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Panagiotis Papadimitroulas

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10 records found

Journal article (2024) - Efstathia Petrou, Konstantinos Chatzipapas, Panagiotis Papadimitroulas, Gustavo Andrade-Miranda, Paraskevi F. Katsakiori, Nikolaos D. Papathanasiou, Dimitris Visvikis, George C. Kagadis
Background: This study investigated alternative, non-invasive methods for human papillomavirus (HPV) detection in head and neck cancers (HNCs). We compared two approaches: analyzing computed tomography (CT) scans with a Deep Learning (DL) model and using radiomic features extracted from CT images with machine learning (ML) models. Methods: Fifty patients with histologically confirmed HNC were included. We first trained a modified ResNet-18 DL model on CT data to predict HPV status. Next, radiomic features were extracted from manually segmented regions of interest near the oropharynx and used to train four ML models (K-Nearest Neighbors, logistic regression, decision tree, random forest) for the same purpose. Results: The CT-based model achieved the highest accuracy (90%) in classifying HPV status. Among the ML models, K-Nearest Neighbors performed best (80% accuracy). Weighted Ensemble methods combining the CT-based model with each ML model resulted in moderate accuracy improvements (70–90%). Conclusions: Our findings suggest that CT scans analyzed by DL models hold promise for non-invasive HPV detection in HNC. Radiomic features, while less accurate in this study, offer a complementary approach. Future research should explore larger datasets and investigate the potential of combining DL and radiomic techniques. ...
Journal article (2023) - Ioanna Stamouli, Thomas Nanos, Konstantinos Chatzipapas, Panagiotis Papadimitroulas, Lydia Aggeliki Zoglopitou, Theodoros Kalathas, Paraskevi F. Katsakiori, Anna Makridou, George C. Kagadis
This study aimed to compare the commercial dosimetric software Planet® Dose (version 3.1.1) from DOSIsoft and the open-source toolkit GATE. Dosimetry was performed for six patients receiving 200 mCi of Lutathera® every 8 weeks for four treatment cycles. For the dose calculation with Planet®, SPECT/CT images were acquired at 4, 24, 72 and 192 h post-injection. After the registration of all the time points to T0, the organs of interest (OOIs) were segmented. Time-activity curves were produced and the absorbed dose was calculated using the bi- and tri-exponential fitting methods. Regarding GATE simulations, the SPECT images of the 24 h time point were utilized for the radiopharmaceutical biodistribution in the OOIs and the attenuation maps were produced using the CT images. For liver and spleen, the average relative difference between GATE and Planet® was 9.6% and 11.1% for biexponential and 12.4% and 30.5% for triexponential fitting, respectively. The right and left kidneys showed differences up to 10.7% and 10.4% for the biexponential and up to 60.6% and 11.9% for the triexponential model, respectively. The absorbed dose calculated with GATE, Planet®(bi-exp) and Planet®(tri-exp) was in agreement with the literature. The results of the bi-exponential fitting were similar to the GATE-resulted calculations, while the tri-exponential fitting had a higher relative difference. ...
Journal article (2023) - Vasileios Eleftheriadis, Georgios Savvidis, Valentina Paneta, Konstantinos Chatzipapas, George C. Kagadis, Panagiotis Papadimitroulas
Objective: A methodology is introduced for the development of an internal dosimetry prediction toolkit for nuclear medical pediatric applications. The proposed study exploits Artificial Intelligence techniques using Monte Carlo simulations as ground truth for accurate prediction of absorbed doses per organ prior to the imaging acquisition considering only personalized anatomical characteristics of any new pediatric patient.

Approach: GATE Monte Carlo simulations were performed using a population of computational pediatric models to calculate the specific absorbed dose rates (SADRs) in several organs. A simulated dosimetry database was developed for 28 pediatric phantoms (age range 2–17 years old, both genders) and 5 different radiopharmaceuticals. Machine Learning regression models were trained on the produced simulated dataset, with leave one out cross validation for the prediction model evaluation. Hyperparameter optimization and ensemble learning techniques for a variation of input features were applied for achieving the best predictive power, leading to the development of a SADR prediction toolkit for any new pediatric patient for the studied organs and radiopharmaceuticals. Main results. SADR values for 30 organs of interest were calculated via Monte Carlo simulations for 28 pediatric phantoms for the cases of five radiopharmaceuticals. The relative percentage uncertainty in the extracted dose values per organ was lower than 2.7%. An internal dosimetry prediction toolkit which can accurately predict SADRs in 30 organs for five different radiopharmaceuticals, with mean absolute percentage error on the level of 8% was developed, with specific focus on pediatric patients, by using Machine Learning regression algorithms, Single or Multiple organ training and Artificial Intelligence ensemble techniques.

