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Ferrer-Sanchez, A., Martin-Guerrero, J., Ruiz de Austri, R., Torres-Forne, A., & Font, J. A. (2024). Gradient-annihilated PINNs for solving Riemann problems: Application to relativistic hydrodynamics. Comput. Meth. Appl. Mech. Eng., 424, 116906–18pp.
Abstract: We present a novel methodology based on Physics-Informed Neural Networks (PINNs) for solving systems of partial differential equations admitting discontinuous solutions. Our method, called Gradient-Annihilated PINNs (GA-PINNs), introduces a modified loss function that forces the model to partially ignore high-gradients in the physical variables, achieved by introducing a suitable weighting function. The method relies on a set of hyperparameters that control how gradients are treated in the physical loss. The performance of our methodology is demonstrated by solving Riemann problems in special relativistic hydrodynamics, extending earlier studies with PINNs in the context of the classical Euler equations. The solutions obtained with the GA-PINN model correctly describe the propagation speeds of discontinuities and sharply capture the associated jumps. We use the relative l(2) error to compare our results with the exact solution of special relativistic Riemann problems, used as the reference ''ground truth'', and with the corresponding error obtained with a second-order, central, shock-capturing scheme. In all problems investigated, the accuracy reached by the GA-PINN model is comparable to that obtained with a shock-capturing scheme, achieving a performance superior to that of the baseline PINN algorithm in general. An additional benefit worth stressing is that our PINN-based approach sidesteps the costly recovery of the primitive variables from the state vector of conserved variables, a well-known drawback of grid-based solutions of the relativistic hydrodynamics equations. Due to its inherent generality and its ability to handle steep gradients, the GA-PINN methodology discussed in this paper could be a valuable tool to model relativistic flows in astrophysics and particle physics, characterized by the prevalence of discontinuous solutions.
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Ahn, C. P. et al, & de Putter, R. (2012). The Ninth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the SDSS-III Baryon Oscillation Spectroscopic Survey. Astrophys. J. Suppl. Ser., 203(2), 21–13pp.
Abstract: The Sloan Digital Sky Survey III (SDSS-III) presents the first spectroscopic data from the Baryon Oscillation Spectroscopic Survey (BOSS). This ninth data release (DR9) of the SDSS project includes 535,995 new galaxy spectra (median z similar to 0.52), 102,100 new quasar spectra (median z similar to 2.32), and 90,897 new stellar spectra, along with the data presented in previous data releases. These spectra were obtained with the new BOSS spectrograph and were taken between 2009 December and 2011 July. In addition, the stellar parameters pipeline, which determines radial velocities, surface temperatures, surface gravities, and metallicities of stars, has been updated and refined with improvements in temperature estimates for stars with T-eff < 5000 K and in metallicity estimates for stars with [Fe/H] > -0.5. DR9 includes new stellar parameters for all stars presented in DR8, including stars from SDSS-I and II, as well as those observed as part of the SEGUE-2. The astrometry error introduced in the DR8 imaging catalogs has been corrected in the DR9 data products. The next data release for SDSS-III will be in Summer 2013, which will present the first data from the APOGEE along with another year of data from BOSS, followed by the final SDSS-III data release in 2014 December.
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Villaescusa-Navarro, F. et al, & Villanueva-Domingo, P. (2023). The CAMELS Project: Public Data Release. Astrophys. J. Suppl. Ser., 265(2), 54–14pp.
Abstract: The Cosmology and Astrophysics with Machine Learning Simulations (CAMELS) project was developed to combine cosmology with astrophysics through thousands of cosmological hydrodynamic simulations and machine learning. CAMELS contains 4233 cosmological simulations, 2049 N-body simulations, and 2184 state-of-the-art hydrodynamic simulations that sample a vast volume in parameter space. In this paper, we present the CAMELS public data release, describing the characteristics of the CAMELS simulations and a variety of data products generated from them, including halo, subhalo, galaxy, and void catalogs, power spectra, bispectra, Lya spectra, probability distribution functions, halo radial profiles, and X-rays photon lists. We also release over 1000 catalogs that contain billions of galaxies from CAMELS-SAM: a large collection of N-body simulations that have been combined with the Santa Cruz semianalytic model. We release all the data, comprising more than 350 terabytes and containing 143,922 snapshots, millions of halos, galaxies, and summary statistics. We provide further technical details on how to access, download, read, and process the data at .
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Clausse, A., Soto, L., & Tarifeño-Saldivia, A. (2015). Influence of the Anode Length on the Neutron Emission of a 50 J Plasma Focus: Modeling and Experiment. IEEE Trans. Plasma Sci., 43(2), 629–636.
