Low-Luminosity Accretion in Black Hole X-ray Binaries and Active Galactic Nuclei

At luminosities below a few percent of Eddington, accreting black holes switch to a hard spectral state which is very different from the soft blackbody-like spectral state that is found at higher luminosities. The hard state is well-described by a two-temperature, optically thin, geometrically thick, advection-dominated accretion flow (ADAF) in which the ions are extremely hot (up to $10^{12}$ K near the black hole), the electrons are also hot ($\sim10^{9-10.5}$ K), and thermal Comptonization dominates the X-ray emission. The radiative efficiency of an ADAF decreases rapidly with decreasing mass accretion rate, becoming extremely low when a source reaches quiescence. ADAFs are expected to have strong outflows, which may explain why relativistic jets are often inferred from the radio emission of these sources. It has been suggested that most of the X-ray emission also comes from a jet, but this is less well established.Comment: To appear in "From X-ray Binaries to Quasars: Black Hole Accretion on All Mass Scales" edited by T. Maccarone, R. Fender, L. Ho, to be published as a special edition of "Astrophysics and Space Science" by Kluwe

Radio emission and jets from microquasars

To some extent, all Galactic binary systems hosting a compact object are potential `microquasars', so much as all galactic nuclei may have been quasars, once upon a time. The necessary ingredients for a compact object of stellar mass to qualify as a microquasar seem to be: accretion, rotation and magnetic field. The presence of a black hole may help, but is not strictly required, since neutron star X-ray binaries and dwarf novae can be powerful jet sources as well. The above issues are broadly discussed throughout this Chapter, with a a rather trivial question in mind: why do we care? In other words: are jets a negligible phenomenon in terms of accretion power, or do they contribute significantly to dissipating gravitational potential energy? How do they influence their surroundings? The latter point is especially relevant in a broader context, as there is mounting evidence that outflows powered by super-massive black holes in external galaxies may play a crucial role in regulating the evolution of cosmic structures. Microquasars can also be thought of as a form of quasars for the impatient: what makes them appealing, despite their low number statistics with respect to quasars, are the fast variability time-scales. In the first approximation, the physics of the jet-accretion coupling in the innermost regions should be set by the mass/size of the accretor: stellar mass objects vary on 10^5-10^8 times shorter time-scales, making it possible to study variable accretion modes and related ejection phenomena over average Ph.D. time-scales. [Abridged]Comment: 28 pages, 13 figures, To appear in Belloni, T. (ed.): The Jet Paradigm - From Microquasars to Quasars, Lect. Notes Phys. 794 (2009

Young and Intermediate-age Distance Indicators

Distance measurements beyond geometrical and semi-geometrical methods, rely mainly on standard candles. As the name suggests, these objects have known luminosities by virtue of their intrinsic proprieties and play a major role in our understanding of modern cosmology. The main caveats associated with standard candles are their absolute calibration, contamination of the sample from other sources and systematic uncertainties. The absolute calibration mainly depends on their chemical composition and age. To understand the impact of these effects on the distance scale, it is essential to develop methods based on different sample of standard candles. Here we review the fundamental properties of young and intermediate-age distance indicators such as Cepheids, Mira variables and Red Clump stars and the recent developments in their application as distance indicators.Comment: Review article, 63 pages (28 figures), Accepted for publication in Space Science Reviews (Chapter 3 of a special collection resulting from the May 2016 ISSI-BJ workshop on Astronomical Distance Determination in the Space Age

Low Complexity Regularization of Linear Inverse Problems

Inverse problems and regularization theory is a central theme in contemporary signal processing, where the goal is to reconstruct an unknown signal from partial indirect, and possibly noisy, measurements of it. A now standard method for recovering the unknown signal is to solve a convex optimization problem that enforces some prior knowledge about its structure. This has proved efficient in many problems routinely encountered in imaging sciences, statistics and machine learning. This chapter delivers a review of recent advances in the field where the regularization prior promotes solutions conforming to some notion of simplicity/low-complexity. These priors encompass as popular examples sparsity and group sparsity (to capture the compressibility of natural signals and images), total variation and analysis sparsity (to promote piecewise regularity), and low-rank (as natural extension of sparsity to matrix-valued data). Our aim is to provide a unified treatment of all these regularizations under a single umbrella, namely the theory of partial smoothness. This framework is very general and accommodates all low-complexity regularizers just mentioned, as well as many others. Partial smoothness turns out to be the canonical way to encode low-dimensional models that can be linear spaces or more general smooth manifolds. This review is intended to serve as a one stop shop toward the understanding of the theoretical properties of the so-regularized solutions. It covers a large spectrum including: (i) recovery guarantees and stability to noise, both in terms of $\ell^2$-stability and model (manifold) identification; (ii) sensitivity analysis to perturbations of the parameters involved (in particular the observations), with applications to unbiased risk estimation ; (iii) convergence properties of the forward-backward proximal splitting scheme, that is particularly well suited to solve the corresponding large-scale regularized optimization problem