Significance: A large simulated dosimetry database was developed and utilized for the training of Machine Learning models. The developed predictive models provide very fast results (<2 s) with an accuracy >90% with respect to the ground truth of Monte Carlo, considering personalized anatomical characteristics and the biodistribution of each radiopharmaceutical. The proposed method is applicable to other medical dosimetry applications in different patients’ populations. ...

A novel platform, based on Geant4-DNA to quantify DNA damage by ionizing radiation

Journal article (2021) - Konstantinos P. Chatzipapas, Panagiotis Papadimitroulas, George Loudos, Niko Papanikolaou, George C. Kagadis
Purpose
This study proposes a novel computational platform that we refer to as IDDRRA (DNA Damage Response to Ionizing RAdiation), which uses Monte Carlo (MC) simulations to score radiation induced DNA damage. MC simulations provide results of high accuracy on the interaction of radiation with matter while scoring the energy deposition based on state-of-the-art physics and chemistry models and probabilistic methods.

Methods
The IDDRRA software is based on the Geant4-DNA toolkit together with new tools that were developed for the purpose of this study, including a new algorithm that was developed in Python for the design of the DNA molecules. New classes were developed in C++ to integrate the GUI and produce the simulation’s output in text format. An algorithm was also developed to analyze the simulation’s output in terms of energy deposition, Single Strand Breaks (SSB), Double Strand Breaks (DSB) and Cluster Damage Sites (CDS). Finally, a new tool was developed to implement probabilistic SSB and DSB repair models using MC techniques.

Results
This article provides the first benchmarks that the user of the IDDRRA tool can use to validate the functionality of the software as well as to provide a starting point to produce different types of DNA simulations. These benchmarks incorporate different kind of particles (e-, e+, protons, electron spectrum) and DNA molecules.

Conclusion
We have developed the IDDRRA tool and demonstrated its use to study various aspects of the modeling and simulation of a DNA irradiation experiment. The tool is expandable and can be expanded by other users with new benchmarks and applications based on the user’s needs and experience. New functionality will be added over time, including the quantification of the indirect damage. ...
Journal article (2021) - Konstantinos P. Chatzipapas, Dimitris Plachouris, Panagiotis Papadimitroulas, Konstantinos A. Mountris, Julien Bert, Dimitris Visvikis, Dimitris Mihailidis, George C. Kagadis
This study aims to validate GATE and GGEMS simulation toolkits for brachytherapy applications and to provide accurate models for six commercial brachytherapy seeds, which will be freely available for research purposes. The AAPM TG-43 guidelines were used for the validation of two Low Dose Rate (LDR), three High Dose Rate (HDR), and one Pulsed Dose Rate (PDR) brachytherapy seeds. Each seed was represented as a 3D model and then simulated in GATE to produce one single Phase-Space (PHSP) per seed. To test the validity of the simulations’ outcome, referenced data (provided by the TG-43) was compared with GATE results. Next, validation of the GGEMS toolkit was achieved by comparing its outcome with the GATE MC simulations, incorporating clinical data. The simulation outcomes on the radial dose function (RDF), anisotropy function (AF), and dose rate constant (DRC) for the six commercial seeds were compared with TG-43 values. The statistical uncertainty was limited to 1% for RDF, to 6% (maximum) for AF, and to 2.7% (maximum) for the DRC. GGEMS provided a good agreement with GATE when compared in different situations: (a) Homogeneous water sphere, (b) heterogeneous CT phantom, and (c) a realistic clinical case. In addition, GGEMS has the advantage of very fast simulations. For the clinical case, where TG-186 guidelines were considered, GATE required 1 h for the simulation while GGEMS needed 162 s to reach the same statistical uncertainty. This study produced accurate models and simulations of their emitted spectrum of commonly used commercial brachytherapy seeds which are freely available to the scientific community. Furthermore, GGEMS was validated as an MC GPU based tool for brachytherapy. More research is deemed necessary for the expansion of brachytherapy seed modeling. ...

