MRI radiomic features are independently associated with overall survival in soft tissue sarcoma

Purpose: Soft tissue sarcomas (STS) represent a heterogeneous group of diseases, and selection of individualized treatments remains a challenge. The goal of this study was to determine whether radiomic features extracted from magnetic resonance (MR) images are independently associated with overall survival (OS) in STS. Methods and Materials: This study analyzed 2 independent cohorts of adult patients with stage II-III STS treated at center 1 (N = 165) and center 2 (N = 61). Thirty radiomic features were extracted from pretreatment T1-weighted contrast-enhanced MR images. Prognostic models for OS were derived on the center 1 cohort and validated on the center 2 cohort. Clinical-only (C), radiomics-only (R), and clinical and radiomics (C+R) penalized Cox models were constructed. Model performance was assessed using Harrell\u27s concordance index. Results: In the R model, tumor volume (hazard ratio [HR], 1.5) and 4 texture features (HR, 1.1-1.5) were selected. In the C+R model, both age (HR, 1.4) and grade (HR, 1.7) were selected along with 5 radiomic features. The adjusted c-indices of the 3 models ranged from 0.68 (C) to 0.74 (C+R) in the derivation cohort and 0.68 (R) to 0.78 (C+R) in the validation cohort. The radiomic features were independently associated with OS in the validation cohort after accounting for age and grade (HR, 2.4; Conclusions: This study found that radiomic features extracted from MR images are independently associated with OS when accounting for age and tumor grade. The overall predictive performance of 3-year OS using a model based on clinical and radiomic features was replicated in an independent cohort. Optimal models using clinical and radiomic features could improve personalized selection of therapy in patients with STS

Radio continuum observations of Class I protostellar disks in Taurus: constraining the greybody tail at centimetre wavelengths

We present deep 1.8 cm (16 GHz) radio continuum imaging of seven young stellar objects in the Taurus molecular cloud. These objects have previously been extensively studied in the sub-mm to NIR range and their SEDs modelled to provide reliable physical and geometrical parametres.We use this new data to constrain the properties of the long-wavelength tail of the greybody spectrum, which is expected to be dominated by emission from large dust grains in the protostellar disk. We find spectra consistent with the opacity indices expected for such a population, with an average opacity index of beta = 0.26+/-0.22 indicating grain growth within the disks. We use spectra fitted jointly to radio and sub-mm data to separate the contributions from thermal dust and radio emission at 1.8 cm and derive disk masses directly from the cm-wave dust contribution. We find that disk masses derived from these flux densities under assumptions consistent with the literature are systematically higher than those calculated from sub-mm data, and meet the criteria for giant planet formation in a number of cases.Comment: submitted MNRA

Nighttime chemical transformation in biomass burning plumes : A box model analysis initialized with aircraft observations

Biomass burning (BB) is a large source of reactive compounds in the atmosphere. While the daytime photochemistry of BB emissions has been studied in some detail, there has been little focus on nighttime reactions despite the potential for substantial oxidative and heterogeneous chemistry. Here, we present the first analysis of nighttime aircraft intercepts of agricultural BB plumes using observations from the NOAA WP-3D aircraft during the 2013 Southeast Nexus (SENEX) campaign. We use these observations in conjunction with detailed chemical box modeling to investigate the formation and fate of oxidants (NO3, N2O5, O3, and OH) and BB volatile organic compounds (BBVOCs), using emissions representative of agricultural burns (rice straw) and western wildfires (ponderosa pine). Field observations suggest NO3 production was approximately 1 ppbv hr–1, while NO3 and N2O5 were at or below 3 pptv, indicating rapid NO3/N2O5 reactivity. Model analysis shows that >99% of NO3/N2O5 loss is due to BBVOC + NO3 reactions rather than aerosol uptake of N2O5. Nighttime BBVOC oxidation for rice straw and ponderosa pine fires is dominated by NO3 (72, 53%, respectively) but O3 oxidation is significant (25, 43%), leading to roughly 55% overnight depletion of the most reactive BBVOCs and NO2