Abstract: A comprehensive set of electric data measured in a small plasma focus (PF) device of 50 J correlated with the corresponding neutron emissions is taken as the base for developing a semiempirical model of the current sheet dynamics and the neutron yield. The model is able to explain the dependence of the neutron yield with the pressure and anode length with good accuracy, and suggests a physical interpretation of the drive parameter commonly used in PF design.
Keywords: Anode; fusion neutrons; modeling; plasma focus (PF); plasma pinch
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Aguiar, P., Rafecas, M., Ortuño, J. E., Kontaxakis, G., Santos, A., Pavia, J., et al. (2010). Geometrical and Monte Carlo projectors in 3D PET reconstruction. Med. Phys., 37(11), 5691–5702.
Abstract: Purpose: In the present work, the authors compare geometrical and Monte Carlo projectors in detail. The geometrical projectors considered were the conventional geometrical Siddon ray-tracer (S-RT) and the orthogonal distance-based ray-tracer (OD-RT), based on computing the orthogonal distance from the center of image voxel to the line-of-response. A comparison of these geometrical projectors was performed using different point spread function (PSF) models. The Monte Carlo-based method under consideration involves an extensive model of the system response matrix based on Monte Carlo simulations and is computed off-line and stored on disk. Methods: Comparisons were performed using simulated and experimental data of the commercial small animal PET scanner rPET. Results: The results demonstrate that the orthogonal distance-based ray-tracer and Siddon ray-tracer using PSF image-space convolutions yield better images in terms of contrast and spatial resolution than those obtained after using the conventional method and the multiray-based S-RT. Furthermore, the Monte Carlo-based method yields slight improvements in terms of contrast and spatial resolution with respect to these geometrical projectors. Conclusions: The orthogonal distance-based ray-tracer and Siddon ray-tracer using PSF image-space convolutions represent satisfactory alternatives to factorizing the system matrix or to the conventional on-the-fly ray-tracing methods for list-mode reconstruction, where an extensive modeling based on Monte Carlo simulations is unfeasible.
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Ballester, F., Granero, D., Perez-Calatayud, J., Venselaar, J. L. M., & Rivard, M. J. (2010). Study of encapsulated Tm-170 sources for their potential use in brachytherapy. Med. Phys., 37(4), 1629–1637.
Abstract: Methods: The authors have assumed a theoretical Tm-170 cylindrical source encapsulated with stainless steel and typical dimensions taken from the currently available HDR Ir-192 brachytherapy sources. The dose-rate distribution was calculated for this source using the GEANT4 Monte Carlo (MC) code considering both photon and electron Tm-170 spectra. The AAPM TG-43 U1 brachytherapy dosimetry parameters were derived. To study general properties of Tm-170 encapsulated sources, spherical sources encapsulated with stainless steel and platinum were also studied. Moreover, the influence of small variations in the active core and capsule dimensions on the dosimetric characteristics was assessed. Treatment times required for a Tm-170 source were compared to those for Ir-192 and Yb-169 for the same contained activity. Results: Due to the energetic beta spectrum and the large electron yield, the bremsstrahlung contribution to the dose was of the same order of magnitude as from the emitted gammas and characteristic x rays. Moreover, the electron spectrum contribution to the dose was significant up to 4 mm from the source center compared to the photon contribution. The dose-rate constant Lambda of the cylindrical source was 1.23 cGy h(-1) U-1. The behavior of the radial dose function showed promise for applications in brachytherapy. Due to the electron spectrum, the anisotropy was large for r < 6 mm. Variations in manufacturing tolerances did not significantly influence the final dosimetry data when expressed in cGy h(-1) U-1. For typical capsule dimensions, maximum reference dose rates of about 0.2, 10, and 2 Gy min(-1) would then be obtained for Tm-170, Ir-192, and Yb-169, respectively, resulting in treatment times greater than those for HDR Ir-192 brachytherapy. Conclusions: The dosimetric characteristics of source designs exploiting the low photon energy of Tm-170 were studied for potential application in HDR-brachytherapy. Dose-rate distributions were obtained for cylindrical and simplified spherical Tm-170 source designs (stainless steel and platinum capsule materials) using MC calculations. Despite the high activity of Tm-170, calculated treatment times were much longer than for Ir-192.
Keywords: brachytherapy; cancer; dosimetry; prosthetics; radioisotopes; thulium
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Rivard, M. J., Granero, D., Perez-Calatayud, J., & Ballester, F. (2010). Influence of photon energy spectra from brachytherapy sources on Monte Carlo simulations of kerma and dose rates in water and air. Med. Phys., 37(2), 869–876.
