Past and present cosmic structure in the SDSS DR7 main sample

We present a chrono-cosmography project, aiming at the inference of the four dimensional formation history of the observed large scale structure from its origin to the present epoch. To do so, we perform a full-scale Bayesian analysis of the northern galactic cap of the Sloan Digital Sky Survey (SDSS) Data Release 7 main galaxy sample, relying on a fully probabilistic, physical model of the non-linearly evolved density field. Besides inferring initial conditions from observations, our methodology naturally and accurately reconstructs non-linear features at the present epoch, such as walls and filaments, corresponding to high-order correlation functions generated by late-time structure formation. Our inference framework self-consistently accounts for typical observational systematic and statistical uncertainties such as noise, survey geometry and selection effects. We further account for luminosity dependent galaxy biases and automatic noise calibration within a fully Bayesian approach. As a result, this analysis provides highly-detailed and accurate reconstructions of the present density field on scales larger than $\sim~3$ Mpc$/h$, constrained by SDSS observations. This approach also leads to the first quantitative inference of plausible formation histories of the dynamic large scale structure underlying the observed galaxy distribution. The results described in this work constitute the first full Bayesian non-linear analysis of the cosmic large scale structure with the demonstrated capability of uncertainty quantification. Some of these results will be made publicly available along with this work. The level of detail of inferred results and the high degree of control on observational uncertainties pave the path towards high precision chrono-cosmography, the subject of simultaneously studying the dynamics and the morphology of the inhomogeneous Universe.Comment: 27 pages, 9 figure

Inferring the post-merger gravitational wave emission from binary neutron star coalescences

We present a robust method to characterize the gravitational wave emission from the remnant of a neutron star coalescence. Our approach makes only minimal assumptions about the morphology of the signal and provides a full posterior probability distribution of the underlying waveform. We apply our method on simulated data from a network of advanced ground-based detectors and demonstrate the gravitational wave signal reconstruction. We study the reconstruction quality for different binary configurations and equations of state for the colliding neutron stars. We show how our method can be used to constrain the yet-uncertain equation of state of neutron star matter. The constraints on the equation of state we derive are complimentary to measurements of the tidal deformation of the colliding neutron stars during the late inspiral phase. In the case of a non-detection of a post-merger signal following a binary neutron star inspiral we show that we can place upper limits on the energy emitted.Comment: 11 pages, 12 figures, final published versio

Bayesian multi-modal model comparison: a case study on the generators of the spike and the wave in generalized spike–wave complexes

We present a novel approach to assess the networks involved in the generation of spontaneous pathological brain activity based on multi-modal imaging data. We propose to use probabilistic fMRI-constrained EEG source reconstruction as a complement to EEG-correlated fMRI analysis to disambiguate between networks that co-occur at the fMRI time resolution. The method is based on Bayesian model comparison, where the different models correspond to different combinations of fMRI-activated (or deactivated) cortical clusters. By computing the model evidence (or marginal likelihood) of each and every candidate source space partition, we can infer the most probable set of fMRI regions that has generated a given EEG scalp data window. We illustrate the method using EEG-correlated fMRI data acquired in a patient with ictal generalized spike–wave (GSW) discharges, to examine whether different networks are involved in the generation of the spike and the wave components, respectively. To this effect, we compared a family of 128 EEG source models, based on the combinations of seven regions haemodynamically involved (deactivated) during a prolonged ictal GSW discharge, namely: bilateral precuneus, bilateral medial frontal gyrus, bilateral middle temporal gyrus, and right cuneus. Bayesian model comparison has revealed the most likely model associated with the spike component to consist of a prefrontal region and bilateral temporal–parietal regions and the most likely model associated with the wave component to comprise the same temporal–parietal regions only. The result supports the hypothesis of different neurophysiological mechanisms underlying the generation of the spike versus wave components of GSW discharges

The Denoised, Deconvolved, and Decomposed Fermi γ\gamma-ray sky - An application of the D3^3PO algorithm

We analyze the 6.5yr all-sky data from the Fermi LAT restricted to gamma-ray photons with energies between 0.6-307.2GeV. Raw count maps show a superposition of diffuse and point-like emission structures and are subject to shot noise and instrumental artifacts. Using the D3PO inference algorithm, we model the observed photon counts as the sum of a diffuse and a point-like photon flux, convolved with the instrumental beam and subject to Poissonian shot noise. D3PO performs a Bayesian inference in this setting without the use of spatial or spectral templates;i.e., it removes the shot noise, deconvolves the instrumental response, and yields estimates for the two flux components separately. The non-parametric reconstruction uncovers the morphology of the diffuse photon flux up to several hundred GeV. We present an all-sky spectral index map for the diffuse component. We show that the diffuse gamma-ray flux can be described phenomenologically by only two distinct components: a soft component, presumably dominated by hadronic processes, tracing the dense, cold interstellar medium and a hard component, presumably dominated by leptonic interactions, following the hot and dilute medium and outflows such as the Fermi bubbles. A comparison of the soft component with the Galactic dust emission indicates that the dust-to-soft-gamma ratio in the interstellar medium decreases with latitude. The spectrally hard component exists in a thick Galactic disk and tends to flow out of the Galaxy at some locations. Furthermore, we find the angular power spectrum of the diffuse flux to roughly follow a power law with an index of 2.47 on large scales, independent of energy. Our first catalog of source candidates includes 3106 candidates of which we associate 1381(1897) with known sources from the 2nd(3rd) Fermi catalog. We observe gamma-ray emission in the direction of a few galaxy clusters hosting radio halos.Comment: re-submission after referee report (A&A); 17 pages, many colorful figures, 4 tables; bug fixed, flux scale now consistent with Fermi, even lower residual level, pDF -> 1DF source catalog, tentative detection of a few clusters of galaxies, online material http://www.mpa-garching.mpg.de/ift/fermi

