Athena X-IFU event reconstruction software: SIRENA

Trabajo presentado a la Conferencia: Exploring the Hot and Energetic Universe: The first scientific conference dedicated to the Athena X-ray observatory; celebrada en Madrid (España) del 8 a 10 de septiembre de 2015.This contribution describes the status and technical details of the SIRENA package, the software currently in development to perform the on board event energy reconstruction for the Athena calorimeter X-IFU. This on board processing will be done in the X-IFU DRE unit and it will consist in an initial triggering of event pulses followed by an analysis (with the SIRENA package) to determine the energy content of such events.The current algorithm used by SIRENA is the optimal filtering technique (also used by ASTRO-H processor) although some other algorithms are also being tested.Here we present these studies and some preliminary results about the energy resolution of the instrument based on simulations done with the SIXTE simulator (http://www.sternwarte.uni-erlangen.de/research/sixte/) in which SIRENA is integrated.This work has been funded by the Spanish Ministries MICINN and MINECO under projects ESP2006-13608-C02-01, AYA2009-08059, AYA2010-21490-C02-01, AYA2012-39767-C02-01, ESP2013-48637-C2-1-P, ESP2014-53672-C3-1-P.Peer Reviewe

Probing X-ray burst -- accretion disk interaction in low mass X-ray binaries through kilohertz quasiperiodic oscillations

The intense radiation flux of Type I X-ray bursts is expected to interact with the accretion flow around neutron stars. High frequency quasiperiodic oscillations (kHz QPOs), observed at frequencies matching orbital frequencies at tens of gravitational radii, offer a unique probe of the innermost disk regions. In this paper, we follow the lower kHz QPOs, in response to Type I X-ray bursts, in two prototypical QPO sources, namely 4U 1636-536 and 4U 1608-522, as observed by the Proportional Counter Array of the Rossi X-ray Timing Explorer. We have selected a sample of 15 bursts for which the kHz QPO frequency can be tracked on timescales commensurable with the burst durations (tens of seconds). We find evidence that the QPOs are affected for over ~200 s during one exceptionally long burst and ~100 s during two others (although at a less significant level), while the burst emission has already decayed to a level that would enable the pre-burst QPO to be detected. On the other hand, for most of our burst-kHz QPO sample, we show that the QPO is detected as soon as the statistics allow and in the best cases, we are able to set an upper limit of ~20 s on the recovery time of the QPO. This diversity of behavior cannot be related to differences in burst peak luminosity. We discuss these results in the framework of recent findings that accretion onto the neutron star may be enhanced during Type I X-ray bursts. The subsequent disk depletion could explain the disappearance of the QPO for ~100 s, as possibly observed in two events. However, alternative scenarios would have to be invoked for explaining the short recovery timescales inferred from most bursts. Clearly the combination of fast timing and spectral information of Type I X-ray bursts holds great potential in the study of the dynamics of the inner accretion flow around neutron stars.Comment: 8 pages, 9 figures, appears in Astronomy & Astrophysics, Volume 567, id.A80, published 07/201

Simulation of Radiative Transfer Within X-ray Microcalorimeter Absorbers

We present Monte Carlo simulations of radiative transfer within the absorbers of X-ray microcalorimeters, utilizing a numerical model for the photon propagation and photon absorption process within the absorber structure. In our model, we include effects of Compton scattering off bound electrons and fluorescence. Scattered or fluorescence photons as well as Auger and photoelectrons escaping the absorber can result in partial energy depositions. By implementing a simplified description of the physical processes compared to existing comprehensive particle transport software frameworks, our model aims to provide representative results at a small computational effort. This approach makes it possible to use our model for quick assessments, parametric studies, and application in other Monte Carlo-based instrument simulators like SIXTE, a software package for X-ray astronomical instrumentation. To study the impact of the energy loss effects on the spectral response of a microcalorimeter, we apply our model to the sensors of the cryogenic X-ray spectrometer X-IFU onboard the future Athena X-ray observatory

