An absorption origin for the soft excess in Seyfert 1 active galactic nuclei

(abridged) The soft excess seen in the X-ray spectra of many high mass accretion rate AGN can be well modelled by reflection from a partially ionised accretion disc. However, the derived parameters are often extreme, both in terms of the underlying spacetime and the reflection geometry, and these models require that the disc is far from hydrostatic equilibrium. An alternative model uses similarly partially ionised, velocity smeared material but seen in absorption, though again the derived velocities are extreme, requiring magnetic driving (in the jet?) rather than a simple line driven disc wind. We find that while both models give comparably good fits to XMM--Newton data, we favour the absorption model as, unlike reflection, all the derived spectral indices are soft. This is as expected by analogy with the correspondingly high mass accretion rate stellar mass black holes. Furthermore, these X-ray spectra are consistent with a one--to--one mapping between AGN type and spectral state, with NLS1's having softer spectra corresponding to the very high state, while the broad line AGN have Gamma~2 as expected for the high/soft state. We also use the simultaneous OM data to derive the ratio of disc to total accretion power which is another tracer of spectral state in X-ray binaries. This does not always show that the disc in NLS1's contributes less than 80 per cent of the total power, as expected for a very high state. We suggest that this is an artifact of the standard disc models used to determine the disc luminosity in our fits. The disc seen in the very high state of black hole binaries is often observed to be distorted from the standard shape, and a similar effect in NLS1's could recover the correspondance between black hole binary spectral state and AGN type.Comment: 12 pages, 12 figures, submitted to MNRA

Universal spectral shape of AGN with high accretion rate

The spectra of radio quiet and NLS1 galaxies show suprising similarity in their shape. They seem to scale only with the accretion rate but not with central black hole mass. We consider two mechanisms modifying the disk spectrum. First, the outer parts of the disk are irradiated by the flux emerging from the inner parts. This is due to the scattering of the flux by the extended hot medium (warm absorber). Second process is connected with the development of the disk warm Comptonizing skin above the disk and/or coronae. Our scenario applies only to object with relatively high luminosity to the Eddington luminosity ratio for which disk evaporation is inefficient.Comment: 4 pages, 5 figures, 1 table, Proc. of the meeting: "The Restless High-Energy Universe" (Amsterdam, The Netherlands

What can we learn about quasars from alpha_OX measurements in galactic black hole binaries?

We draw a comparison between AGN and Galactic black hole binaries using a uniform description of spectral energy distribution of these two classes of accreting X-ray sources. We parametrize spectra of GBHs with an alpha_GBH parameter which we define as a slope of a nominal power law function between 3 and 20 keV. We show that this parameter can be treated as an equivalent of the X-ray loudness, alpha_OX, used to describe AGN spectra. We do not find linear correlation between the alpha_GBH and disc flux (similar to that between alpha_OX and optical/UV luminosity found in AGN). Instead, we show that alpha_GBH follows a well defined pattern during a GBH outburst. We find that alpha_GBH tend to cluster around 1, 1.5 and 2, which correspond to a hard, very high/intermediate and soft spectral state, respectively. We conclude that majority of the observed Type 1 radio quiet AGN are in a spectral state corresponding to a very high/intermediate state of GBHs. The same conclusion is valid for radio loud AGN. We also study variations of the spectral slopes (alpha_GBH and the X-ray photon index, Gamma) as a function of disc and Comptonization fluxes. We discuss these dependencies in the context of correlations of alpha_OX and Gamma with the optical/UV and X-ray 2 keV fluxes considered for AGN and quasars.Comment: 10 pages, 7 figures, accepted for publication in MNRA

Compton scattering as the explanation of the peculiar X-ray properties of Cyg X-3

