Local Disk Research Articles

Hot-starting software containers for STAR aligner.

BackgroundUsing software containers has become standard practice to reproducibly deploy and execute biomedical workflows on the cloud. However, some applications that contain time-consuming initialization steps will produce unnecessary costs for repeated executions.FindingsWe demonstrate that hot-starting from containers that have been frozen after the application has already begun execution can speed up bioinformatics workflows by avoiding repetitive initialization steps. We use an open-source tool called Checkpoint and Restore in Userspace (CRIU) to save the state of the containers as a collection of checkpoint files on disk after it has read in the indices. The resulting checkpoint files are migrated to the host, and CRIU is used to regenerate the containers in that ready-to-run hot-start state. As a proof-of-concept example, we create a hot-start container for the spliced transcripts alignment to a reference (STAR) aligner and deploy this container to align RNA sequencing data. We compare the performance of the alignment step with and without checkpoints on cloud platforms using local and network disks.ConclusionsWe demonstrate that hot-starting Docker containers from snapshots taken after repetitive initialization steps are completed significantly speeds up the execution of the STAR aligner on all experimental platforms, including Amazon Web Services, Microsoft Azure, and local virtual machines. Our method can be potentially employed in other bioinformatics applications in which a checkpoint can be inserted after a repetitive initialization phase.

The Effectiveness of Module and Compact Disc Poem Teaching Based on Local Wisdom

.

Comparison of Transforaminal Lumbar Interbody Fusion Using the Boomerang-Shaped Cage with Traditional Posterior Lumbar Interbody Fusion for Lumbar Spondylolisthesis.

Introduction This study aimed to compare the clinical and radiological results of transforaminal lumbar interbody fusion (TLIF) with a boomerang-shaped cage and traditional posterior lumbar interbody fusion (PLIF) according to fused level and elucidate whether TLIF could replace PLIF at all lumbar levels. Methods The study investigated 128 patients with lumbar spondylolisthesis who underwent a single-level TLIF or traditional PLIF. Intraoperative blood loss, operative time, and recovery rate were analyzed. Percent slip, disc height, and local lordosis at the fused level were measured using X-ray images from preoperation to the final follow-up. Results No significant differences in recovery rate were observed at any level. The operative time and intraoperative blood loss were significantly less in the TLIF group at the L4/5 and L5/S1 levels. There were no significant differences in disc height or local lordosis at the L3/4 and L4/5 levels, and a satisfactory level of maintenance after the operation was achieved in both groups. However, at the L5/S1 level, postoperative maintenance after TLIF could not be achieved, and the obtained disc height and local lordosis in TLIF significantly decreased. Conclusions Compared with traditional PLIF, TLIF was a less invasive procedure with a shorter operative time and lesser blood loss. TLIF could obtain similar local lordosis and disc height as PLIF at the L3/4 and L4/5 levels. At the L5/S1 level, the postoperative maintenance of local lordosis and disc height after TLIF was inferior to that after PLIF. On the basis of our results, we do not recommend performing TLIF at only the L5/S1 level.

Millisecond Pulsar Origin of the Galactic Center Excess and Extended Gamma-Ray Emission from Andromeda: A Closer Look

Abstract A new measurement of a spatially extended gamma-ray signal from the center of the Andromeda galaxy (M31) has recently been published by the Fermi-LAT collaboration, reporting that the emission broadly resembles the so-called Galactic center excess (GCE) of the Milky Way (MW). The weight of the evidence is steadily accumulating on a millisecond pulsar (MSPs) origin for the GCE. These elements prompt us to compare these observations with what is, perhaps, the simplest model for an MSP population, which is solely obtained by rescaling of the MSP luminosity function that is determined in the local MW disk via the respective stellar mass of the systems. Remarkably, we find that without free fitting parameters, this model can account for both the energetics and the morphology of the GCE within uncertainties. For M31, the estimated luminosity due to primordial MSPs is expected to only contribute about a quarter of the detected emission, although a stronger contribution cannot be excluded given the large uncertainties. If correct, the model predicts that the M31 disk emission due to MSPs is not far below the present upper bound. We also discuss additional refinements of this simple model. Using the correlation between globular cluster gamma-ray luminosity and stellar encounter rate, we gauge the dynamical MSP formation in the bulge. This component is expected to contribute to the GCE only at a level of ≲5%, it could affect the signal’s morphology. We also comment on the limitations of our model and on future perspectives for improved diagnostics.

