions, are often cancer drivers. Thus, eliciting chromatin conformation is important, yet challenging due to compaction, dynamics and scale. However, a variety of recent assays, in particular Hi-C, have generated new details of chromatin structure, spawning a number of novel biological findings. Many findings have resulted from analyses on the level of native contact data as generated by the assays. Alternatively, reconstruction based approaches often proceed by first converting contact frequencies into distances, then generating a three dimensional (3D) chromatin configuration that best recapitulates these distances. Subsequent analyses can enrich contact level analyses via superposition of genomic attributes on the reconstruction. But, such advantages depend on the accuracy of the reconstruction which, absent gold standards, is inherently difficult to assess. Attempts at accuracy evaluation have relied on simulation and/or FISH imaging that typically features a handful of low resolution probes. While newly advanced multiplexed FISH imaging offers possibilities for refined 3D reconstruction accuracy evaluation, availability of such data is limited due to assay complexity and the resolution thereof is appreciably lower than the reconstructions being assessed. Accordingly, there is demand for new methods of reconstruction accuracy appraisal. RESULTS:Here we explore the potential of recently proposed stationary distributions, hereafter StatDns, derived from Hi-C contact matrices, to serve as a basis for reconstruction accuracy assessment. Current usage of such StatDns has focussed on the identification of highly interactive regions (HIRs): computationally defined regions of the genome purportedly involved in numerous long-range intra-chromosomal contacts. Consistent identification of HIRs would be informative with respect to inferred 3D architecture since the corresponding regions of the reconstruction would have an elevated number of k nearest neighbors (kNNs). More generally, we anticipate a monotone decreasing relationship between StatDn values and kNN distances. After initially evaluating the reproducibility of StatDns across replicate Hi-C data sets, we use this implied StatDn - kNN relationship to gauge the utility of StatDns for reconstruction validation, making recourse to both real and simulated examples. CONCLUSIONS:Our analyses demonstrate that, as constructed, StatDns do not provide a suitable measure for assessing the accuracy of 3D genome reconstructions. Whether this is attributable to specific choices surrounding normalization in defining StatDns or to the logic underlying their very formulation remains to be determined

Bisous model - detecting filamentary patterns in point processes

The cosmic web is a highly complex geometrical pattern, with galaxy clusters at the intersection of filaments and filaments at the intersection of walls. Identifying and describing the filamentary network is not a trivial task due to the overwhelming complexity of the structure, its connectivity and the intrinsic hierarchical nature. To detect and quantify galactic filaments we use the Bisous model, which is a marked point process built to model multi-dimensional patterns. The Bisous filament finder works directly with the galaxy distribution data and the model intrinsically takes into account the connectivity of the filamentary network. The Bisous model generates the visit map (the probability to find a filament at a given point) together with the filament orientation field. Using these two fields, we can extract filament spines from the data. Together with this paper we publish the computer code for the Bisous model that is made available in GitHub. The Bisous filament finder has been successfully used in several cosmological applications and further development of the model will allow to detect the filamentary network also in photometric redshift surveys, using the full redshift posterior. We also want to encourage the astro-statistical community to use the model and to connect it with all other existing methods for filamentary pattern detection and characterisation.Comment: 12 pages, 6 figures, accepted by Astronomy and Computin

Galaxy filaments as pearl necklaces

Context. Galaxies in the Universe form chains (filaments) that connect groups and clusters of galaxies. The filamentary network includes nearly half of the galaxies and is visually the most striking feature in cosmological maps. Aims. We study the distribution of galaxies along the filamentary network, trying to find specific patterns and regularities. Methods. Galaxy filaments are defined by the Bisous model, a marked point process with interactions. We use the two-point correlation function and the Rayleigh Z-squared statistic to study how galaxies and galaxy groups are distributed along the filaments. Results. We show that galaxies and groups are not uniformly distributed along filaments, but tend to form a regular pattern. The characteristic length of the pattern is around 7 Mpc/h. A slightly smaller characteristic length 4 Mpc/h can also be found, using the Z-squared statistic. Conclusions. We find that galaxy filaments in the Universe are like pearl necklaces, where the pearls are galaxy groups distributed more or less regularly along the filaments. We propose that this well defined characteristic scale could be used to test various cosmological models and to probe environmental effects on the formation and evolution of galaxies.Comment: 8 pages, 9 figures, 1 table, accepted for publication in A&

Flux- and volume-limited groups/clusters for the SDSS galaxies: catalogues and mass estimation

We provide flux-limited and volume-limited galaxy group and cluster catalogues, based on the spectroscopic sample of the SDSS data release 10 galaxies. We used a modified friends-of-friends (FoF) method with a variable linking length in the transverse and radial directions to identify as many realistic groups as possible. The flux-limited catalogue incorporates galaxies down to m_r = 17.77 mag. It includes 588193 galaxies and 82458 groups. The volume-limited catalogues are complete for absolute magnitudes down to M_r = -18.0, -18.5, -19.0, -19.5, -20.0, -20.5, and -21.0; the completeness is achieved within different spatial volumes, respectively. Our analysis shows that flux-limited and volume-limited group samples are well compatible to each other, especially for the larger groups/clusters. Dynamical mass estimates, based on radial velocity dispersions and group extent in the sky, are added to the extracted groups. The catalogues can be accessed via http://cosmodb.to.ee and the Strasbourg Astronomical Data Center (CDS).Comment: 16 pages, 18 figures, 2 tables, accepted for publication in A&

