2022 |
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Sonia Baeza, Debora Gil, I.Garcia Olive, M.Salcedo, J.Deportos, Carles Sanchez, et al. (2022). A novel intelligent radiomic analysis of perfusion SPECT/CT images to optimize pulmonary embolism diagnosis in COVID-19 patients. EJNMMI-PHYS - EJNMMI Physics, 9(1, Article 84), 1–17.
Abstract: Background: COVID-19 infection, especially in cases with pneumonia, is associated with a high rate of pulmonary embolism (PE). In patients with contraindications for CT pulmonary angiography (CTPA) or non-diagnostic CTPA, perfusion single-photon emission computed tomography/computed tomography (Q-SPECT/CT) is a diagnostic alternative. The goal of this study is to develop a radiomic diagnostic system to detect PE based only on the analysis of Q-SPECT/CT scans.
Methods: This radiomic diagnostic system is based on a local analysis of Q-SPECT/CT volumes that includes both CT and Q-SPECT values for each volume point. We present a combined approach that uses radiomic features extracted from each scan as input into a fully connected classifcation neural network that optimizes a weighted crossentropy loss trained to discriminate between three diferent types of image patterns (pixel sample level): healthy lungs (control group), PE and pneumonia. Four types of models using diferent confguration of parameters were tested.
Results: The proposed radiomic diagnostic system was trained on 20 patients (4,927 sets of samples of three types of image patterns) and validated in a group of 39 patients (4,410 sets of samples of three types of image patterns). In the training group, COVID-19 infection corresponded to 45% of the cases and 51.28% in the test group. In the test group, the best model for determining diferent types of image patterns with PE presented a sensitivity, specifcity, positive predictive value and negative predictive value of 75.1%, 98.2%, 88.9% and 95.4%, respectively. The best model for detecting
pneumonia presented a sensitivity, specifcity, positive predictive value and negative predictive value of 94.1%, 93.6%, 85.2% and 97.6%, respectively. The area under the curve (AUC) was 0.92 for PE and 0.91 for pneumonia. When the results obtained at the pixel sample level are aggregated into regions of interest, the sensitivity of the PE increases to 85%, and all metrics improve for pneumonia.
Conclusion: This radiomic diagnostic system was able to identify the diferent lung imaging patterns and is a frst step toward a comprehensive intelligent radiomic system to optimize the diagnosis of PE by Q-SPECT/CT.
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2021 |
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Marta Ligero, Alonso Garcia Ruiz, Cristina Viaplana, Guillermo Villacampa, Maria V Raciti, Jaid Landa, et al. (2021). A CT-based radiomics signature is associated with response to immune checkpoint inhibitors in advanced solid tumors. Radiology, 299(1), 109–119.
Abstract: Background Reliable predictive imaging markers of response to immune checkpoint inhibitors are needed. Purpose To develop and validate a pretreatment CT-based radiomics signature to predict response to immune checkpoint inhibitors in advanced solid tumors. Materials and Methods In this retrospective study, a radiomics signature was developed in patients with advanced solid tumors (including breast, cervix, gastrointestinal) treated with anti-programmed cell death-1 or programmed cell death ligand-1 monotherapy from August 2012 to May 2018 (cohort 1). This was tested in patients with bladder and lung cancer (cohorts 2 and 3). Radiomics variables were extracted from all metastases delineated at pretreatment CT and selected by using an elastic-net model. A regression model combined radiomics and clinical variables with response as the end point. Biologic validation of the radiomics score with RNA profiling of cytotoxic cells (cohort 4) was assessed with Mann-Whitney analysis. Results The radiomics signature was developed in 85 patients (cohort 1: mean age, 58 years ± 13 [standard deviation]; 43 men) and tested on 46 patients (cohort 2: mean age, 70 years ± 12; 37 men) and 47 patients (cohort 3: mean age, 64 years ± 11; 40 men). Biologic validation was performed in a further cohort of 20 patients (cohort 4: mean age, 60 years ± 13; 14 men). The radiomics signature was associated with clinical response to immune checkpoint inhibitors (area under the curve [AUC], 0.70; 95% CI: 0.64, 0.77; P < .001). In cohorts 2 and 3, the AUC was 0.67 (95% CI: 0.58, 0.76) and 0.67 (95% CI: 0.56, 0.77; P < .001), respectively. A radiomics-clinical signature (including baseline albumin level and lymphocyte count) improved on radiomics-only performance (AUC, 0.74 [95% CI: 0.63, 0.84; P < .001]; Akaike information criterion, 107.00 and 109.90, respectively). Conclusion A pretreatment CT-based radiomics signature is associated with response to immune checkpoint inhibitors, likely reflecting the tumor immunophenotype. © RSNA, 2021 Online supplemental material is available for this article. See also the editorial by Summers in this issue.
