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Hirn, J., Garcia, J. E., Montesinos-Navarro, A., Sanchez-Martin, R., Sanz, V., & Verdu, M. (2022). A deep Generative Artificial Intelligence system to predict species coexistence patterns. Methods Ecol. Evol., 13, 1052–1061.
Abstract: Predicting coexistence patterns is a current challenge to understand diversity maintenance, especially in rich communities where these patterns' complexity is magnified through indirect interactions that prevent their approximation with classical experimental approaches. We explore cutting-edge Machine Learning techniques called Generative Artificial Intelligence (GenAI) to predict species coexistence patterns in vegetation patches, training generative adversarial networks (GAN) and variational AutoEncoders (VAE) that are then used to unravel some of the mechanisms behind community assemblage. The GAN accurately reproduces real patches' species composition and plant species' affinity to different soil types, and the VAE also reaches a high level of accuracy, above 99%. Using the artificially generated patches, we found that high-order interactions tend to suppress the positive effects of low-order interactions. Finally, by reconstructing successional trajectories, we could identify the pioneer species with larger potential to generate a high diversity of distinct patches in terms of species composition. Understanding the complexity of species coexistence patterns in diverse ecological communities requires new approaches beyond heuristic rules. Generative Artificial Intelligence can be a powerful tool to this end as it allows to overcome the inherent dimensionality of this challenge.
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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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Assam, I., Vijande, J., Ballester, F., Perez-Calatayud, J., Poppe, B., & Siebert, F. A. (2022). Evaluation of dosimetric effects of metallic artifact reduction and tissue assignment on Monte Carlo dose calculations for I-125 prostate implants. Med. Phys., 49, 6195–6208.
Abstract: Purpose Monte Carlo (MC) simulation studies, aimed at evaluating the magnitude of tissue heterogeneity in I-125 prostate permanent seed implant brachytherapy (BT), customarily use clinical post-implant CT images to generate a virtual representation of a realistic patient model (virtual patient model). Metallic artifact reduction (MAR) techniques and tissue assignment schemes (TAS) are implemented on the post-implant CT images to mollify metallic artifacts due to BT seeds and to assign tissue types to the voxels corresponding to the bright seed spots and streaking artifacts, respectively. The objective of this study is to assess the combined influence of MAR and TAS on MC absorbed dose calculations in post-implant CT-based phantoms. The virtual patient models used for I-125 prostate implant MC absorbed dose calculations in this study are derived from the CT images of an external radiotherapy prostate patient without BT seeds and prostatic calcifications, thus averting the need to implement MAR and TAS. Methods The geometry of the IsoSeed I25.S17plus source is validated by comparing the MC calculated results of the TG-43 parameters for the line source approximation with the TG-43U1S2 consensus data. Four MC absorbed dose calculations are performed in two virtual patient models using the egs_brachy MC code: (1) TG-43-based D-w,w-TG(43), (2) D-w,D-w-MBDC that accounts for interseed scattering and attenuation (ISA), (3) D-m,D-m that examines ISA and tissue heterogeneity by scoring absorbed dose in tissue, and (4) D-w,D-m that unlike D-m,D-m scores absorbed dose in water. The MC absorbed doses (1) and (2) are simulated in a TG-43 patient phantom derived by assigning the densities of every voxel to 1.00 g cm(-3) (water), whereas MC absorbed doses (3) and (4) are scored in the TG-186 patient phantom generated by mapping the mass density of each voxel to tissue according to a CT calibration curve. The MC absorbed doses calculated in this study are compared with VariSeed v8.0 calculated absorbed doses. To evaluate the dosimetric effect of MAR and TAS, the MC absorbed doses of this work (independent of MAR and TAS) are compared to the MC absorbed doses of different I-125 source models from previous studies that were calculated with different MC codes using post-implant CT-based phantoms generated by implementing MAR and TAS on post-implant CT images. Results The very good agreement of TG-43 parameters of this study and the published consensus data within 3% validates the geometry of the IsoSeed I25.S17plus source. For the clinical studies, the TG-43-based calculations show a D-90 overestimation of more than 4% compared to the more realistic MC methods due to ISA and tissue composition. The results of this work generally show few discrepancies with the post-implant CT-based dosimetry studies with respect to the D-90 absorbed dose metric parameter. These discrepancies are mainly Type B uncertainties due to the different I-125 source models and MC codes. Conclusions The implementation of MAR and TAS on post-implant CT images have no dosimetric effect on the I-125 prostate MC absorbed dose calculation in post-implant CT-based phantoms.
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Biagi, N., Francesconi, S., Gessner, M., Bellini, M., & Zavatta, A. (2022). Remote Phase Sensing by Coherent Single Photon Addition. Adv. Quantum Technol., 5(12), 2200039–9pp.