On the origin of <i>Halipeurus heraldicus</i> on Round Island petrels: cophylogenetic relationships between petrels and their chewing lice

Lice phylogenetic relationships have often been used to elucidate host relationships and vice versa. In this study, we investigate the louse genus Halipeurus which parasitizes bird hosts in the families Procellariidae, Hydrobatidae and Pelecanoididae. The presence of two lice species on Pterodroma arminjoniana in different breeding grounds (Halipeurus heraldicus on Round Island, off Mauritius in the Indian Ocean and Halipeurus kermadecensis on Trindade Island in the Atlantic Ocean) has led to some confusion in the distribution of Pt. arminjoniana and its close relatives Pt. heraldica and Pt. neglecta. By using a cophylogenetic approach that incorporates uncertainties in phylogenetic reconstructions, we show significant overall coevolution between Halipeurus lice and their hosts. However, the study also indicates that the presence of H. heraldicus on Pt. arminjoniana and Pt. neglecta on Round Island and on Pt. heraldica on Gambier Island are the result of a host switch whereas H. kermadecensis is the ancestral parasite of Pt. arminjoniana. This suggests that H. kermadecensis was lost during or after colonisation of Round Island by Pt. arminjoniana. We conclude that cophylogenetic analyses are central to inferring the evolutionary history and biogeographical patterns of hosts and their parasites

How to understand the cell by breaking it: network analysis of gene perturbation screens

Modern high-throughput gene perturbation screens are key technologies at the forefront of genetic research. Combined with rich phenotypic descriptors they enable researchers to observe detailed cellular reactions to experimental perturbations on a genome-wide scale. This review surveys the current state-of-the-art in analyzing perturbation screens from a network point of view. We describe approaches to make the step from the parts list to the wiring diagram by using phenotypes for network inference and integrating them with complementary data sources. The first part of the review describes methods to analyze one- or low-dimensional phenotypes like viability or reporter activity; the second part concentrates on high-dimensional phenotypes showing global changes in cell morphology, transcriptome or proteome.Comment: Review based on ISMB 2009 tutorial; after two rounds of revisio

From sea to land and beyond : new insights into the evolution of euthyneuran Gastropoda (Mollusca)

Background The Euthyneura are considered to be the most successful and diverse group of Gastropoda. Phylogenetically, they are riven with controversy. Previous morphology-based phylogenetic studies have been greatly hampered by rampant parallelism in morphological characters or by incomplete taxon sampling. Based on sequences of nuclear 18S rRNA and 28S rRNA as well as mitochondrial 16S rRNA and COI DNA from 56 taxa, we reconstructed the phylogeny of Euthyneura utilising Maximum Likelihood and Bayesian inference methods. The evolution of colonization of freshwater and terrestrial habitats by pulmonate Euthyneura, considered crucial in the evolution of this group of Gastropoda, is reconstructed with Bayesian approaches. Results We found several well supported clades within Euthyneura, however, we could not confirm the traditional classification, since Pulmonata are paraphyletic and Opistobranchia are either polyphyletic or paraphyletic with several clades clearly distinguishable. Sacoglossa appear separately from the rest of the Opisthobranchia as sister taxon to basal Pulmonata. Within Pulmonata, Basommatophora are paraphyletic and Hygrophila and Eupulmonata form monophyletic clades. Pyramidelloidea are placed within Euthyneura rendering the Euthyneura paraphyletic. Conclusion Based on the current phylogeny, it can be proposed for the first time that invasion of freshwater by Pulmonata is a unique evolutionary event and has taken place directly from the marine environment via an aquatic pathway. The origin of colonisation of terrestrial habitats is seeded in marginal zones and has probably occurred via estuaries or semi-terrestrial habitats such as mangroves

Constraints on reionisation from the z=7.5 QSO ULASJ1342+0928

The recent detection of ULASJ1342+0928, a bright QSO at $z=7.54$, provides a powerful probe of the ionisation state of the intervening intergalactic medium, potentially allowing us to set strong constraints on the epoch of reionisation (EoR). Here we quantify the presence of Ly$\alpha$ damping wing absorption from the EoR in the spectrum of ULASJ1342+0928. Our Bayesian framework simultaneously accounts for uncertainties on: (i) the intrinsic QSO emission (obtained from reconstructing the Ly$\alpha$ profile from a covariance matrix of emission lines) and (ii) the distribution of HII regions during reionisation (obtained from three different 1.6$^3$ Gpc$^3$ simulations spanning the range of plausible EoR morphologies). Our analysis is complementary to that in the discovery paper (Ba\~nados et al.) and the accompanying method paper (Davies et al.) as it focuses solely on the damping wing imprint redward of Ly$\alpha$ ($1218 < \lambda < 1230$\AA), and uses a different methodology for (i) and (ii). We recover weak evidence for damping wing absorption. Our intermediate EoR model yields a volume-weighted neutral hydrogen fraction at $z=7.5$ of $\bar{x}_{\rm HI} = 0.21\substack{+0.17 \\ -0.19}$ (68 per cent). The constraints depend weakly on the EoR morphology. Our limits are lower than those presented previously, though they are consistent at ~1-1.5$\sigma$. We attribute this difference to: (i) a lower amplitude intrinsic Ly$\alpha$ profile obtained from our reconstruction pipeline, driven by correlations with other high-ionisation lines in the spectrum which are relatively weak; and (ii) only considering transmission redward of Ly$\alpha$ when computing the likelihood, which reduces the available constraining power but makes the results less model-dependent. Our results are consistent with previous estimates of the EoR history, and support the picture of a moderately extended EoR.Comment: 7 pages, 3 figures. Submitted to MNRAS, comments welcom