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.
|
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.
|
Saad Minhas, Zeba Khanam, Shoaib Ehsan, Klaus McDonald Maier, & Aura Hernandez-Sabate. (2022). Weather Classification by Utilizing Synthetic Data. SENS - Sensors, 22(9), 3193.
Abstract: Weather prediction from real-world images can be termed a complex task when targeting classification using neural networks. Moreover, the number of images throughout the available datasets can contain a huge amount of variance when comparing locations with the weather those images are representing. In this article, the capabilities of a custom built driver simulator are explored specifically to simulate a wide range of weather conditions. Moreover, the performance of a new synthetic dataset generated by the above simulator is also assessed. The results indicate that the use of synthetic datasets in conjunction with real-world datasets can increase the training efficiency of the CNNs by as much as 74%. The article paves a way forward to tackle the persistent problem of bias in vision-based datasets.
Keywords: Weather classification; synthetic data; dataset; autonomous car; computer vision; advanced driver assistance systems; deep learning; intelligent transportation systems
|
Debora Gil, Katerine Diaz, Carles Sanchez, & Aura Hernandez-Sabate. (2020). Early Screening of SARS-CoV-2 by Intelligent Analysis of X-Ray Images.
Abstract: Future SARS-CoV-2 virus outbreak COVID-XX might possibly occur during the next years. However the pathology in humans is so recent that many clinical aspects, like early detection of complications, side effects after recovery or early screening, are currently unknown. In spite of the number of cases of COVID-19, its rapid spread putting many sanitary systems in the edge of collapse has hindered proper collection and analysis of the data related to COVID-19 clinical aspects. We describe an interdisciplinary initiative that integrates clinical research, with image diagnostics and the use of new technologies such as artificial intelligence and radiomics with the aim of clarifying some of SARS-CoV-2 open questions. The whole initiative addresses 3 main points: 1) collection of standardize data including images, clinical data and analytics; 2) COVID-19 screening for its early diagnosis at primary care centers; 3) define radiomic signatures of COVID-19 evolution and associated pathologies for the early treatment of complications. In particular, in this paper we present a general overview of the project, the experimental design and first results of X-ray COVID-19 detection using a classic approach based on HoG and feature selection. Our experiments include a comparison to some recent methods for COVID-19 screening in X-Ray and an exploratory analysis of the feasibility of X-Ray COVID-19 screening. Results show that classic approaches can outperform deep-learning methods in this experimental setting, indicate the feasibility of early COVID-19 screening and that non-COVID infiltration is the group of patients most similar to COVID-19 in terms of radiological description of X-ray. Therefore, an efficient COVID-19 screening should be complemented with other clinical data to better discriminate these cases.
|
Debora Gil, Antonio Esteban Lansaque, Agnes Borras, & Carles Sanchez. (2019). Enhancing virtual bronchoscopy with intra-operative data using a multi-objective GAN. IJCAR - International Journal of Computer Assisted Radiology and Surgery, 7(1).
Abstract: This manuscript has been withdrawn by bioRxiv due to upload of an incorrect version of the manuscript by the authors. Therefore, this manuscript should not be cited as reference for this project.
|
Debora Gil, Carles Sanchez, Agnes Borras, Marta Diez-Ferrer, & Antoni Rosell. (2019). Segmentation of Distal Airways using Structural Analysis. Plos - PloS one, 14(12).
Abstract: Segmentation of airways in Computed Tomography (CT) scans is a must for accurate support of diagnosis and intervention of many pulmonary disorders. In particular, lung cancer diagnosis would benefit from segmentations reaching most distal airways. We present a method that combines descriptors of bronchi local appearance and graph global structural analysis to fine-tune thresholds on the descriptors adapted for each bronchial level. We have compared our method to the top performers of the EXACT09 challenge and to a commercial software for biopsy planning evaluated in an own-collected data-base of high resolution CT scans acquired under different breathing conditions. Results on EXACT09 data show that our method provides a high leakage reduction with minimum loss in airway detection. Results on our data-base show the reliability across varying breathing conditions and a competitive performance for biopsy planning compared to a commercial solution.
|
Marta Ligero, Guillermo Torres, Carles Sanchez, Katerine Diaz, Raquel Perez, & Debora Gil. (2019). Selection of Radiomics Features based on their Reproducibility. In 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (pp. 403–408).