A review of Morlet wavelet analysis of radial profiles of Saturn's rings.

Spiral waves propagating in Saturn's rings have wavelengths that vary with radial position within the disc. The best-quality observations of these waves have the form of radial profiles centred on a particular azimuth. In that context, the wavelength of a given spiral wave is seen to change substantially with position along the one-dimensional profile. In this paper, we review the use of Morlet wavelet analysis to understand these waves. When signal to noise is high and the cause of the wave is well understood, wavelet analysis has been used to solve for wave parameters that are diagnostic of local disc properties. Waves that are not readily perceptible in the spatial domain signal can be clearly identified. Furthermore, filtering in wavelet space, followed by the reverse wavelet transform, has been used to isolate the part of the signal that is of interest. When the cause of the wave is not known, comparing the phases of the complex-valued wavelet transforms from many profiles has been used to determine wave parameters that cannot be determined from any single profile. When signal to noise is low, co-adding wavelet transforms while manipulating the phase has been used to boost a wave's signal above detection limits.This article is part of the theme issue 'Redundancy rules: the continuous wavelet transform comes of age'.

Neutral versus ionized gas kinematics at z ≃ 2.6: the AGN-host starburst galaxy PKS 0529-549

We present a multiwavelength study of the AGN-host starburst galaxy PKS 0529-549 at z~2.6. We use (1) new ALMA observations of the dust continuum and of the [CI] 370 um line, tracing molecular gas, (2) SINFONI spectroscopy of the [OIII] 5007 Ang line, tracing ionized gas, and (3) ATCA radio continuum images, tracing synchrotron emission. Both [CI] and [OIII] show regular velocity gradients, but their systemic velocities and position angles differ by ~300 km/s and ~30 degrees, respectively. The [CI] is consistent with a rotating disc, aligned with the dust and stellar continuum, while the [OIII] likely traces an outflow, aligned with two AGN-driven radio lobes. We model the [CI] cube using 3D disc models, which give best-fit rotation velocities V~310 km/s and velocity dispersions sigma<30 km/s. Hence, the [CI] disc has V/sigma>10 and is not particularly turbulent, similar to local galaxy discs. The dynamical mass (~10^11 Msun) is comparable to the baryonic mass within the errors. This suggests that baryons dominate the inner galaxy dynamics, similar to massive galaxies at z=0. Remarkably, PKS 0529-549 lies on the local baryonic Tully-Fisher relation, indicating that at least some massive galaxies are already in place and kinematically relaxed at z~2.6. This work highlights the potential of the [CI] line to trace galaxy dynamics at high z, as well as the importance of multiwavelength data to interpret gas kinematics.

Molecular gas in AzTEC/C159: a star-forming disk galaxy 1.3 Gyr after the Big Bang