General Overview of Black Hole Accretion Theory

I provide a broad overview of the basic theoretical paradigms of black hole accretion flows. Models that make contact with observations continue to be mostly based on the four decade old alpha stress prescription of Shakura & Sunyaev (1973), and I discuss the properties of both radiatively efficient and inefficient models, including their local properties, their expected stability to secular perturbations, and how they might be tied together in global flow geometries. The alpha stress is a prescription for turbulence, for which the only existing plausible candidate is that which develops from the magnetorotational instability (MRI). I therefore also review what is currently known about the local properties of such turbulence, and the physical issues that have been elucidated and that remain uncertain that are relevant for the various alpha-based black hole accretion flow models.Comment: To be published in Space Science Reviews and as hard cover in the Space Sciences Series of ISSI: The Physics of Accretion on to Black Holes (Springer Publisher

Nucleosomes in gene regulation: theoretical approaches

This work reviews current theoretical approaches of biophysics and bioinformatics for the description of nucleosome arrangements in chromatin and transcription factor binding to nucleosomal organized DNA. The role of nucleosomes in gene regulation is discussed from molecular-mechanistic and biological point of view. In addition to classical problems of this field, actual questions of epigenetic regulation are discussed. The authors selected for discussion what seem to be the most interesting concepts and hypotheses. Mathematical approaches are described in a simplified language to attract attention to the most important directions of this field

Common variants near MC4R are associated with fat mass, weight and risk of obesity.

To identify common variants influencing body mass index (BMI), we analyzed genome-wide association data from 16,876 individuals of European descent. After previously reported variants in FTO, the strongest association signal (rs17782313, P = 2.9 x 10(-6)) mapped 188 kb downstream of MC4R (melanocortin-4 receptor), mutations of which are the leading cause of monogenic severe childhood-onset obesity. We confirmed the BMI association in 60,352 adults (per-allele effect = 0.05 Z-score units; P = 2.8 x 10(-15)) and 5,988 children aged 7-11 (0.13 Z-score units; P = 1.5 x 10(-8)). In case-control analyses (n = 10,583), the odds for severe childhood obesity reached 1.30 (P = 8.0 x 10(-11)). Furthermore, we observed overtransmission of the risk allele to obese offspring in 660 families (P (pedigree disequilibrium test average; PDT-avg) = 2.4 x 10(-4)). The SNP location and patterns of phenotypic associations are consistent with effects mediated through altered MC4R function. Our findings establish that common variants near MC4R influence fat mass, weight and obesity risk at the population level and reinforce the need for large-scale data integration to identify variants influencing continuous biomedical traits

Associations of autozygosity with a broad range of human phenotypes

In many species, the offspring of related parents suffer reduced reproductive success, a phenomenon known as inbreeding depression. In humans, the importance of this effect has remained unclear, partly because reproduction between close relatives is both rare and frequently associated with confounding social factors. Here, using genomic inbreeding coefficients (F-ROH) for >1.4 million individuals, we show that F-ROH is significantly associated (p <0.0005) with apparently deleterious changes in 32 out of 100 traits analysed. These changes are associated with runs of homozygosity (ROH), but not with common variant homozygosity, suggesting that genetic variants associated with inbreeding depression are predominantly rare. The effect on fertility is striking: F-ROH equivalent to the offspring of first cousins is associated with a 55% decrease [95% CI 44-66%] in the odds of having children. Finally, the effects of F-ROH are confirmed within full-sibling pairs, where the variation in F-ROH is independent of all environmental confounding.Peer reviewe

Fine-mapping of prostate cancer susceptibility loci in a large meta-analysis identifies candidate causal variants

Prostate cancer is a polygenic disease with a large heritable component. A number of common, low-penetrance prostate cancer risk loci have been identified through GWAS. Here we apply the Bayesian multivariate variable selection algorithm JAM to fine-map 84 prostate cancer susceptibility loci, using summary data from a large European ancestry meta-analysis. We observe evidence for multiple independent signals at 12 regions and 99 risk signals overall. Only 15 original GWAS tag SNPs remain among the catalogue of candidate variants identified; the remainder are replaced by more likely candidates. Biological annotation of our credible set of variants indicates significant enrichment within promoter and enhancer elements, and transcription factor-binding sites, including AR, ERG and FOXA1. In 40 regions at least one variant is colocalised with an eQTL in prostate cancer tissue. The refined set of candidate variants substantially increase the proportion of familial relative risk explained by these known susceptibility regions, which highlights the importance of fine-mapping studies and has implications for clinical risk profiling. © 2018 The Author(s).Prostate cancer is a polygenic disease with a large heritable component. A number of common, low-penetrance prostate cancer risk loci have been identified through GWAS. Here we apply the Bayesian multivariate variable selection algorithm JAM to fine-map 84 prostate cancer susceptibility loci, using summary data from a large European ancestry meta-analysis. We observe evidence for multiple independent signals at 12 regions and 99 risk signals overall. Only 15 original GWAS tag SNPs remain among the catalogue of candidate variants identified; the remainder are replaced by more likely candidates. Biological annotation of our credible set of variants indicates significant enrichment within promoter and enhancer elements, and transcription factor-binding sites, including AR, ERG and FOXA1. In 40 regions at least one variant is colocalised with an eQTL in prostate cancer tissue. The refined set of candidate variants substantially increase the proportion of familial relative risk explained by these known susceptibility regions, which highlights the importance of fine-mapping studies and has implications for clinical risk profiling. © 2018 The Author(s).Peer reviewe