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Mireia Sole, Joan Blanco, Debora Gil, Oliver Valero, Alvaro Pascual, B. Cardenas, et al. (2021). Chromosomal positioning in spermatogenic cells is influenced by chromosomal factors associated with gene activity, bouquet formation, and meiotic sex-chromosome inactivation. Chromosoma, 130, 163–175.
Abstract: Chromosome territoriality is not random along the cell cycle and it is mainly governed by intrinsic chromosome factors and gene expression patterns. Conversely, very few studies have explored the factors that determine chromosome territoriality and its influencing factors during meiosis. In this study, we analysed chromosome positioning in murine spermatogenic cells using three-dimensionally fluorescence in situ hybridization-based methodology, which allows the analysis of the entire karyotype. The main objective of the study was to decipher chromosome positioning in a radial axis (all analysed germ-cell nuclei) and longitudinal axis (only spermatozoa) and to identify the chromosomal factors that regulate such an arrangement. Results demonstrated that the radial positioning of chromosomes during spermatogenesis was cell-type specific and influenced by chromosomal factors associated to gene activity. Chromosomes with specific features that enhance transcription (high GC content, high gene density and high numbers of predicted expressed genes) were preferentially observed in the inner part of the nucleus in virtually all cell types. Moreover, the position of the sex chromosomes was influenced by their transcriptional status, from the periphery of the nucleus when its activity was repressed (pachytene) to a more internal position when it is partially activated (spermatid). At pachytene, chromosome positioning was also influenced by chromosome size due to the bouquet formation. Longitudinal chromosome positioning in the sperm nucleus was not random either, suggesting the importance of ordered longitudinal positioning for the release and activation of the paternal genome after fertilisation.
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Sonia Baeza, R.Domingo, M.Salcedo, G.Moragas, J.Deportos, I.Garcia Olive, et al. (2021). Artificial Intelligence to Optimize Pulmonary Embolism Diagnosis During Covid-19 Pandemic by Perfusion SPECT/CT, a Pilot Study. American Journal of Respiratory and Critical Care Medicine, .
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2020 |
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Aura Hernandez-Sabate, Lluis Albarracin, & F. Javier Sanchez. (2020). Graph-Based Problem Explorer: A Software Tool to Support Algorithm Design Learning While Solving the Salesperson Problem. MATH - Mathematics, 1595.
Abstract: In this article, we present a sequence of activities in the form of a project in order to promote
learning on design and analysis of algorithms. The project is based on the resolution of a real problem, the salesperson problem, and it is theoretically grounded on the fundamentals of mathematical modelling. In order to support the students’ work, a multimedia tool, called Graph-based Problem Explorer (GbPExplorer), has been designed and refined to promote the development of computer literacy in engineering and science university students. This tool incorporates several modules to allow coding different algorithmic techniques solving the salesman problem. Based on an educational design research along five years, we observe that working with GbPExplorer during the project provides students with the possibility of representing the situation to be studied in the form of graphs and analyze them from a computational point of view.
Keywords: STEM education; Project-based learning; Coding; software tool
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