We studied the molecular gas properties of AzTEC/C159, a star-forming disk galaxy at z = 4.567, in order to better constrain the nature of the high-redshift end of the submillimeter-selected galaxy (SMG) population. We secured 12CO molecular line detections for the J = 2 →1 and J = 5 →4 transitions using the Karl G. Jansky Very Large Array (VLA) and the NOrthern Extended Millimeter Array (NOEMA) interferometer. The broad (FWHM ~ 750 km s−1) and tentative double-peaked profiles of the two 12CO lines are consistent with an extended molecular gas reservoir, which is distributed in a rotating disk, as previously revealed from [CII] 158 μm line observations. Based on the 12CO(2 →1) emission line, we derived L′CO=(3.4±0.6)×1010 K km s−1 pc2, which yields a molecular gas mass of MH2(αCO/4.3)=(1.5±0.3)×1011 M⊙ and unveils a gas-rich system with μgas(αCO/4.3)≡MH2/M⋆=3.3±0.7. The extreme star formation efficiency of AzTEC/C159, parametrized by the ratio LIR/L′CO=(216±80) L⊙ (K km s−1 pc2)−1, is comparable to merger-driven starbursts such as local ultra-luminous infrared galaxies and SMGs. Likewise, the 12CO(5 →4)/CO(2 →1) line brightness temperature ratio of r52 = 0.55 ± 0.15 is consistent with high-excitation conditions as observed in SMGs. Based on mass budget considerations, we constrained the value for the L′CO – H2 mass conversion factor in AzTEC/C159, that is, αCO=3.9−1.3+2.7 M⊙ K−1 km−1 s pc−2, which is consistent with a self-gravitating molecular gas distribution as observed in local star-forming disk galaxies. Cold gas streams from cosmological filaments might be fueling a gravitationally unstable gas-rich disk in AzTEC/C159, which breaks into giant clumps and forms stars as efficiently as in merger-driven systems and generates high gas excitation. These results support the evolutionary connection between AzTEC/C159-like systems and massive quiescent disk galaxies at z ~ 2.

Building a scientific workflow framework to enable real‐time machine learning and visualization

SummaryNowadays, we have entered the era of big data. In the area of high performance computing, large‐scale simulations can generate huge amounts of data with potentially critical information. However, these data are usually saved in intermediate files and are not instantly visible until advanced data analytics techniques are applied after reading all simulation data from persistent storages (eg, local disks or a parallel file system). This approach puts users in a situation where they spend long time on waiting for running simulations while not knowing the status of the running job. In this paper, we build a new computational framework to couple scientific simulations with multi‐step machine learning processes and in‐situ data visualizations. We also design a new scalable simulation‐time clustering algorithm to automatically detect fluid flow anomalies. This computational framework is built upon different software components and provides plug‐in data analysis and visualization functions over complex scientific workflows. With this advanced framework, users can monitor and get real‐time notifications of special patterns or anomalies from ongoing extreme‐scale turbulent flow simulations.

Disc-Aware Ensemble Network for Glaucoma Screening From Fundus Image

Glaucoma is a chronic eye disease that leads to irreversible vision loss. Most of the existing automatic screening methods first segment the main structure and subsequently calculate the clinical measurement for the detection and screening of glaucoma. However, these measurement-based methods rely heavily on the segmentation accuracy and ignore various visual features. In this paper, we introduce a deep learning technique to gain additional image-relevant information and screen glaucoma from the fundus image directly. Specifically, a novel disc-aware ensemble network for automatic glaucoma screening is proposed, which integrates the deep hierarchical context of the global fundus image and the local optic disc region. Four deep streams on different levels and modules are, respectively, considered as global image stream, segmentation-guided network, local disc region stream, and disc polar transformation stream. Finally, the output probabilities of different streams are fused as the final screening result. The experiments on two glaucoma data sets (SCES and new SINDI data sets) show that our method outperforms other state-of-the-art algorithms.

Low-mass planet migration in magnetically torqued dead zones – II. Flow-locked and runaway migration, and a torque prescription

We examine the migration of low mass planets in laminar protoplanetary discs, threaded by large scale magnetic fields in the dead zone that drive radial gas flows. As shown in Paper I, a dynamical corotation torque arises due to the flow-induced asymmetric distortion of the corotation region and the evolving vortensity contrast between the librating horseshoe material and background disc flow. Using simulations of laminar torqued discs containing migrating planets, we demonstrate the existence of the four distinct migration regimes predicted in Paper I. In two regimes, the migration is approximately locked to the inward or outward radial gas flow, and in the other regimes the planet undergoes outward runaway migration that eventually settles to fast steady migration. In addition, we demonstrate torque and migration reversals induced by midplane magnetic stresses, with a bifurcation dependent on the disc surface density. We develop a model for fast migration, and show why the outward runaway saturates to a steady speed, and examine phenomenologically its termination due to changing local disc conditions. We also develop an analytical model for the corotation torque at late times that includes viscosity, for application to discs that sustain modest turbulence. Finally, we use the simulation results to develop torque prescriptions for inclusion in population synthesis models of planet formation.