Abstract: A remote phase sensing scheme is proposed, inspired by the high sensitivity of the entanglement produced by coherent multimode photon addition on the phase set in the remote heralding apparatus. By exploring the case of delocalized photon addition over two modes containing identical coherent states, the optimal observable to perform remote phase estimation from heralded quadrature measurements is derived. The technique is experimentally tested with calibration measurements and then used for estimating a remote phase with a sensitivity that is found to scale with the intensity of the local coherent states, which never interacted with the sample.
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Peppa, V., Thomson, R. M., Enger, S. A., Fonseca, G. P., Lee, C. N., Lucero, J. N. E., et al. (2023). A MC-based anthropomorphic test case for commissioning model-based dose calculation in interstitial breast 192-Ir HDR brachytherapy. Med. Phys., 50(7), 4675–4687.
Abstract: PurposeTo provide the first clinical test case for commissioning of Ir-192 brachytherapy model-based dose calculation algorithms (MBDCAs) according to the AAPM TG-186 report workflow. Acquisition and Validation MethodsA computational patient phantom model was generated from a clinical multi-catheter Ir-192 HDR breast brachytherapy case. Regions of interest (ROIs) were contoured and digitized on the patient CT images and the model was written to a series of DICOM CT images using MATLAB. The model was imported into two commercial treatment planning systems (TPSs) currently incorporating an MBDCA. Identical treatment plans were prepared using a generic Ir-192 HDR source and the TG-43-based algorithm of each TPS. This was followed by dose to medium in medium calculations using the MBDCA option of each TPS. Monte Carlo (MC) simulation was performed in the model using three different codes and information parsed from the treatment plan exported in DICOM radiation therapy (RT) format. Results were found to agree within statistical uncertainty and the dataset with the lowest uncertainty was assigned as the reference MC dose distribution. Data Format and Usage NotesThe dataset is available online at ,. Files include the treatment plan for each TPS in DICOM RT format, reference MC dose data in RT Dose format, as well as a guide for database users and all files necessary to repeat the MC simulations. Potential ApplicationsThe dataset facilitates the commissioning of brachytherapy MBDCAs using TPS embedded tools and establishes a methodology for the development of future clinical test cases. It is also useful to non-MBDCA adopters for intercomparing MBDCAs and exploring their benefits and limitations, as well as to brachytherapy researchers in need of a dosimetric and/or a DICOM RT information parsing benchmark. Limitations include specificity in terms of radionuclide, source model, clinical scenario, and MBDCA version used for its preparation.
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Beaulieu, L., Ballester, F., Granero, D., Tedgren, A. C., Haworth, A., Lowenstein, J. R., et al. (2023). AAPM WGDCAB Report 372: A joint AAPM, ESTRO, ABG, and ABS report on commissioning of model-based dose calculation algorithms in brachytherapy. Med. Phys., 50(8), e946–e960.
Abstract: The introduction of model-based dose calculation algorithms (MBDCAs) in brachytherapy provides an opportunity for a more accurate dose calculation and opens the possibility for novel, innovative treatment modalities. The joint AAPM, ESTRO, and ABG Task Group 186 (TG-186) report provided guidance to early adopters. However, the commissioning aspect of these algorithms was described only in general terms with no quantitative goals. This report, from the Working Group on Model-Based Dose Calculation Algorithms in Brachytherapy, introduced a field-tested approach to MBDCA commissioning. It is based on a set of well-characterized test cases for which reference Monte Carlo (MC) and vendor-specific MBDCA dose distributions are available in a Digital Imaging and Communications in Medicine-Radiotherapy (DICOM-RT) format to the clinical users. The key elements of the TG-186 commissioning workflow are now described in detail, and quantitative goals are provided. This approach leverages the well-known Brachytherapy Source Registry jointly managed by the AAPM and the Imaging and Radiation Oncology Core (IROC) Houston Quality Assurance Center (with associated links at ESTRO) to provide open access to test cases as well as step-by-step user guides. While the current report is limited to the two most widely commercially available MBDCAs and only for Ir-192-based afterloading brachytherapy at this time, this report establishes a general framework that can easily be extended to other brachytherapy MBDCAs and brachytherapy sources. The AAPM, ESTRO, ABG, and ABS recommend that clinical medical physicists implement the workflow presented in this report to validate both the basic and the advanced dose calculation features of their commercial MBDCAs. Recommendations are also given to vendors to integrate advanced analysis tools into their brachytherapy treatment planning system to facilitate extensive dose comparisons. The use of the test cases for research and educational purposes is further encouraged.
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Fletcher, E. M., Ballester, F., Beaulieu, L., Morrison, H., Poher, A., Rivard, M. J., et al. (2024). Generation and comparison of 3D dosimetric reference datasets for COMS eye plaque brachytherapy using model-based dose calculations. Med. Phys., 51, 694–706.