Dust Devil Tracks

Dust devils that leave dark- or light-toned tracks are common on Mars and they can also be found on the Earth’s surface. Dust devil tracks (hereinafter DDTs) are ephemeral surface features with mostly sub-annual lifetimes. Regarding their size, DDT widths can range between ∼1 m and ∼1 km, depending on the diameter of dust devil that created the track, and DDT lengths range from a few tens of meters to several kilometers, limited by the duration and horizontal ground speed of dust devils. DDTs can be classified into three main types based on their morphology and albedo in contrast to their surroundings; all are found on both planets: (a) dark continuous DDTs, (b) dark cycloidal DDTs, and (c) bright DDTs. Dark continuous DDTs are the most common type on Mars. They are characterized by their relatively homogenous and continuous low albedo surface tracks. Based on terrestrial and martian in situ studies, these DDTs most likely form when surficial dust layers are removed to expose larger-grained substrate material (coarse sands of ≥500 μm in diameter). The exposure of larger-grained materials changes the photometric properties of the surface; hence leading to lower albedo tracks because grain size is photometrically inversely proportional to the surface reflectance. However, although not observed so far, compositional differences (i.e., color differences) might also lead to albedo contrasts when dust is removed to expose substrate materials with mineralogical differences. For dark continuous DDTs, albedo drop measurements are around 2.5 % in the wavelength range of 550–850 nm on Mars and around 0.5 % in the wavelength range from 300–1100 nm on Earth. The removal of an equivalent layer thickness around 1 μm is sufficient for the formation of visible dark continuous DDTs on Mars and Earth. The next type of DDTs, dark cycloidal DDTs, are characterized by their low albedo pattern of overlapping scallops. Terrestrial in situ studies imply that they are formed when sand-sized material that is eroded from the outer vortex area of a dust devil is redeposited in annular patterns in the central vortex region. This type of DDT can also be found in on Mars in orbital image data, and although in situ studies are lacking, terrestrial analog studies, laboratory work, and numerical modeling suggest they have the same formation mechanism as those on Earth. Finally, bright DDTs are characterized by their continuous track pattern and high albedo compared to their undisturbed surroundings. They are found on both planets, but to date they have only been analyzed in situ on Earth. Here, the destruction of aggregates of dust, silt and sand by dust devils leads to smooth surfaces in contrast to the undisturbed rough surfaces surrounding the track. The resulting change in photometric properties occurs because the smoother surfaces have a higher reflectance compared to the surrounding rough surface, leading to bright DDTs. On Mars, the destruction of surficial dust-aggregates may also lead to bright DDTs. However, higher reflective surfaces may be produced by other formation mechanisms, such as dust compaction by passing dust devils, as this may also cause changes in photometric properties. On Mars, DDTs in general are found at all elevations and on a global scale, except on the permanent polar caps. DDT maximum areal densities occur during spring and summer in both hemispheres produced by an increase in dust devil activity caused by maximum insolation. Regionally, dust devil densities vary spatially likely controlled by changes in dust cover thicknesses and substrate materials. This variability makes it difficult to infer dust devil activity from DDT frequencies. Furthermore, only a fraction of dust devils leave tracks. However, DDTs can be used as proxies for dust devil lifetimes and wind directions and speeds, and they can also be used to predict lander or rover solar panel clearing events. Overall, the high DDT frequency in many areas on Mars leads to drastic albedo changes that affect large-scale weather patterns

Evidence of population-level impacts and resiliency for Gulf of Mexico shelf taxa following the Deepwater Horizon oil spill

The goal of this paper was to review the evidence of population-level impacts of the Deepwater Horizon Oil Spill (DWH) on Gulf of Mexico (GOM) continental shelf taxa, as well as evidence of resiliency following the DWH. There is considerable environmental and biological evidence that GOM shelf taxa were exposed to and suffered direct and indirect impacts of the DWH. Numerous assessments, from mesocosm studies to analysis of biopsied tissue or tissue samples from necropsied animals, revealed a constellation of physiological effects related to DWH impacts on GOM biota, some of which clearly or likely resulted in mortality. While the estimated concentrations of hydrocarbons in shelf waters and sediments were orders of magnitude lower than measured in inshore or deep GOM environments, the level of mortality observed or predicted was substantial for many shelf taxa. In some cases, such as for zooplankton, community shifts following the spill were ephemeral, likely reflecting high rates of population turnover and productivity. In other taxa, such as GOM reef fishes, impacts of the spill are confounded with other stressors, such as fishing mortality or the appearance and rapid population growth of invasive lionfish (Pterois spp.). In yet others, such as cetaceans, modeling efforts to predict population-level effects of the DWH made conservative assumptions given the species’ protected status, which post-DWH population assessments either failed to detect or population increases were estimated. A persistent theme that emerged was the lack of precise population-level data or assessments prior to the DWH for many taxa, but even when data or assessments did exist, examining evidence of population resiliency was confounded by other stressors impacting GOM biota. Unless efforts are made to increase the resolution of the data or precision of population assessments, difficulties will likely remain in estimating the scale of population-level effects or resiliency in the case of future large-scale environmental catastrophes