Analysis of changes in cervical spinal curvature and intervertebral disk space height following ACDF surgery in a group of 100 patients followed up for 12 months

We analysed 100 patients following anterior cervical discectomy and fusion with interbody stabilisation with PEEK cages. Radiographs obtained preoperatively and during the 12-month follow-up were compared to track changes in overall and local cervical lordosis and disk space height. Subsidence was defined as cage migration ≥ 3 mm into the adjacent endplates. Mean change in operated disk space height was 1.13 ± 1.33 mm. Subsidence was detected in 10.23% of the operated spaces. Mean change in overall cervical lordosis was 1.31 ± 5.71 degrees, and mean change in local lordosis was 0.19 ± 4.71 degrees. Change in overall cervical lordosis correlated with change in local lordosis (r = 0.61, p < 0.01). The greatest changes in lordosis and disk space height were noted immediately post-surgery. Baseline values were approximated gradually over time, but the post-operative values at 12 months were still higher than baseline. Disk space height change did not correlate with changes in patient-reported pain intensity at baseline (VAS 0) vs. at 12 months post-operatively (VAS 12) (r = 0.12, p < 0.05) or changes in the Neck Disability Index (NDI) at baseline (NDI 0) vs. at 12 months post-operatively (NDI 12) (r = −0.02, p = 0.05). Changes in overall cervical lordosis did not directly influence treatment outcomes assessed by comparing VAS 0 vs. VAS 12 (r = 0.13, p = 0.24) or NDI 0 vs. NDI 12 (r = −0.0005, p = 0.96). Surgical outcomes depend primarily on adequate decompression of the spinal cord and nerve roots. Post-operative radiological changes did not directly influence patients’ pain level or quality of life.

Pebble-isolation mass: Scaling law and implications for the formation of super-Earths and gas giants

The growth of a planetary core by pebble accretion stops at the so-called pebble isolation mass, when the core generates a pressure bump that traps drifting pebbles outside its orbit. The value of the pebble isolation mass is crucial in determining the final planet mass. If the isolation mass is very low, gas accretion is protracted and the planet remains at a few Earth masses with a mainly solid composition. For higher values of the pebble isolation mass, the planet might be able to accrete gas from the protoplanetary disc and grow into a gas giant. Previous works have determined a scaling of the pebble isolation mass with cube of the disc aspect ratio. Here, we expand on previous measurements and explore the dependency of the pebble isolation mass on all relevant parameters of the protoplanetary disc. We use 3D hydrodynamical simulations to measure the pebble isolation mass and derive a simple scaling law that captures the dependence on the local disc structure and the turbulent viscosity parameter α. We find that small pebbles, coupled to the gas, with Stokes number τf &lt; 0.005 can drift through the partial gap at pebble isolation mass. However, as the planetary mass increases, particles must be decreasingly smaller to penetrate the pressure bump. Turbulent diffusion of particles, however, can lead to an increase of the pebble isolation mass by a factor of two, depending on the strength of the background viscosity and on the pebble size. We finally explore the implications of the new scaling law of the pebble isolation mass on the formation of planetary systems by numerically integrating the growth and migration pathways of planets in evolving protoplanetary discs. Compared to models neglecting the dependence of the pebble isolation mass on the α-viscosity, our models including this effect result in higher core masses for giant planets. These higher core masses are more similar to the core masses of the giant planets in the solar system.