Abstract: Methods: For Ir-192, I-125, and Pd-103, the authors considered from two to five published spectra. Spherical sources approximating common brachytherapy sources were assessed. Kerma and dose results from GEANT4, MCNP5, and PENELOPE-2008 were compared for water and air. The dosimetric influence of Ir-192, I-125, and Pd-103 spectral choice was determined. Results: For the spectra considered, there were no statistically significant differences between kerma or dose results based on Monte Carlo code choice when using the same spectrum. Water-kerma differences of about 2%, 2%, and 0.7% were observed due to spectrum choice for Ir-192, I-125, and Pd-103, respectively (independent of radial distance), when accounting for photon yield per Bq. Similar differences were observed for air-kerma rate. However, their ratio (as used in the dose-rate constant) did not significantly change when the various photon spectra were selected because the differences compensated each other when dividing dose rate by air-kerma strength. Conclusions: Given the standardization of radionuclide data available from the National Nuclear Data Center (NNDC) and the rigorous infrastructure for performing and maintaining the data set evaluations, NNDC spectra are suggested for brachytherapy simulations in medical physics applications.
Keywords: biomedical materials; brachytherapy; dosimetry; iodine; iridium; Monte Carlo methods; palladium; radioisotopes
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Ballester, F., Tedgren, A. C., Granero, D., Haworth, A., Mourtada, F., Fonseca, G. P., et al. (2015). A generic high-dose rate Ir-192 brachytherapy source for evaluation of model-based dose calculations beyond the TG-43 formalism. Med. Phys., 42(6), 3048–3062.
Abstract: Purpose: In order to facilitate a smooth transition for brachytherapy dose calculations from the American Association of Physicists in Medicine (AAPM) Task Group No. 43 (TG-43) formalism to model-based dose calculation algorithms (MBDCAs), treatment planning systems (TPSs) using a MBDCA require a set of well-defined test case plans characterized by Monte Carlo (MC) methods. This also permits direct dose comparison to TG-43 reference data. Such test case plans should be made available for use in the software commissioning process performed by clinical end users. To this end, a hypothetical, generic high-dose rate (HDR) Ir-192 source and a virtual water phantom were designed, which can be imported into a TPS. Methods: A hypothetical, generic HDR Ir-192 source was designed based on commercially available sources as well as a virtual, cubic water phantom that can be imported into any TPS in DICOM format. The dose distribution of the generic Ir-192 source when placed at the center of the cubic phantom, and away from the center under altered scatter conditions, was evaluated using two commercial MBDCAs [Oncentra (R) Brachy with advanced collapsed-cone engine (ACE) and BrachyVision AcuRos (TM)]. Dose comparisons were performed using state-of-the-art MC codes for radiation transport, including ALGEBRA, BrachyDose, GEANT4, MCNP5, MCNP6, and pENELopE2008. The methodologies adhered to recommendations in the AAPM TG-229 report on high-energy brachytherapy source dosimetry. TG-43 dosimetry parameters, an along-away dose-rate table, and primary and scatter separated (PSS) data were obtained. The virtual water phantom of (201)(3) voxels (1 mm sides) was used to evaluate the calculated dose distributions. Two test case plans involving a single position of the generic HDR Ir-192 source in this phantom were prepared: (i) source centered in the phantom and (ii) source displaced 7 cm laterally from the center. Datasets were independently produced by different investigators. MC results were then compared against dose calculated using TG-43 and MBDCA methods. Results: TG-43 and PSS datasets were generated for the generic source, the PSS data for use with the ACE algorithm. The dose-rate constant values obtained from seven MC simulations, performed independently using different codes, were in excellent agreement, yielding an average of 1.1109 +/- 0.0004 cGy/(h U) (k = 1, Type A uncertainty). MC calculated dose-rate distributions for the two plans were also found to be in excellent agreement, with differences within type A uncertainties. Differences between commercial MBDCA and MC results were test, position, and calculation parameter dependent. On average, however, these differences were within 1% for ACUROS and 2% for ACE at clinically relevant distances. Conclusions: A hypothetical, generic HDR Ir-192 source was designed and implemented in two commercially available TPSs employing different MBDCAs. Reference dose distributions for this source were benchmarked and used for the evaluation of MBDCA calculations employing a virtual, cubic water phantom in the form of a CT DICOM image series. The implementation of a generic source of identical design in all TPSs using MBDCAs is an important step toward supporting univocal commissioning procedures and direct comparisons between TPSs.
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Candela-Juan, C., Vijande, J., Garcia-Martinez, T., Niatsetski, Y., Nauta, G., Schuurman, J., et al. (2015). Comparison and uncertainty evaluation of different calibration protocols and ionization chambers for low-energy surface brachytherapy dosimetry. Med. Phys., 42(8), 4954–4964.