Abstract: PurposeA joint Working Group of the American Association of Physicists in Medicine (AAPM), the European Society for Radiotherapy and Oncology (ESTRO), and the Australasian Brachytherapy Group (ABG) was created to aid in the transition from the AAPM TG-43 dose calculation formalism, the current standard, to model-based dose calculations. This work establishes the first test cases for low-energy photon-emitting brachytherapy using model-based dose calculation algorithms (MBDCAs).Acquisition and Validation MethodsFive test cases are developed: (1) a single model 6711 125I brachytherapy seed in water, 13 seeds (2) individually and (3) in combination in water, (4) the full Collaborative Ocular Melanoma Study (COMS) 16-mm eye plaque in water, and (5) the full plaque in a realistic eye phantom. Calculations are done with four Monte Carlo (MC) codes and a research version of a commercial treatment planning system (TPS). For all test cases, local agreement of MC codes was within & SIM;2.5% and global agreement was & SIM;2% (4% for test case 5). MC agreement was within expected uncertainties. Local agreement of TPS with MC was within 5% for test case 1 and & SIM;20% for test cases 4 and 5, and global agreement was within 0.4% for test case 1 and 10% for test cases 4 and 5.Data Format and Usage NotesDose distributions for each set of MC and TPS calculations are available online () along with input files and all other information necessary to repeat the calculations.Potential ApplicationsThese data can be used to support commissioning of MBDCAs for low-energy brachytherapy as recommended by TGs 186 and 221 and AAPM Report 372. This work additionally lays out a sample framework for the development of test cases that can be extended to other applications beyond eye plaque brachytherapy.
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ANTARES Collaboration(Reeb, N. et al), Alves, S., Carretero, V., Colomer, M., Hernandez-Rey, J. J., Khan-Chowdhury, N. R., et al. (2023). Studying bioluminescence flashes with the ANTARES deep-sea neutrino telescope. Limnol. Oceanogr. Meth., 21(11), 734–760.
Abstract: We develop a novel technique to exploit the extensive data sets provided by underwater neutrino telescopes to gain information on bioluminescence in the deep sea. The passive nature of the telescopes gives us the unique opportunity to infer information on bioluminescent organisms without actively interfering with them. We propose a statistical method that allows us to reconstruct the light emission of individual organisms, as well as their location and movement. A mathematical model is built to describe the measurement process of underwater neutrino telescopes and the signal generation of the biological organisms. The Metric Gaussian Variational Inference algorithm is used to reconstruct the model parameters using photon counts recorded by photomultiplier tubes. We apply this method to synthetic data sets and data collected by the ANTARES neutrino telescope. The telescope is located 40 km off the French coast and fixed to the sea floor at a depth of 2475 m. The runs with synthetic data reveal that we can model the emitted bioluminescent flashes of the organisms. Furthermore, we find that the spatial resolution of the localization of light sources highly depends on the configuration of the telescope. Precise measurements of the efficiencies of the detectors and the attenuation length of the water are crucial to reconstruct the light emission. Finally, the application to ANTARES data reveals the first localizations of bioluminescent organisms using neutrino telescope data.
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Piriz, G. H., Gonzalez-Sprinberg, G. A., Ballester, F., & Vijande, J. (2024). Dosimetry of Large Field Valencia applicators for Cobalt-60-based brachytherapy. Med. Phys., , 5pp.
Abstract: BackgroundNon-melanoma skin cancer is one of the most common types of cancer and one of the main approaches is brachytherapy. For small lesions, the treatment of this cancer with brachytherapy can be done with two commercial applicators, one of these is the Large Field Valencia Applicators (LFVA).PurposeThe aim of this study is to test the capabilities of the LFVA to use clinically 60Co sources instead of the 192Ir ones. This study was designed for the same dwell positions and weights for both sources.MethodsThe Penelope Monte Carlo code was used to evaluate dose distribution in a water phantom when a 60Co source is considered. The LFVA design and the optimized dwell weights reported for the case of 192Ir are maintained with the only exception of the dwell weight of the central position, that was increased. 2D dose distributions, field flatness, symmetry and the leakage dose distribution around the applicator were calculated.ResultsWhen comparing the dose distributions of both sources, field flatness and symmetry remain unchanged. The only evident difference is an increase of the penumbra regions for all depths when using the 60Co source. Regarding leakage, the maximum dose within the air volume surrounding the applicator is in the order of 20% of the prescription dose for the 60Co source, but it decreases to less than 5% at about 1 cm distance.ConclusionsFlatness and symmetry remains unaltered as compared with 192Ir sources, while an increase in leakage has been observed. This proves the feasibility of using the LFVA in a larger range of clinical applications.
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