Abstract: Dimensionality reduction is key to alleviate machine learning artifacts in clinical applications with Small Sample Size (SSS) unbalanced datasets. Existing methods rely on either the probabilistic distribution of training data or the discriminant power of the reduced space, disregarding the impact of repeatability and uncertainty in features.In the present study is proposed the use of reproducibility of radiomics features to select features with high inter-class correlation coefficient (ICC). The reproducibility includes the variability introduced in the image acquisition, like medical scans acquisition parameters and convolution kernels, that affects intensity-based features and tumor annotations made by physicians, that influences morphological descriptors of the lesion.For the reproducibility of radiomics features three studies were conducted on cases collected at Vall Hebron Oncology Institute (VHIO) on responders to oncology treatment. The studies focused on the variability due to the convolution kernel, image acquisition parameters, and the inter-observer lesion identification. The features selected were those features with a ICC higher than 0.7 in the three studies.The selected features based on reproducibility were evaluated for lesion malignancy classification using a different database. Results show better performance compared to several state-of-the-art methods including Principal Component Analysis (PCA), Kernel Discriminant Analysis via QR decomposition (KDAQR), LASSO, and an own built Convolutional Neural Network.
|
Debora Gil, & Antoni Rosell. (2019). Advances in Artificial Intelligence – How Lung Cancer CT Screening Will Progress? In World Lung Cancer Conference.
Abstract: Invited speaker
|
Antonio Esteban Lansaque. (2019). An Endoscopic Navigation System for Lung Cancer Biopsy (Debora Gil, & Carles Sanchez, Eds.). Ph.D. thesis, Ediciones Graficas Rey, .
Abstract: Lung cancer is one of the most diagnosed cancers among men and women. Actually,
lung cancer accounts for 13% of the total cases with a 5-year global survival
rate in patients. Although Early detection increases survival rate from 38% to 67%, accurate diagnosis remains a challenge. Pathological confirmation requires extracting a sample of the lesion tissue for its biopsy. The preferred procedure for tissue biopsy is called bronchoscopy. A bronchoscopy is an endoscopic technique for the internal exploration of airways which facilitates the performance of minimal invasive interventions with low risk for the patient. Recent advances in bronchoscopic devices have increased their use for minimal invasive diagnostic and intervention procedures, like lung cancer biopsy sampling. Despite the improvement in bronchoscopic device quality, there is a lack of intelligent computational systems for supporting in-vivo clinical decision during examinations. Existing technologies fail to accurately reach the lesion due to several aspects at intervention off-line planning and poor intra-operative guidance at exploration time. Existing guiding systems radiate patients and clinical staff,might be expensive and achieve a suboptimlal 70% of yield boost. Diagnostic yield could be improved reducing radiation and costs by developing intra-operative support systems able to guide the bronchoscopist to the lesion during the intervention. The goal of this PhD thesis is to develop an image-based navigation systemfor intra-operative guidance of bronchoscopists to a target lesion across a path previously planned on a CT-scan. We propose a 3D navigation system which uses the anatomy of video bronchoscopy frames to locate the bronchoscope within the airways. Once the bronchoscope is located, our navigation system is able to indicate the bifurcation which needs to be followed to reach the lesion. In order to facilitate an off-line validation
as realistic as possible, we also present a method for augmenting simulated virtual bronchoscopies with the appearance of intra-operative videos. Experiments performed on augmented and intra-operative videos, prove that our algorithm can be speeded up for an on-line implementation in the operating room.
|
Debora Gil, Antonio Esteban Lansaque, Agnes Borras, Esmitt Ramirez, & Carles Sanchez. (2020). Intraoperative Extraction of Airways Anatomy in VideoBronchoscopy. ACCESS - IEEE Access, 8, 159696–159704.
Abstract: A main bottleneck in bronchoscopic biopsy sampling is to efficiently reach the lesion navigating across bronchial levels. Any guidance system should be able to localize the scope position during the intervention with minimal costs and alteration of clinical protocols. With the final goal of an affordable image-based guidance, this work presents a novel strategy to extract and codify the anatomical structure of bronchi, as well as, the scope navigation path from videobronchoscopy. Experiments using interventional data show that our method accurately identifies the bronchial structure. Meanwhile, experiments using simulated data verify that the extracted navigation path matches the 3D route.
|
Saad Minhas, Aura Hernandez-Sabate, Shoaib Ehsan, & Klaus McDonald Maier. (2022). Effects of Non-Driving Related Tasks during Self-Driving mode. TITS - IEEE Transactions on Intelligent Transportation Systems, 23(2), 1391–1399.