Orbital alignment of circumbinary planets that form in misaligned circumbinary discs: the case of Kepler-413b

Although most of the circumbinary planets detected by the Kepler spacecraft are on orbits that are closely aligned with the binary orbital plane, the systems Kepler-413 and Kepler-453 exhibit small misalignments of $\sim 2.5^\circ$. One possibility is that these planets formed in a circumbinary disc whose midplane was inclined relative to the binary orbital plane. Such a configuration is expected to lead to a warped and twisted disc, and our aim is to examine the inclination evolution of planets embedded in these discs. We employed 3D hydrodynamical simulations that examine the disc response to the presence of a modestly inclined binary with parameters that match the Kepler-413 system, as a function of disc parameters and binary inclinations. The discs all develop slowly varying warps, and generally display very small amounts of twist. Very slow solid body precession occurs because a large outer disc radius is adopted. Simulations of planets embedded in these discs resulted in the planet aligning with the binary orbit plane for disc masses close to the minimum mass solar nebular, such that nodal precession of the planet was controlled by the binary. For higher disc masses, the planet maintains near coplanarity with the local disc midplane. Our results suggest that circumbinary planets born in tilted circumbinary discs should align with the binary orbit plane as the disc ages and loses mass, even if the circumbinary disc remains misaligned from the binary orbit. This result has important implications for understanding the origins of the known circumbinary planets.

I didn't see that! An examination of internet browser cache behaviour following website visits

By default, all major web browsing applications cache visited website content to the local disk to improve browser efficiency and enhance user experience. As a result of this action, the cache provides a window of opportunity for the digital forensic practitioner to establish the nature of the content which was hosted on the websites which had been visited. Cache content is often evidential during cases surrounding Indecent Images of Children (IIoC) where it is often assumed that cached IIoC is a record of the content viewed by a defendant via their browser. However, this may not always be the case. This article investigates web browser cache behaviour in an attempt to identify whether it is possible to definitively establish what quantity of cached content was viewable by a user following a visit to a website. Both the Mozilla Firefox and Google Chrome browser caches are analysed following visits to 10 test websites in order to quantify cache behaviour. Results indicate that the volume of locally cached content differs between both web browsers and websites visited, with instances of images cached which would not have been viewable by the user upon landing on a website. Further, the number of cached images appears to be effected by how much of a website a user scrolls through.

Angular Momentum Evolution of Stellar Disks at High Redshifts

Abstract The stellar disk size of a galaxy depends on the ratio of the disk stellar mass to the halo mass, m ⋆ ≡ M ⋆/M dh, and the fraction of the dark halo angular momentum transferred to the stellar disk, j ⋆ ≡ J ⋆/J dh. Since m ⋆ and j ⋆ are determined by many star formation–related processes, measuring j ⋆ and m ⋆ at various redshifts is essential to understanding the formation history of disk galaxies. We use the 3D-HST GOODS-S, COSMOS, and AEGIS imaging data and photo-z catalog to examine j ⋆ and m ⋆ for star-forming galaxies at z ∼ 2–4, when disks are actively forming. We find that the j ⋆/m ⋆ ratio is ≃0.77 ± 0.06 for all three redshifts over the entire mass range examined, 8 × 1010 &lt; M dh/h −1 M ⊙ &lt; 2 × 1012, with a possible (&lt;30%) decrease with mass. This high ratio is close to those of local disk galaxies, descendants of our galaxies in terms of M dh growth, implying a nearly constant j ⋆/m ⋆ over the past 12 Gyr. These results are remarkable because mechanisms controlling angular momentum transfer to disks such as inflows and feedback depend on both cosmic time and halo mass, and, indeed, theoretical studies tend to predict j ⋆/m ⋆ changing with redshift and mass. It is found that some of the recent theoretical galaxy formation simulations predict a smaller j ⋆/m ⋆ than our values. We also find that a significant fraction of our galaxies appears to be unstable against bar formation.