Collapse of a molecular cloud core to stellar densities: stellar core and outflow formation in radiation magnetohydrodynamics simulations (dataset)

This repository contains the datasets from the original smoothed particle hydrodynamics (SPH) calculations for the associated paper, including most dump files. It also includes all of the scripts for generating the figures that appear in the paper. These are contained either in the Figure_Generation.zip file or in the Paper.zip file. The former mainly contains SPLASH scripts (see below) for generating images from the SPH dump files. The latter mainly contains the final (or intermediate) SPLASH figures, plus the data files and scripts for making the other figures (line plots). Line plots use supermongo scripts. There are 5 main SPH calculations discussed in the paper, using 3 million SPH particles (3M) and with magnetic mass-to-flux ratios of 5, 10, 20, 100, and infinity (e.g. MF05). The outputs from each calculation are found in the zip files that begin with RMHD_MF*. For example, RMHD_MF05_3M.zip contains all the output (and executable) from the 3 million particle calculation with mass-to-flux ratio 5, except the dump files. The dump files are contained in a series of zip files such as: RMHD_MF05_3M_0200_0219.zip which contains 20 dump files, numbers 200 to 219. The dump files are included in groups to allow downloads in reasonably small (~20 GB) chunks, since the entire repository is ~3 TB. Also included is the output from the 1 million particle, mass-to-flux ratio 5 calculation (which was used for resolution testing in the Appendix of the paper). Only the single dump file from the 10 million particle calculation which was used to generate figure 22 is included in the respository (within the Figure_Generation.zip file) because the dump files from the entire calculation occupied another 1 TB of disk space. The SPH dump files for each calculation begin at TEST000 at time zero and then are numbered sequentially. The spacing in time is not regular (it generally decreases). The SPH dump files are Fortran binary files, written in big endian format and generated by the sphNG code. They can be read, visualised, and manipulated using the free, publicly available SPLASH visualisation code (which reads sphNG dump files), written by Daniel Price, that can be downloaded from: http://users.monash.edu.au/~dprice/splash/ Finally, the MovieAll.zip file contains the SPLASH scripts for generating the density movies associated with the paper that can be found at: http://www.astro.ex.ac.uk/people/mbate/Animations/stellarcore.htmlThis is the dataset that was used to produce the paper published in MNRAS. It contains the output from each of the SPH simulations, including dump files and the scripts used to generate the figures for the paper. To view the paper follow the DOI above or http://hdl.handle.net/10871/14622University of Exeter Visiting International Academic FellowshipMonash UniversityAustralian Research Council Discovery Project GrantEndeavour IPRS and APA postgraduate research scholarshipsUniversity of Exeter Supercomputer: jointly funded by Science and Technology Facilities Council (STFC), Large Facilities Capital Fund of BIS, and the University of ExeterDiRac Complexity computer: jointly funded by Science and Technology Facilities Council (STFC) and the Large Facilities Capital Fund of BI

Euclid preparation. TBD. The effect of linear redshift-space distortions in photometric galaxy clustering and its cross-correlation with cosmic shear