Abstract: Purpose: A surface electronic brachytherapy (EBT) device is in fact an x-ray source collimated with specific applicators. Low-energy (<100 kVp) x-ray beam dosimetry faces several challenges that need to be addressed. A number of calibration protocols have been published for x-ray beam dosimetry. The media in which measurements are performed are the fundamental difference between them. The aim of this study was to evaluate the surface dose rate of a low-energy x-ray source with small field applicators using different calibration standards and different small-volume ionization chambers, comparing the values and uncertainties of each methodology. Methods: The surface dose rate of the EBT unit Esteya (Elekta Brachytherapy, The Netherlands), a 69.5 kVp x-ray source with applicators of 10, 15, 20, 25, and 30 mm diameter, was evaluated using the AAPM TG-61 (based on air kerma) and International Atomic Energy Agency (IAEA) TRS-398 (based on absorbed dose to water) dosimetry protocols for low-energy photon beams. A plane parallel T34013 ionization chamber (PTW Freiburg, Germany) calibrated in terms of both absorbed dose to water and air kerma was used to compare the two dosimetry protocols. Another PTW chamber of the same model was used to evaluate the reproducibility between these chambers. Measurements were also performed with two different Exradin A20 (Standard Imaging, Inc., Middleton, WI) chambers calibrated in terms of air kerma. Results: Differences between surface dose rates measured in air and in water using the T34013 chamber range from 1.6% to 3.3%. No field size dependence has been observed. Differences are below 3.7% when measurements with the A20 and the T34013 chambers calibrated in air are compared. Estimated uncertainty (with coverage factor k = 1) for the T34013 chamber calibrated in water is 2.2%-2.4%, whereas it increases to 2.5% and 2.7% for the A20 and T34013 chambers calibrated in air, respectively. The output factors, measured with the PTW chambers, differ by less than 1.1% for any applicator size when compared to the output factors that were measured with the A20 chamber. Conclusions: Measurements using both dosimetric protocols are consistent, once the overall uncertainties are considered. There is also consistency between measurements performed with both chambers calibrated in air. Both the T34013 and A20 chambers have negligible stem effect. Any x-ray surface brachytherapy system, including Esteya, can be characterized using either one of these calibration protocols and ionization chambers. Having less correction factors, lower uncertainty, and based on measurements, performed in closer to clinical conditions, the TRS-398 protocol seems to be the preferred option.
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Albiol, A., Corbi, A., & Albiol, F. (2017). Automatic intensity windowing of mammographic images based on a perceptual metric. Med. Phys., 44(4), 1369–1378.
Abstract: Purpose: Initial auto-adjustment of the window level WL and width WW applied to mammographic images. The proposed intensity windowing (IW) method is based on the maximization of the mutual information (MI) between a perceptual decomposition of the original 12-bit sources and their screen displayed 8-bit version. Besides zoom, color inversion and panning operations, IW is the most commonly performed task in daily screening and has a direct impact on diagnosis and the time involved in the process. Methods: The authors present a human visual system and perception-based algorithm named GRAIL (Gabor-relying adjustment of image levels). GRAIL initially measures a mammogram's quality based on the MI between the original instance and its Gabor-filtered derivations. From this point on, the algorithm performs an automatic intensity windowing process that outputs the WL/WW that best displays each mammogram for screening. GRAIL starts with the default, high contrast, wide dynamic range 12-bit data, and then maximizes the graphical information presented in ordinary 8-bit displays. Tests have been carried out with several mammogram databases. They comprise correlations and an ANOVA analysis with the manual IW levels established by a group of radiologists. A complete MATLAB implementation of GRAIL is available at . Results: Auto-leveled images show superior quality both perceptually and objectively compared to their full intensity range and compared to the application of other common methods like global contrast stretching (GCS). The correlations between the human determined intensity values and the ones estimated by our method surpass that of GCS. The ANOVA analysis with the upper intensity thresholds also reveals a similar outcome. GRAIL has also proven to specially perform better with images that contain micro-calcifications and/or foreign X-ray-opaque elements and with healthy BI-RADS A-type mammograms. It can also speed up the initial screening time by a mean of 4.5 s per image. Conclusions: A novel methodology is introduced that enables a quality-driven balancing of the WL/WW of mammographic images. This correction seeks the representation that maximizes the amount of graphical information contained in each image. The presented technique can contribute to the diagnosis and the overall efficiency of the breast screening session by suggesting, at the beginning, an optimal and customized windowing setting for each mammogram.
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