Chemical evolution with rotating massive star yields – I. The solar neighbourhood and the s-process elements

We present a comprehensive study of the abundance evolution of the elements from H to U in the Milky Way halo and local disk. We use a consistent chemical evolution model, metallicity dependent isotopic yields from low and intermediate mass stars and yields from massive stars which include, for the first time, the combined effect of metallicity, mass loss and rotation for a large grid of stellar masses and for all stages of stellar evolution. The yields of massive stars are weighted by a metallicity dependent function of the rotational velocities, constrained by observations as to obtain a primary-like $^{14}$N behavior at low metallicity and to avoid overproduction of s-elements at intermediate metallicities. We show that the solar system isotopic composition can be reproduced to better than a factor of two for isotopes up to the Fe-peak, and at the 10\% level for most pure s-isotopes, both light ones (resulting from the weak s-process in rotating massive stars) and the heavy ones (resulting from the main s-process in low and intermediate mass stars). We conclude that the light element primary process (LEPP), invoked to explain the apparent abundance deficiency of the s-elements with A< 100, is not necessary. We also reproduce the evolution of the heavy to light s-elements abundance ratio ([hs/ls]) - recently observed in unevolved thin disk stars - as a result of the contribution of rotating massive stars at sub-solar metallicities. We find that those stars produce primary F and dominate its solar abundance and we confirm their role in the observed primary behavior of N. In contrast, we show that their action is insufficient to explain the small observed values of C12/C13 in halo red giants, which is rather due to internal processes in those stars.

Numerical Simulations of Multiphase Winds and Fountains from Star-forming Galactic Disks. I. Solar Neighborhood TIGRESS Model

Abstract Gas blown away from galactic disks by supernova (SN) feedback plays a key role in galaxy evolution. We investigate outflows utilizing the solar neighborhood model of our high-resolution, local galactic disk simulation suite, TIGRESS. In our numerical implementation, star formation and SN feedback are self-consistently treated and well resolved in the multiphase, turbulent, magnetized interstellar medium. Bursts of star formation produce spatially and temporally correlated SNe that drive strong outflows, consisting of hot ( ) winds and warm ( ) fountains. The hot gas at distance from the midplane has mass and energy fluxes nearly constant with d. The hot flow escapes our local Cartesian box barely affected by gravity, and is expected to accelerate up to terminal velocity of . The mean mass and energy loading factors of the hot wind are 0.1 and 0.02, respectively. For warm gas, the mean outward mass flux through is comparable to the mean star formation rate, but only a small fraction of this gas is at velocity . Thus, the warm outflows eventually fall back as inflows. The warm fountain flows are created by expanding hot superbubbles at at larger d neither ram pressure acceleration nor cooling transfers significant momentum or energy flux from the hot wind to the warm outflow. The velocity distribution at launching near is a better representation of warm outflows than a single mass loading factor, potentially enabling development of subgrid models for warm galactic winds in arbitrary large-scale galactic potentials.

Study of the Transition from MRI to Magnetic Turbulence via Parasitic Instability by a High-order MHD Simulation Code

Abstract Magnetic turbulence in accretion disks under ideal magnetohydrodynamic (MHD) conditions is expected to be driven by the magneto-rotational instability (MRI) followed by secondary parasitic instabilities. We develop a three-dimensional ideal MHD code that can accurately resolve turbulent structures, and carry out simulations with a net vertical magnetic field in a local shearing box disk model to investigate the role of parasitic instabilities in the formation process of magnetic turbulence. Our simulations reveal that a highly anisotropic Kelvin–Helmholtz (K–H) mode parasitic instability evolves just before the first peak in turbulent stress and then breaks large-scale shear flows created by MRI. The wavenumber of the enhanced parasitic instability is larger than the theoretical estimate, because the shear flow layers sometimes become thinner than those assumed in the linear analysis. We also find that interaction between antiparallel vortices caused by the K–H mode parasitic instability induces small-scale waves that break the shear flows. On the other hand, at repeated peaks in the nonlinear phase, anisotropic wavenumber spectra are observed only in the small wavenumber region and isotropic waves dominate at large wavenumbers unlike for the first peak. Restructured channel flows due to MRI at the peaks in nonlinear phase seem to be collapsed by the advection of small-scale shear structures into the restructured flow and resultant mixing.