Cosmological surveys planned for the current decade will provide us with unparalleled observations of the distribution of galaxies on cosmic scales, by means of which we can probe the underlying large-scale structure (LSS) of the Universe. This will allow us to test the concordance cosmological model and its extensions. However, precision pushes us to high levels of accuracy in the theoretical modelling of the LSS observables, in order not to introduce biases in the estimation of cosmological parameters. In particular, effects such as redshift-space distortions (RSD) can become relevant in the computation of harmonic-space power spectra even for the clustering of the photometrically selected galaxies, as it has been previously shown in literature studies. In this work, we investigate the contribution of linear RSD, as formulated in the Limber approximation by arXiv:1902.07226, in forecast cosmological analyses with the photometric galaxy sample of the Euclid survey, in order to assess their impact and quantify the bias on the measurement of cosmological parameters that neglecting such an effect would cause. We perform this task by producing mock power spectra for photometric galaxy clustering and weak lensing, as expected to be obtained from the Euclid survey. We then use a Markov chain Monte Carlo approach to obtain the posterior distributions of cosmological parameters from such simulated observations. We find that neglecting the linear RSD leads to significant biases both when using galaxy correlations alone and when these are combined with cosmic shear, in the so-called 3$\times$2pt approach. Such biases can be as large as $5\,\sigma$-equivalent when assuming an underlying $\Lambda$CDM cosmology. When extending the cosmological model to include the equation-of-state parameters of dark energy, we find that the extension parameters can be shifted by more than $1\,\sigma$.Comment: 15 pages, 5 figures. To be submitted in A&

Euclid preparation. XXIX. Water ice in spacecraft part I: The physics of ice formation and contamination

Molecular contamination is a well-known problem in space flight. Water is the most common contaminant and alters numerous properties of a cryogenic optical system. Too much ice means that Euclid's calibration requirements and science goals cannot be met. Euclid must then be thermally decontaminated, a long and risky process. We need to understand how iced optics affect the data and when a decontamination is required. This is essential to build adequate calibration and survey plans, yet a comprehensive analysis in the context of an astrophysical space survey has not been done before. In this paper we look at other spacecraft with well-documented outgassing records, and we review the formation of thin ice films. A mix of amorphous and crystalline ices is expected for Euclid. Their surface topography depends on the competing energetic needs of the substrate-water and the water-water interfaces, and is hard to predict with current theories. We illustrate that with scanning-tunnelling and atomic-force microscope images. Industrial tools exist to estimate contamination, and we must understand their uncertainties. We find considerable knowledge errors on the diffusion and sublimation coefficients, limiting the accuracy of these tools. We developed a water transport model to compute contamination rates in Euclid, and find general agreement with industry estimates. Tests of the Euclid flight hardware in space simulators did not pick up contamination signals; our in-flight calibrations observations will be much more sensitive. We must understand the link between the amount of ice on the optics and its effect on Euclid's data. Little research is available about this link, possibly because other spacecraft can decontaminate easily, quenching the need for a deeper understanding. In our second paper we quantify the various effects of iced optics on spectrophotometric data.Comment: 35 pages, 22 figures, A&A in press. Changes to previous version: language edits, added Z. Bolag as author in the arxiv PDF (was listed in the ASCII author list and in the journal PDF, but not in the arxiv PDF). This version is identical to the journal versio

Euclid preparation. XXXI. The effect of the variations in photometric passbands on photometric-redshift accuracy

The technique of photometric redshifts has become essential for the exploitation of multi-band extragalactic surveys. While the requirements on photo-zs for the study of galaxy evolution mostly pertain to the precision and to the fraction of outliers, the most stringent requirement in their use in cosmology is on the accuracy, with a level of bias at the sub-percent level for the Euclid cosmology mission. A separate, and challenging, calibration process is needed to control the bias at this level of accuracy. The bias in photo-zs has several distinct origins that may not always be easily overcome. We identify here one source of bias linked to the spatial or time variability of the passbands used to determine the photometric colours of galaxies. We first quantified the effect as observed on several well-known photometric cameras, and found in particular that, due to the properties of optical filters, the redshifts of off-axis sources are usually overestimated. We show using simple simulations that the detailed and complex changes in the shape can be mostly ignored and that it is sufficient to know the mean wavelength of the passbands of each photometric observation to correct almost exactly for this bias; the key point is that this mean wavelength is independent of the spectral energy distribution of the source}. We use this property to propose a correction that can be computationally efficiently implemented in some photo-z algorithms, in particular template-fitting. We verified that our algorithm, implemented in the new photo-z code Phosphoros, can effectively reduce the bias in photo-zs on real data using the CFHTLS T007 survey, with an average measured bias Delta z over the redshift range 0.4<z<0.7 decreasing by about 0.02, specifically from Delta z~0.04 to Delta z~0.02 around z=0.5. Our algorithm is also able to produce corrected photometry for other applications.Comment: 19 pages, 13 figures; Accepted for publication in A&