Quantifying the radiobiological damage using monte carlo simulations

Review (2020) - Konstantinos P. Chatzipapas, Panagiotis Papadimitroulas, Dimitris Emfietzoglou, Spyridon A. Kalospyros, Megumi Hada, Alexandros G. Georgakilas, George C. Kagadis
Ionizing radiation is a common tool in medical procedures. Monte Carlo (MC) techniques are widely used when dosimetry is the matter of investigation. The scientific community has invested, over the last 20 years, a lot of effort into improving the knowledge of radiation biology. The present article aims to summarize the understanding of the field of DNA damage response (DDR) to ionizing radiation by providing an overview on MC simulation studies that try to explain several aspects of radiation biology. The need for accurate techniques for the quantification of DNA damage is crucial, as it becomes a clinical need to evaluate the outcome of various applications including both low-and high-energy radiation medical procedures. Understanding DNA repair processes would improve radiation therapy procedures. Monte Carlo simulations are a promising tool in radiobiology studies, as there are clear prospects for more advanced tools that could be used in multidisciplinary studies, in the fields of physics, medicine, biology and chemistry. Still, lot of effort is needed to evolve MC simulation tools and apply them in multiscale studies starting from small DNA segments and reaching a population of cells. ...
Journal article (2019) - Konstantinos P. Chatzipapas, Panagiotis Papadimitroulas, Mohammad Obeidat, Kristen A. McConnell, Neil Kirby, George Loudos, Niko Papanikolaou, George C. Kagadis
Purpose
This study aims to standardize the simulation procedure in measuring DNA double-strand breaks (DSBs), by using advanced Monte Carlo toolkits, and newly introduced experimental methods for DNA DSB measurement.

Methods
For the experimental quantification of DNA DSB, an innovative DNA dosimeter was used to produce experimental data. GATE in combination with Geant4-DNA toolkit were exploited to simulate the experimental environment. The PDB4DNA example of Geant4-DNA was upgraded and investigated. Parameters of the simulation such energy threshold (ET) for a strand break and base pair threshold (BPT) for a DSB were evaluated, depending on the dose.

Results
Simulations resulted to minimum differentiation in comparison to experimental data for ET = 19 ± 1 eV and BPT = 10 bp, and high differentiation for ET<17.5 eV or ET>22.5 eV and BPT = 10 bp. There was also small differentiation for ET = 17.5 eV and BPT = 6 bp. Uncertainty has been kept lower than 3%.

Conclusions
This study includes first results on the quantification of DNA double-strand breaks. The energy spectrum of a LINAC was simulated and used for the first time to irradiate DNA molecules. Simulation outcome was validated on experimental data that were produced by a prototype DNA dosimeter. ...
Review (2019) - Panagiotis Papadimitroulas, Theodora Kostou, Konstantinos Chatzipapas, Dimitris Visvikis, Konstantinos A. Mountris, Vincent Jaouen, Konstantinos Katsanos, Athanasios Diamantopoulos, George C. Kagadis
Pediatric patient-specific dosimetry of ionizing radiation is of great scientific and social interest. Children provide a higher relative cancer-risk from exposure to ionizing radiation compared to adults. The proposed study reviews the recent techniques applied in pediatric imaging and therapy applications for dosimetry purposes. Modern medicine makes use of advance computational tools for the personalization of internal and external dosimetry, especially in the sensitive group of children. Several groups of pediatric computational models have been developed which are combined with Monte Carlo (MC) simulations, machine learning (ML) techniques, and image processing algorithms for accurate dosimetry assessment. More specifically, this paper reviews the dosimetry applications in pediatric diagnostic procedures, including computed tomography and nuclear medicine applications. Right afterward, the most recent applications in therapeutic brachytherapy protocols are presented, which is a rather sensitive procedure in pediatrics. Finally, modern tools for dosimetry optimization are discussed, reviewing the most indicative applications with: 1) MC simulations for pediatric dosimetry assessment; 2) pediatric computational models, widely used in medical applications; and 3) ML techniques that provide an alternative method for estimating individualized absorbed doses. ...
Journal article (2017) - Konstantinos Chatzipapas, Panagiotis Papadimitroulas, Mohammad Ali Obeidat, Neil Kirby, George Loudos, Niko Papanikolaou, George C. Kagadis
The investigation of biological effects in living tissues requires the modeling of physical, chemical, and physico-chemical interactions. Strong effort has been given in the 3D modeling of DNA structure, such as to describe the cell nucleus. In 2015, a new application, Geant4-DNA was presented, enabling the atomic level description of DNA molecules and the possibility of evaluating the direct damage induced on the DNA molecule by ionizing radiation [1]. Recently, a DNA Double-Strand Break (DSB) dosimeter was developed for the detection and quantification of DNA-DSBs after irradiation[2]. Our goal is to validate the simulated data, and standardize the experimental procedure for measuring the biological damage.