We consider implications of a possible presence of a Thomson-thick, low-temperature, plasma cloud surrounding the compact object in the binary system Cyg X-3. The presence of such a cloud was earlier inferred from the energy-independent orbital modulation of the X-ray flux and the lack of high frequencies in its power spectra. Here, we study the effect of Compton scattering by the cloud on the X-ray energy and power spectra, concentrating on the hard spectral state. The process reduces the energy of the high-energy break/cut-off in the energy spectra, which allows us to determine the Thomson optical depth. This, together with the observed cut-off in the power spectrum, determines the size of the plasma to be 2x10^9 cm. At this size, the cloud will be in thermal equilibrium in the photon field of the X-ray source, which yields the cloud temperature of 3 keV, which refines the determination of the Thomson optical depth to 7. At these parameters, thermal bremsstrahlung emission of the cloud becomes important as well. The physical origin of the cloud is likely to be collision of the very strong stellar wind of the companion Wolf-Rayet star with a small accretion disc formed by the wind accretion. Our model thus explains the peculiar X-ray energy and power spectra of Cyg X-3.Comment: MNRAS, the version as printed, the title and abstract change

Is the soft excess in active galactic nuclei real?

We systematically analyse all publicly available XMM–Newton spectra of radio-quiet PG quasars. The soft X-ray excess in these objects is well modelled by an additional, cool, Compton scattering region. However, the remarkably constant temperature derived for this component over the whole sample requires a puzzling fine tuning of the parameters. Instead, we propose that the soft excess is an artifact of strong, relativistically smeared, partially ionized absorption. The strong jump in opacity at 0.7 keV from O vii, O viii and iron can lead to an apparent soft excess below this energy, which is trivially constant since it depends on atomic processes. This can have a dramatic effect on the derived spectrum, which has implications for fitting the relativistic smearing of the reflected iron line emission from the disc

Thermal proteome profiling of breast cancer cells reveals proteasomal activation by CDK4/6 inhibitor palbociclib

Palbociclib is a CDK4/6 inhibitor approved for metastatic estrogen receptor-positive breast cancer. In addition to G1 cell cycle arrest, palbociclib treatment results in cell senescence, a phenotype that is not readily explained by CDK4/6 inhibition. In order to identify a molecular mechanism responsible for palbociclib-induced senescence, we performed thermal proteome profiling of MCF7 breast cancer cells. In addition to affecting known CDK4/6 targets, palbociclib induces a thermal stabilization of the 20S proteasome, despite not directly binding to it. We further show that palbociclib treatment increases proteasome activity independently of the ubiquitin pathway. This leads to cellular senescence, which can be counteracted by proteasome inhibitors. Palbociclib-induced proteasome activation and senescence is mediated by reduced proteasomal association of ECM29. Loss of ECM29 activates the proteasome, blocks cell proliferation, and induces a senescence-like phenotype. Finally, we find that ECM29 mRNA levels are predictive of relapse-free survival in breast cancer patients treated with endocrine therapy. In conclusion, thermal proteome profiling identifies the proteasome and ECM29 protein as mediators of palbociclib activity in breast cancer cells

GRS 1915+105: the distance, radiative processes and energy-dependent variability

We present an exhaustive analysis of five broad-band observations of GRS 1915+105 in two variability states, chi and omega, observed simultaneously by the PCA, HEXTE and OSSE. We find all the spectra well fitted by Comptonization of disc blackbody photons, with very strong evidence for the presence of a nonthermal electron component in the Comptonizing plasma. Both the energy and the power spectra in the chi state are typical to the very high/intermediate state of black-hole binaries. The spectrum of the omega state is characterized by a strong blackbody component Comptonized by thermal electrons and a weak nonthermal tail. We then calculate rms spectra (fractional variability as functions of energy) for the PCA data. We accurately model the rms spectra by coherent superposition of variability in the components implied by the spectral fits, namely a less variable blackbody and more variable Comptonization. The latter dominates at high energies, resulting in a flattening of the rms at high energies in most of the data. This is also the case for the spectra of the QPOs present in the chi state. Then, some of our data require a radial dependence of the rms of the disc blackbody. We also study the distance to the source, and find 11 kpc as the most likely value, contrary to a recent claim of a much lower value.Comment: Accepted to MNRAS, landscape table in a separate fil

