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Valdes-Cortez, C., Niatsetski, Y., Perez-Calatayud, J., Ballester, F., & Vijande, J. (2022). A Monte Carlo study of the relative biological effectiveness in surface brachytherapy. Med. Phys., 49, 5576–5588.
Abstract: Purpose This work aims to simulate clustered DNA damage from ionizing radiation and estimate the relative biological effectiveness (RBE) for radionuclide (rBT)- and electronic (eBT)-based surface brachytherapy through a hybrid Monte Carlo (MC) approach, using realistic models of the sources and applicators. Methods Damage from ionizing radiation has been studied using the Monte Carlo Damage Simulation algorithm using as input the primary electron fluence simulated using a state-of-the-art MC code, PENELOPE-2018. Two Ir-192 rBT applicators, Valencia and Leipzig, one Co-60 source with a Freiburg Flap applicator (reference source), and two eBT systems, Esteya and INTRABEAM, have been included in this study implementing full realizations of their geometries as disclosed by the manufacturer. The role played by filtration and tube kilovoltage has also been addressed. Results For rBT, an RBE value of about 1.01 has been found for the applicators and phantoms considered. In the case of eBT, RBE values for the Esteya system show an almost constant RBE value of about 1.06 for all depths and materials. For INTRABEAM, variations in the range of 1.12-1.06 are reported depending on phantom composition and depth. Modifications in the Esteya system, filtration, and tube kilovoltage give rise to variations in the same range. Conclusions Current clinical practice does not incorporate biological effects in surface brachytherapy. Therefore, the same absorbed dose is administered to the patients independently on the particularities of the rBT or eBT system considered. The almost constant RBE values reported for rBT support that assumption regardless of the details of the patient geometry, the presence of a flattening filter in the applicator design, or even significant modifications in the photon energy spectra above 300 keV. That is not the case for eBT, where a clear dependence on the eBT system and the characteristics of the patient geometry are reported. A complete study specific for each eBT system, including detailed applicator characteristics (size, shape, filtering, among others) and common anatomical locations, should be performed before adopting an existing RBE value.
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SCiMMA and SNEWS Collaborations(Baxter, A. L. et al), & Colomer, M. (2022). Collaborative experience between scientific software projects using Agile Scrum development. Softw.-Pract. Exp., 52, 2077–2096.
Abstract: Developing sustainable software for the scientific community requires expertise in software engineering and domain science. This can be challenging due to the unique needs of scientific software, the insufficient resources for software engineering practices in the scientific community, and the complexity of developing for evolving scientific contexts. While open-source software can partially address these concerns, it can introduce complicating dependencies and delay development. These issues can be reduced if scientists and software developers collaborate. We present a case study wherein scientists from the SuperNova Early Warning System collaborated with software developers from the Scalable Cyberinfrastructure for Multi-Messenger Astrophysics project. The collaboration addressed the difficulties of open-source software development, but presented additional risks to each team. For the scientists, there was a concern of relying on external systems and lacking control in the development process. For the developers, there was a risk in supporting a user-group while maintaining core development. These issues were mitigated by creating a second Agile Scrum framework in parallel with the developers' ongoing Agile Scrum process. This Agile collaboration promoted communication, ensured that the scientists had an active role in development, and allowed the developers to evaluate and implement the scientists' software requirements. The collaboration provided benefits for each group: the scientists actuated their development by using an existing platform, and the developers utilized the scientists' use-case to improve their systems. This case study suggests that scientists and software developers can avoid scientific computing issues by collaborating and that Agile Scrum methods can address emergent concerns.
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Aliaga, R. J. (2017). Real-Time Estimation of Zero Crossings of Sampled Signals for Timing Using Cubic Spline Interpolation. IEEE Trans. Nucl. Sci., 64(8), 2414–2422.
Abstract: A scheme is proposed for hardware estimation of the location of zero crossings of sampled signals with subsample resolution for timing applications, which consists of interpolating the signal with a cubic spline near the zero crossing and then finding the root of the resulting polynomial. An iterative algorithm based on the bisection method is presented that obtains one bit of the result per step and admits an efficient digital implementation using fixed-point representation. In particular, the root estimation iteration involves only two additions, and the initial values can be obtained from finite impulse response (FIR) filters with certain symmetry properties. It is shown that this allows online real-time estimation of timestamps in free-running sampling detector systems with improved accuracy with respect to the more common linear interpolation. The method is evaluated with simulations using ideal and real timing signals, and estimates are given for the resource usage and speed of its implementation.
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Carrio, F. (2022). The Data Acquisition System for the ATLAS Tile Calorimeter Phase-II Upgrade Demonstrator. IEEE Trans. Nucl. Sci., 69(4), 687–695.