The X-IFU end-to-end simulations performed for the TES array optimization exercise

Trabajo presentado a la Conferencia: Exploring the Hot and Energetic Universe: The first scientific conference dedicated to the Athena X-ray observatory; celebrada en Madrid (España) del 8 a 10 de septiembre de 2015.-- et al.The focal plane assembly of the Athena X-ray Integral Field Unit (X-IFU) includes as the baseline an array of ~4000 single size calorimeters based on Transition Edge Sensors (TES). Other sensor array configurations could however be considered, combining TES of different properties (e.g. size). In attempting to improve the X-IFU performance in terms of field of view, count rate performance, and even spectral resolution, two alternative TES array configurations to the baseline have been simulated, each combining a small and a large pixel array. With the X-IFU end-to-end simulator, a sub-sample of the Athena core science goals, selected by the X-IFU science team as potentially driving the optimal TES array configuration, has been simulated for the results to be scientifically assessed and compared. In this contribution, we will describe the simulation set-up for the various array configurations, and highlight some of the results of the test cases simulated.Peer Reviewe

ATHENA X-IFU RMF with extended Line Spread Function

The present document describes the current implementation of the extended LSF model in the Athena X-IFU RMF and its usage for X-ray data analysi

GPU Supported Simulation of Transition-Edge Sensor Arrays

Abstract We present numerical simulations of full transition-edge sensor (TES) arrays utilizing graphical processing units (GPUs). With the support of GPUs, it is possible to perform simulations of large pixel arrays to assist detector development. Comparisons with TES small-signal and noise theory confirm the representativity of the simulated data. In order to demonstrate the capabilities of this approach, we present its implementation in xifusim, a simulator for the X-ray Integral Field Unit, a cryogenic X-ray spectrometer on board the future Athena X-ray observatory

Elevated MACC1 expression in colorectal cancer is driven by chromosomal instability and is associated with molecular subtype and worse patient survival

Metastasis-Associated in Colon Cancer 1 (MACC1) is a strong prognostic biomarker inducing proliferation, migration, invasiveness, and metastasis of cancer cells. The context of MACC1 dysregulation in cancers is, however, still poorly understood. Here, we investigated whether chromosomal instability and somatic copy number alterations (SCNA) frequently occurring in CRC contribute to MACC1 dysregulation, with prognostic and predictive impacts. Using the Oncotrack and Charité CRC cohorts of CRC patients, we showed that elevated MACC1 mRNA expression was tightly dependent on increased MACC1 gene SCNA and was associated with metastasis and shorter metastasis free survival. Deep analysis of the COAD-READ TCGA cohort revealed elevated MACC1 expression due to SCNA for advanced tumors exhibiting high chromosomal instability (CIN), and predominantly classified as CMS2 and CMS4 transcriptomic subtypes. For that cohort, we validated that elevated MACC1 mRNA expression correlated with reduced disease-free and overall survival. In conclusion, this study gives insights into the context of MACC1 expression in CRC. Increased MACC1 expression is largely driven by CIN, SCNA gains, and molecular subtypes, potentially determining the molecular risk for metastasis that might serve as a basis for patient-tailored treatment decisions

The Athena X-IFU Instrument Simulator xifusim

We present the instrument simulator xifusim developed for the X-ray Integral Field Unit X-IFU aboard the planned Athena mission. xifusim aims to be an accurate representation of the entire instrument, starting from a full simulation of the Transition-Edge Sensor (TES) array receiving impact photons unconstrained by the small signal limit. Its output current is then propagated through the entire readout chain, including multiplexing, amplification and the digital readout. The final output consists of triggered records, which can be post-processed to reconstruct the photon energies. The readout chain itself is separated into individual, modular blocks with several possible models for each, allowing the simulation of different readout schemes or models of varying physical accuracy at the expense of run time. New models are implemented as necessary to enable studies of the overall readout chain. Such studies are also facilitated by fine-grained control of the simulation output, including the internal state of intermediate simulation blocks. In addition to its modularity, xifusim also allows the manipulation of certain internal parameters during a run, enabling the simulation of readout chain characterization measurements, environmental drifts or various kinds of crosstalk.Open Access funding enabled and organized by Projekt DEAL.Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347Ministerio de Ciencia e Innovación http://dx.doi.org/10.13039/501100004837Friedrich-Alexander-Universität Erlangen-Nürnberg (1041