Abstract: Perception reaction time and mental workload have proven to be crucial in manual driving. Moreover, in highly automated cars, where most of the research is focusing on Level 4 Autonomous driving, take-over performance is also a key factor when taking road safety into account. This study aims to investigate how the immersion in non-driving related tasks affects the take-over performance of drivers in given scenarios. The paper also highlights the use of virtual simulators to gather efficient data that can be crucial in easing the transition between manual and autonomous driving scenarios. The use of Computer Aided Simulations is of absolute importance in this day and age since the automotive industry is rapidly moving towards Autonomous technology. An experiment comprising of 40 subjects was performed to examine the reaction times of driver and the influence of other variables in the success of take-over performance in highly automated driving under different circumstances within a highway virtual environment. The results reflect the relationship between reaction times under different scenarios that the drivers might face under the circumstances stated above as well as the importance of variables such as velocity in the success on regaining car control after automated driving. The implications of the results acquired are important for understanding the criteria needed for designing Human Machine Interfaces specifically aimed towards automated driving conditions. Understanding the need to keep drivers in the loop during automation, whilst allowing drivers to safely engage in other non-driving related tasks is an important research area which can be aided by the proposed study.
|
|
Debora Gil, & Guillermo Torres. (2020). A multi-shape loss function with adaptive class balancing for the segmentation of lung structures. In 34th International Congress and Exhibition on Computer Assisted Radiology & Surgery.
|
Guillermo Torres, Sonia Baeza, Carles Sanchez, Ignasi Guasch, Antoni Rosell, & Debora Gil. (2022). An Intelligent Radiomic Approach for Lung Cancer Screening. APPLSCI - Applied Sciences, 12(3), 1568.
Abstract: The efficiency of lung cancer screening for reducing mortality is hindered by the high rate of false positives. Artificial intelligence applied to radiomics could help to early discard benign cases from the analysis of CT scans. The available amount of data and the fact that benign cases are a minority, constitutes a main challenge for the successful use of state of the art methods (like deep learning), which can be biased, over-fitted and lack of clinical reproducibility. We present an hybrid approach combining the potential of radiomic features to characterize nodules in CT scans and the generalization of the feed forward networks. In order to obtain maximal reproducibility with minimal training data, we propose an embedding of nodules based on the statistical significance of radiomic features for malignancy detection. This representation space of lesions is the input to a feed
forward network, which architecture and hyperparameters are optimized using own-defined metrics of the diagnostic power of the whole system. Results of the best model on an independent set of patients achieve 100% of sensitivity and 83% of specificity (AUC = 0.94) for malignancy detection.
Keywords: Lung cancer; Early diagnosis; Screening; Neural networks; Image embedding; Architecture optimization
|
Debora Gil, Aura Hernandez-Sabate, Julien Enconniere, Saryani Asmayawati, Pau Folch, Juan Borrego-Carazo, et al. (2022). E-Pilots: A System to Predict Hard Landing During the Approach Phase of Commercial Flights. ACCESS - IEEE Access, 10, 7489–7503.
Abstract: More than half of all commercial aircraft operation accidents could have been prevented by executing a go-around. Making timely decision to execute a go-around manoeuvre can potentially reduce overall aviation industry accident rate. In this paper, we describe a cockpit-deployable machine learning system to support flight crew go-around decision-making based on the prediction of a hard landing event.
This work presents a hybrid approach for hard landing prediction that uses features modelling temporal dependencies of aircraft variables as inputs to a neural network. Based on a large dataset of 58177 commercial flights, the results show that our approach has 85% of average sensitivity with 74% of average specificity at the go-around point. It follows that our approach is a cockpit-deployable recommendation system that outperforms existing approaches.
|
Jose Elias Yauri, Aura Hernandez-Sabate, Pau Folch, & Debora Gil. (2021). Mental Workload Detection Based on EEG Analysis. In Artificial Intelligent Research and Development. Proceedings 23rd International Conference of the Catalan Association for Artificial Intelligence. (Vol. 339, pp. 268–277).
Abstract: The study of mental workload becomes essential for human work efficiency, health conditions and to avoid accidents, since workload compromises both performance and awareness. Although workload has been widely studied using several physiological measures, minimising the sensor network as much as possible remains both a challenge and a requirement.
Electroencephalogram (EEG) signals have shown a high correlation to specific cognitive and mental states like workload. However, there is not enough evidence in the literature to validate how well models generalize in case of new subjects performing tasks of a workload similar to the ones included during model’s training.
In this paper we propose a binary neural network to classify EEG features across different mental workloads. Two workloads, low and medium, are induced using two variants of the N-Back Test. The proposed model was validated in a dataset collected from 16 subjects and shown a high level of generalization capability: model reported an average recall of 81.81% in a leave-one-out subject evaluation.
Keywords: Cognitive states; Mental workload; EEG analysis; Neural Networks.
|