Changes of Atterberg limits and electrochemical behaviors of clays with dispersants as conditioning agents for EPB shield tunnelling

Clay clogging frequently happens during tunnelling with an earth pressure balance (EPB) shield in clayey ground and results in local disk cutter housings. It could even completely clog shield chambers with a blocked cutterhead. Dispersants are commonly adopted as conditioning agents to reduce clay stickiness, which is related to clay consistency determined based on the Atterberg limits. This paper investigates changes of Atterberg limits of clays with dispersant content and their electrochemical mechanism on evaluating clay conditioning approach for EPB shield tunnelling. Soils consisting of bentonite, kaolin and their mixtures were conditioned respectively with two different dispersants including sodium hexametaphosphate and sodium polyacrylate. They were then tested for determining their Atterberg limits, Zeta potential and repulsive energy. The results show that the liquid limit and plasticity index decreased significantly due to the addition of the dispersants, but these decreases became less obvious with a higher dispersant content. The effect of sodium hexametaphosphate was more significant than that of sodium polyacrylate on the clays at the same dispersant content, but the latter had quicker conditioning effect. The amount of the negative charge of the clayey particles increased and the Zeta potential decreased with an increase of dispersant content. The reduction of Zeta potential induced by the sodium hexametaphosphate was greater than that induced by the sodium polyacrylate at the identical dispersant content. The decrease of Zeta potential increased the peak value of the total repulsive energy, leading to reductions of the Atterberg limits of the clays. The reduction of plasticity index leads to less water required to transform clay from “soft” to “very soft” or “liquid” region and shorter time required for the response of clay to dispersant.

X-ray radiative transfer in protoplanetary disks

Context. The X-ray luminosities of T Tauri stars are about two to four orders of magnitude higher than the luminosity of the contemporary Sun. As these stars are born in clusters, their disks are not only irradiated by their parent star but also by an X-ray background field produced by the cluster members. Aims. We aim to quantify the impact of X-ray background fields produced by young embedded clusters on the chemical structure of disks. Further, we want to investigate the importance of the dust for X-ray radiative transfer in disks. Methods. We present a new X-ray radiative transfer module for the radiation thermo-chemical disk code PRODIMO (PROtoplanetary DIsk MOdel), which includes X-ray scattering and absorption by both the gas and dust component. The X-ray dust opacities can be calculated for various dust compositions and dust-size distributions. For the X-ray radiative transfer we consider irradiation by the star and by X-ray background fields. To study the impact of X-rays on the chemical structure of disks we use the well established disk ionization tracers N2H+ and HCO+. Results. For evolved dust populations (e.g. grain growth), X-ray opacities are mostly dominated by the gas; only for photon energies E ≳ 5−10 keV do dust opacities become relevant. Consequently the local disk X-ray radiation field is only affected in dense regions close to the disk midplane. X-ray background fields can dominate the local X-ray disk ionization rate for disk radii r ≳ 20 au. However, the N2H+ and HCO+ column densities are only significantly affected in cases of low cosmic-ray ionization rates (≲10-19 s-1), or if the background flux is at least a factor of ten higher than the flux level of ≈10-5 erg cm-2 s-1 expected for clusters typical for the solar vicinity. Conclusions. Observable signatures of X-ray background fields in low-mass star-formation regions, like Taurus, are only expected for cluster members experiencing a strong X-ray background field (e.g. due to their location within the cluster). For the majority of the cluster members, the X-ray background field has relatively little impact on the disk chemical structure.