Abstract: The tile calorimeter (TileCal) is the central hadronic calorimeter of the ATLAS experiment at the large hadron collider (LHC). In 2025, the LHC will be upgraded leading to the high luminosity LHC (HL-LHC). The HL-LHC will deliver an instantaneous luminosity up to seven times larger than the LHC nominal luminosity. The ATLAS Phase-II upgrade (2025-2027) will accommodate the subdetectors to the HL-LHC requirements. As part of this upgrade, the majority of the TileCal on-detector and off-detector electronics will be replaced using a new readout strategy, where the on-detector electronics will digitize and transmit digitized detector data to the off-detector electronics at the bunch crossing frequency (40 MHz). In the counting rooms, the off-detector electronics will compute reconstructed trigger objects for the first-level trigger and will store the digitized samples in pipelined buffers until the reception of a trigger acceptance signal. The off-detector electronics will also distribute the LHC clock to the on-detector electronics embedded within the digital data stream. The TileCal Phase-II upgrade project has undertaken an extensive research and development program that includes the development of a Demonstrator module to evaluate the performance of the new clock and readout architecture envisaged for the HL-LHC. The Demonstrator module equipped with the latest version of the on-detector electronics was built and inserted into the ATLAS experiment. The Demonstrator module is operated and read out using a Tile PreProcessor (TilePPr) Demonstrator which enables backward compatibility with the present ATLAS Trigger and Data AcQuisition (TDAQ), and the timing, trigger, and command (TTC) systems. This article describes in detail the main hardware and firmware components of the clock distribution and data acquisition systems for the Demonstrator module, focusing on the TilePPr Demonstrator.
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Mendoza, S., & Olmo, G. J. (2015). Astrophysical constraints and insights on extended relativistic gravity. Astrophys. Space Sci., 357(2), 133–6pp.
Abstract: We give precise details to support that observations of gravitational lensing at scales of individual, groups and clusters of galaxies can be understood in terms of nonNewtonian gravitational interactions with a relativistic structure compatible with the Einstein Equivalence Principle. This result is derived on very general grounds without knowing the underlying structure of the gravitational field equations. As such, any developed gravitational theory built to deal with these astrophysical scales needs to reproduce the obtained results of this article.
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Angles-Castillo, A., Perucho, M., Marti, J. M., & Laing, R. A. (2021). On the deceleration of Fanaroff-Riley Class I jets: mass loading of magnetized jets by stellar winds. Mon. Not. Roy. Astron. Soc., 500(1), 1512–1530.
Abstract: In this paper, we present steady-state relativistic magnetohydrodynamic simulations that include a mass-load term to study the process of jet deceleration. The mass load mimics the injection of a proton-electron plasma from stellar winds within the host galaxy into initially pair plasma jets, with mean stellar mass-losses ranging from 10(-14) to 10(-9) M-circle dot yr(-1). The spatial jet evolution covers similar to 500 pc from jet injection in the grid at 10 pc from the jet nozzle. Our simulations use a relativistic gas equation of state and a pressure profile for the ambient medium. We compare these simulations with previous dynamical simulations of relativistic, non-magnetized jets. Our results show that toroidal magnetic fields can prevent fast jet expansion and the subsequent embedding of further stars via magnetic tension. In this sense, magnetic fields avoid a runaway deceleration process. Furthermore, when the mass load is large enough to increase the jet density and produce fast, differential jet expansion, the conversion of magnetic energy flux into kinetic energy flux (i.e. magnetic acceleration), helps to delay the deceleration process with respect to non-magnetized jets. We conclude that the typical stellar population in elliptical galaxies cannot explain jet deceleration in classical Fanaroff-Riley type I radio galaxies. However, we observe a significant change in the jet composition, thermodynamical parameters, and energy dissipation along its evolution, even for moderate values of the mass load.
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Panes, B., Eckner, C., Hendriks, L., Caron, S., Dijkstra, K., Johannesson, G., et al. (2021). Identification of point sources in gamma rays using U-shaped convolutional neural networks and a data challenge. Astron. Astrophys., 656, A62–18pp.
Abstract: Context. At GeV energies, the sky is dominated by the interstellar emission from the Galaxy. With limited statistics and spatial resolution, accurately separating point sources is therefore challenging. Aims. Here we present the first application of deep learning based algorithms to automatically detect and classify point sources from gamma-ray data. For concreteness we refer to this approach as AutoSourceID. Methods. To detect point sources, we utilized U-shaped convolutional networks for image segmentation and k-means for source clustering and localization. We also explored the Centroid-Net algorithm, which is designed to find and count objects. Using two algorithms allows for a cross check of the results, while a combination of their results can be used to improve performance. The training data are based on 9.5 years of exposure from The Fermi Large Area Telescope (Fermi-LAT) and we used source properties of active galactic nuclei (AGNs) and pulsars (PSRs) from the fourth Fermi-LAT source catalog in addition to several models of background interstellar emission. The results of the localization algorithm are fed into a classification neural network that is trained to separate the three general source classes (AGNs, PSRs, and FAKE sources). Results. We compared our localization algorithms qualitatively with traditional methods and find them to have similar detection thresholds. We also demonstrate the robustness of our source localization algorithms to modifications in the interstellar emission models, which presents a clear advantage over traditional methods. The classification network is able to discriminate between the three classes with typical accuracy of similar to 70%, as long as balanced data sets are used in classification training. We published online our training data sets and analysis scripts and invite the community to join the data challenge aimed to improve the localization and classification of gamma-ray point sources.