Induced two-photon decay of the 2s level and the rate of cosmological hydrogen recombination

Induced emission due to the presence of soft CMB photons slightly increases the two-photon decay rate of the 2s level of hydrogen defining the rate of cosmological recombination. This correspondingly changes the degree of ionization, the visibility function and the resulting primordial temperature anisotropies and polarization of the CMB on the percent level. These changes exceed the precision of the widely used CMBFAST and CAMB codes by more than one order of magnitude and can be easily taken into account.Comment: 5 pages, 5 figure, accepted by Astronomy and Astrophysic

Recovering 3D structural properties of galaxies from SDSS-like photometry

Because of the 3D nature of galaxies, an algorithm for constructing spatial density distribution models of galaxies on the basis of galaxy images has many advantages over surface density distribution approximations. We present a method for deriving spatial structure and overall parameters of galaxies from images and estimate its accuracy and derived parameter degeneracies on a sample of idealised model galaxies. The test galaxies consist of a disc-like component and a spheroidal component with varying proportions and properties. Both components are assumed to be axially symmetric and coplanar. We simulate these test galaxies as if observed in the SDSS project through ugriz filters, thus gaining a set of realistically imperfect images of galaxies with known intrinsic properties. These artificial SDSS galaxies were thereafter remodelled by approximating the surface brightness distribution with a 2D projection of a bulge+disc spatial distribution model and the restored parameters were compared to the initial ones. Down to the r-band limiting magnitude 18, errors of the restored integral luminosities and colour indices remain within 0.05 mag and errors of the luminosities of individual components within 0.2 mag. Accuracy of the restored bulge-to-disc ratios (B/D) is within 40% in most cases, and becomes worse for galaxies with low B/D, but the general balance between bulges and discs is not shifted systematically. Assuming that the intrinsic disc axial ratio is < 0.3, the inclination angles can be estimated with errors < 5deg for most of the galaxies with B/D < 2 and with errors < 15deg up to B/D = 6. Errors of the recovered sizes of the galactic components are below 10% in most cases. In general, models of disc components are more accurate than models of spheroidal components for geometrical reasons.Comment: 15 pages, 13 figures, accepted for publication in RA

Models of infrared spectra of Sakurai's Object (V4334 Sgr) in 1997

Theoretical spectral energy distributions computed for a grid of hydrogen-deficient and carbon-rich model atmospheres have been compared with the observed infrared (1--2.5 $\mu$m) spectra of V4334 Sgr (Sakurai's Object) on 1997 April 21 and July 13. The comparison yields an effective temperature of \Tef = 5500 $\pm$ 200 K for the April date and \Tef = 5250 $\pm$ 200 K for July. The observed spectra are well fitted by Asplund et al. (1999) abundances, except that the carbon abundance is higher by 0.3 dex. Hot dust produces significant excess continuum at the long wavelength ends of the 1997 spectra. \keywords{Stars: individual: V4334 Sgr (Sakurai's Object) -- Stars: AGB and post-AGB evolution -- Stars: model atmospheres -- Stars: energy distributions -- Stars: effective temperatures}Comment: 6 pages, 7 eps figs, accepted for A

Near-Infrared Spectroscopy of Carbon-Enhanced Metal-Poor Stars. I. A SOAR/OSIRIS Pilot Study

We report on an abundance analysis for a pilot study of seven Carbon-Enhanced Metal-Poor (CEMP) stars, based on medium-resolution optical and near-infrared spectroscopy. The optical spectra are used to estimate [Fe/H], [C/Fe], [N/Fe], and [Ba/Fe] for our program stars. The near-infrared spectra, obtained during a limited early science run with the new SOAR 4.1m telescope and the Ohio State Infrared Imager and Spectrograph (OSIRIS), are used to obtain estimates of [O/Fe] and 12C/13C. The chemical abundances of CEMP stars are of importance for understanding the origin of CNO in the early Galaxy, as well as for placing constraints on the operation of the astrophysical s-process in very low-metallicity Asymptotic Giant Branch (AGB) stars. This pilot study includes a few stars with previously measured [Fe/H], [C/Fe], [N/Fe],[O/Fe], 12C/13C, and [Ba/Fe], based on high-resolution optical spectra obtained with large-aperture telescopes. Our analysis demonstrates that we are able to achieve reasonably accurate determinations of these quantities for CEMP stars from moderate-resolution optical and near-infrared spectra. This opens the pathway for the study of significantly larger samples of CEMP stars in the near future. Furthermore, the ability to measure [Ba/Fe] for (at least the cooler) CEMP stars should enable one to separate stars that are likely to be associated with s-process enhancements (the CEMP-s stars) from those that do not exhibit neutron-capture enhancements (the CEMP-no stars).Comment: 27 pages, including 5 tables, 6 figures, accepted for publication in The Astronomical Journa