Patterns of energy-dependent variability from Comptonization

We study fractional variability as a function of energy from black-hole X-ray binaries on timescales from milliseconds to hundreds of seconds. We build a theoretical model of energy-dependent variability in which the X-ray energy spectrum varies in response to a changing physical parameter. We compare these models to rms spectra obtained from RXTE PCA observations of black-hole binaries XTE J1550-564 and XTE J1650-500. We show that two main variability models are consistent with the data: variable seed photon input in the hard state and variable power in the Comptonized component in the soft and very high states. The lack of clear reflection features in the rms spectra implies that the reflection and the X-ray continuum, when integrated over Fourier frequencies, are correlated and vary with similar fractional amplitudes. Our models predict two important features of rms spectra, not possible to be clearly seen by the PCA due sensitivity limits. At soft X-rays, >~3 keV, we predict the presence of a break in the rms spectrum at energy directly related to the seed photon temperature. At higher energies, ~20--30 keV, we predict a peak in the rms spectrum originating from the variability of the spectrum produced by a hybrid thermal/non-thermal electron distribution. If these features are confirmed by broad-band observations, they will impose important constraints on the origin of the seed photons for Comptonization and the electron distribution in the hot plasma.Comment: 11 pages, 12 figures, revised version, accepted for publication in MNRA

Physics of accretion in the millisecond pulsar XTE J1751-305

We have undertaken an extensive study of X-ray data from the accreting millisecond pulsar XTE J1751-305 observed by RXTE and XMM-Newton during its 2002 outburst. In all aspects this source is similar to a prototypical millisecond pulsar SAX J1808.4-3658, except for the higher peak luminosity of 13 per cent of Eddington, and the optical depth of the hard X-ray source larger by factor ~2. Its broad-band X-ray spectrum can be modelled by three components. We interpret the two soft components as thermal emission from a colder (kT ~ 0.6 keV) accretion disc and a hotter (~1 keV) spot on the neutron star surface. We interpret the hard component as thermal Comptonization in plasma of temperature ~40 keV and optical depth of ~1.5 in a slab geometry. The plasma is heated by the accretion shock as the material collimated by the magnetic field impacts on to the surface. The seed photons for Comptonization are provided by the hotspot, not by the disc. The Compton reflection is weak and the disc is probably truncated into an optically thin flow above the magnetospheric radius. Rotation of the emission region with the star creates an almost sinusoidal pulse profile with rms amplitude of 3.3 per cent. The energy-dependent soft phase lags can be modelled by two pulsating components shifted in phase, which is naturally explained by a different character of emission of the optically thick spot and optically thin shock combined with the action of the Doppler boosting.Comment: Accepted for publication in MNRAS, 15 pages, 16 figures (references corrected

How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

An RNA-seq experiment with 48 biological replicates in each of 2 conditions was performed to determine the number of biological replicates ($n_r$) required, and to identify the most effective statistical analysis tools for identifying differential gene expression (DGE). When $n_r=3$, seven of the nine tools evaluated give true positive rates (TPR) of only 20 to 40 percent. For high fold-change genes ($|log_{2}(FC)|\gt2$) the TPR is $\gt85$ percent. Two tools performed poorly; over- or under-predicting the number of differentially expressed genes. Increasing replication gives a large increase in TPR when considering all DE genes but only a small increase for high fold-change genes. Achieving a TPR $\gt85$% across all fold-changes requires $n_r\gt20$. For future RNA-seq experiments these results suggest $n_r\gt6$, rising to $n_r\gt12$ when identifying DGE irrespective of fold-change is important. For $6 \lt n_r \lt 12$, superior TPR makes edgeR the leading tool tested. For $n_r \ge12$, minimizing false positives is more important and DESeq outperforms the other tools.Comment: 21 Pages and 4 Figures in main text. 9 Figures in Supplement attached to PDF. Revision to correct a minor error in the abstrac