In the present study, we investigated the PDB4DNA tool and developed a new G4-DNA class for the quantification of DSBs after irradiation. Experimental measures were used for testing the G4-DNA classes. A DNA molecule (1329bp, the largest in PDBlib) was irradiated with 3 different absorbed doses equal to 10, 25 and 50Gy. In our simulation study, we used a structure of a single DNA molecule (based on experimental data), and irradiated it multiple times to quantify the probability of DSBs.

The simulations, on G4-DNA DSB quantification, resulted in DSB probabilities equal to 9.0%, 17.0%, and 31% for doses 10Gy, 25Gy, and 50Gy respectively. Thus, the statistical difference between experimental and simulated DSBs was calculated to 8.09%, 9.23%, and 13.43% accordingly. Comparing our simulations with the standard used PDB4DNA class, differences varied from 40–70%.

This is a preliminary study for the modeling, and the quantification of DNA-DSBs based on experimental data. The limitations of this study need to be addressed, such as the modeling of multiple DNA molecules for accurate statistical simulations, and chemical reactions need to be taken into account for the total quantification of the biological damage on DNA structures. ...
Journal article (2016) - Konstantinos Chatzipapas, Panagiotis Papadimitroulas, George Loudos, N Papanikolaou, G Kagadis
Purpose:
Pediatric tumors are generally treated with multi-modal procedures. Brachytherapy can be used with pediatric tumors, especially given that in this patient population low toxicity on normal tissues is critical as is the suppression of the probability for late malignancies. Our goal is to validate the GATE toolkit on realistic brachytherapy applications, and evaluate brachytherapy plans on pediatrics for accurate dosimetry on sensitive and critical organs of interest.

Methods:
The GATE Monte Carlo (MC) toolkit was used. Two High Dose Rate (HDR) 192Ir brachytherapy sources were simulated (Nucletron mHDR-v1 and Varian VS2000), and fully validated using the AAPM and ESTRO protocols. A realistic brachytherapy plan was also simulated using the XCAT anthropomorphic computational model .The simulated data were compared to the clinical dose points. Finally, a 14 years old girl with vaginal rhabdomyosarcoma was modelled based on clinical procedures for the calculation of the absorbed dose per organ.

Results:
The MC simulations resulted in accurate dosimetry in terms of dose rate constant (Λ), radial dose gL(r) and anisotropy function F(r,θ) for both sources. The simulations were executed using ∼1010 number of primaries resulting in statistical uncertainties lower than 2%.The differences between the theoretical values and the simulated ones ranged from 0.01% up to 3.3%, with the largest discrepancy (6%) being observed in the dose rate constant calculation. The simulated DVH using an adult female XCAT model was also compared to a clinical one resulting in differences smaller than 5%. Finally, a realistic pediatric brachytherapy simulation was performed to evaluate the absorbed dose per organ and to calculate DVH with respect to heterogeneities of the human anatomy.

Conclusion:
GATE is a reliable tool for brachytherapy simulations both for source modeling and for dosimetry in anthropomorphic voxelized models. Our project aims to evaluate a variety of pediatric brachytherapy schemes using a population of pediatric phantoms for several pathological cases. ...