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Stoppa, F., Vreeswijk, P., Bloemen, S., Bhattacharyya, S., Caron, S., Johannesson, G., et al. (2022). AutoSourceID-Light Fast optical source localization via U-Net and Laplacian of Gaussian. Astron. Astrophys., 662, A109–8pp.
Abstract: Aims. With the ever-increasing survey speed of optical wide-field telescopes and the importance of discovering transients when they are still young, rapid and reliable source localization is paramount. We present AutoSourceID-Light (ASID-L), an innovative framework that uses computer vision techniques that can naturally deal with large amounts of data and rapidly localize sources in optical images. Methods. We show that the ASID-L algorithm based on U-shaped networks and enhanced with a Laplacian of Gaussian filter provides outstanding performance in the localization of sources. A U-Net network discerns the sources in the images from many different artifacts and passes the result to a Laplacian of Gaussian filter that then estimates the exact location. Results. Using ASID-L on the optical images of the MeerLICHT telescope demonstrates the great speed and localization power of the method. We compare the results with SExtractor and show that our method outperforms this more widely used method. ASID-L rapidly detects more sources not only in low- and mid-density fields, but particularly in areas with more than 150 sources per square arcminute. The training set and code used in this paper are publicly available.
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AGATA Collaboration(Akkoyun, S. et al), Algora, A., Barrientos, D., Domingo-Pardo, C., Egea, F. J., Gadea, A., et al. (2012). AGATA-Advanced GAmma Tracking Array. Nucl. Instrum. Methods Phys. Res. A, 668, 26–58.
Abstract: The Advanced GAmma Tracking Array (AGATA) is a European project to develop and operate the next generation gamma-ray spectrometer. AGATA is based on the technique of gamma-ray energy tracking in electrically segmented high-purity germanium crystals. This technique requires the accurate determination of the energy, time and position of every interaction as a gamma ray deposits its energy within the detector volume. Reconstruction of the full interaction path results in a detector with very high efficiency and excellent spectral response. The realisation of gamma-ray tracking and AGATA is a result of many technical advances. These include the development of encapsulated highly segmented germanium detectors assembled in a triple cluster detector cryostat, an electronics system with fast digital sampling and a data acquisition system to process the data at a high rate. The full characterisation of the crystals was measured and compared with detector-response simulations. This enabled pulse-shape analysis algorithms, to extract energy, time and position, to be employed. In addition, tracking algorithms for event reconstruction were developed. The first phase of AGATA is now complete and operational in its first physics campaign. In the future AGATA will be moved between laboratories in Europe and operated in a series of campaigns to take advantage of the different beams and facilities available to maximise its science output. The paper reviews all the achievements made in the AGATA project including all the necessary infrastructure to operate and support the spectrometer.
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Stoppa, F., Ruiz de Austri, R., Vreeswijk, P., Bhattacharyya, S., Caron, S., Bloemen, S., et al. (2023). AutoSourceID-FeatureExtractor Optical image analysis using a two-step mean variance estimation network for feature estimation and uncertainty characterisation. Astron. Astrophys., 680, A108–14pp.
Abstract: Aims. In astronomy, machine learning has been successful in various tasks such as source localisation, classification, anomaly detection, and segmentation. However, feature regression remains an area with room for improvement. We aim to design a network that can accurately estimate sources' features and their uncertainties from single-band image cutouts, given the approximated locations of the sources provided by the previously developed code AutoSourceID-Light (ASID-L) or other external catalogues. This work serves as a proof of concept, showing the potential of machine learning in estimating astronomical features when trained on meticulously crafted synthetic images and subsequently applied to real astronomical data.Methods. The algorithm presented here, AutoSourceID-FeatureExtractor (ASID-FE), uses single-band cutouts of 32x32 pixels around the localised sources to estimate flux, sub-pixel centre coordinates, and their uncertainties. ASID-FE employs a two-step mean variance estimation (TS-MVE) approach to first estimate the features and then their uncertainties without the need for additional information, for example the point spread function (PSF). For this proof of concept, we generated a synthetic dataset comprising only point sources directly derived from real images, ensuring a controlled yet authentic testing environment.Results. We show that ASID-FE, trained on synthetic images derived from the MeerLICHT telescope, can predict more accurate features with respect to similar codes such as SourceExtractor and that the two-step method can estimate well-calibrated uncertainties that are better behaved compared to similar methods that use deep ensembles of simple MVE networks. Finally, we evaluate the model on real images from the MeerLICHT telescope and the Zwicky Transient Facility (ZTF) to test its transfer learning abilities.
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