The Athena X-IFU Instrument Simulator xifusim

We present the instrument simulator xifusim developed for the X-ray Integral Field Unit X-IFU aboard the planned Athena mission. xifusim aims to be an accurate representation of the entire instrument, starting from a full simulation of the Transition-Edge Sensor (TES) array receiving impact photons unconstrained by the small signal limit. Its output current is then propagated through the entire readout chain, including multiplexing, amplification and the digital readout. The final output consists of triggered records, which can be post-processed to reconstruct the photon energies. The readout chain itself is separated into individual, modular blocks with several possible models for each, allowing the simulation of different readout schemes or models of varying physical accuracy at the expense of run time. New models are implemented as necessary to enable studies of the overall readout chain. Such studies are also facilitated by fine-grained control of the simulation output, including the internal state of intermediate simulation blocks. In addition to its modularity, xifusim also allows the manipulation of certain internal parameters during a run, enabling the simulation of readout chain characterization measurements, environmental drifts or various kinds of crosstalk.Bundesministerium für Wirtschaft und Technologie under DLR Grant Number 50 QR 1903.Spanish Ministry MCIU under project RTI2018-096686-B-C21 (MCIU/AEI/FEDER, UE), co-funded by FEDER funds.Open Access funding enabled and organized by Projekt DEAL.Peer reviewe

Correlating Global Gene Regulation to Angiogenesis in the Developing Chick Extra-Embryonic Vascular System

International audienceBACKGROUND: Formation of blood vessels requires the concerted regulation of an unknown number of genes in a spatial-, time- and dosage-dependent manner. Determining genes, which drive vascular maturation is crucial for the identification of new therapeutic targets against pathological angiogenesis. METHOLOGY/PRINCIPAL FINDINGS: We accessed global gene regulation throughout maturation of the chick chorio-allantoic membrane (CAM), a highly vascularized tissue, using pan genomic microarrays. Seven percent of analyzed genes showed a significant change in expression (>2-fold, FDR<5%) with a peak occurring from E7 to E10, when key morphogenetic and angiogenic genes such as BMP4, SMO, HOXA3, EPAS1 and FGFR2 were upregulated, reflecting the state of an activated endothelium. At later stages, a general decrease in gene expression occurs, including genes encoding mitotic factors or angiogenic mediators such as CYR61, EPAS1, MDK and MYC. We identified putative human orthologs for 77% of significantly regulated genes and determined endothelial cell enrichment for 20% of the orthologs in silico. Vascular expression of several genes including ENC1, FSTL1, JAM2, LDB2, LIMS1, PARVB, PDE3A, PRCP, PTRF and ST6GAL1 was demonstrated by in situ hybridization. Up to 9% of the CAM genes were also overexpressed in human organs with related functions, such as placenta and lung or the thyroid. 21-66% of CAM genes enriched in endothelial cells were deregulated in several human cancer types (P<.0001). Interfering with PARVB (encoding parvin, beta) function profoundly changed human endothelial cell shape, motility and tubulogenesis, suggesting an important role of this gene in the angiogenic process. CONCLUSIONS/SIGNIFICANCE: Our study underlines the complexity of gene regulation in a highly vascularized organ during development. We identified a restricted number of novel genes enriched in the endothelium of different species and tissues, which may play crucial roles in normal and pathological angiogenesis