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Author Mireia Sole; Joan Blanco; Debora Gil; Oliver Valero; B. Cardenas; G. Fonseka; E. Anton; Alvaro Pascual; Richard Frodsham; Zaida Sarrate edit  doi
openurl 
  Title Time to match; when do homologous chromosomes become closer? Type Journal Article
  Year (down) 2022 Publication Chromosoma Abbreviated Journal CHRO  
  Volume Issue Pages  
  Keywords  
  Abstract In most eukaryotes, pairing of homologous chromosomes is an essential feature of meiosis that ensures homologous recombination and segregation. However, when the pairing process begins, it is still under investigation. Contrasting data exists in Mus musculus, since both leptotene DSB-dependent and preleptotene DSB-independent mechanisms have been described. To unravel this contention, we examined homologous pairing in pre-meiotic and meiotic Mus musculus cells using a threedimensional fuorescence in situ hybridization-based protocol, which enables the analysis of the entire karyotype using DNA painting probes. Our data establishes in an unambiguously manner that 73.83% of homologous chromosomes are already paired at premeiotic stages (spermatogonia-early preleptotene spermatocytes). The percentage of paired homologous chromosomes increases to 84.60% at mid-preleptotene-zygotene stage, reaching 100% at pachytene stage. Importantly, our results demonstrate a high percentage of homologous pairing observed before the onset of meiosis; this pairing does not occur randomly, as the percentage was higher than that observed in somatic cells (19.47%) and between nonhomologous chromosomes (41.1%). Finally, we have also observed that premeiotic homologous pairing is asynchronous and independent of the chromosome size, GC content, or presence of NOR regions.  
  Address August, 2022  
  Corporate Author Thesis  
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  Series Editor Series Title Abbreviated Series Title  
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  ISSN ISBN Medium  
  Area Expedition Conference  
  Notes IAM; 601.139; 600.145; 600.096 Approved no  
  Call Number Admin @ si @ SBG2022 Serial 3719  
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Author Oriol Ramos Terrades; Albert Berenguel; Debora Gil edit   pdf
doi  openurl
  Title A Flexible Outlier Detector Based on a Topology Given by Graph Communities Type Journal Article
  Year (down) 2022 Publication Big Data Research Abbreviated Journal BDR  
  Volume 29 Issue Pages 100332  
  Keywords Classification algorithms; Detection algorithms; Description of feature space local structure; Graph communities; Machine learning algorithms; Outlier detectors  
  Abstract Outlier detection is essential for optimal performance of machine learning methods and statistical predictive models. Their detection is especially determinant in small sample size unbalanced problems, since in such settings outliers become highly influential and significantly bias models. This particular experimental settings are usual in medical applications, like diagnosis of rare pathologies, outcome of experimental personalized treatments or pandemic emergencies. In contrast to population-based methods, neighborhood based local approaches compute an outlier score from the neighbors of each sample, are simple flexible methods that have the potential to perform well in small sample size unbalanced problems. A main concern of local approaches is the impact that the computation of each sample neighborhood has on the method performance. Most approaches use a distance in the feature space to define a single neighborhood that requires careful selection of several parameters, like the number of neighbors.
This work presents a local approach based on a local measure of the heterogeneity of sample labels in the feature space considered as a topological manifold. Topology is computed using the communities of a weighted graph codifying mutual nearest neighbors in the feature space. This way, we provide with a set of multiple neighborhoods able to describe the structure of complex spaces without parameter fine tuning. The extensive experiments on real-world and synthetic data sets show that our approach outperforms, both, local and global strategies in multi and single view settings.
 
  Address August 28, 2022  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
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  ISSN ISBN Medium  
  Area Expedition Conference  
  Notes DAG; IAM; 600.140; 600.121; 600.139; 600.145; 600.159 Approved no  
  Call Number Admin @ si @ RBG2022a Serial 3718  
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Author Saad Minhas; Aura Hernandez-Sabate; Shoaib Ehsan; Klaus McDonald Maier edit  doi
openurl 
  Title Effects of Non-Driving Related Tasks during Self-Driving mode Type Journal Article
  Year (down) 2022 Publication IEEE Transactions on Intelligent Transportation Systems Abbreviated Journal TITS  
  Volume 23 Issue 2 Pages 1391-1399  
  Keywords  
  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.  
  Address Feb. 2022  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
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  Area Expedition Conference  
  Notes IAM; 600.139; 600.145 Approved no  
  Call Number Admin @ si @ MHE2022 Serial 3468  
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Author Saad Minhas; Zeba Khanam; Shoaib Ehsan; Klaus McDonald Maier; Aura Hernandez-Sabate edit  doi
openurl 
  Title Weather Classification by Utilizing Synthetic Data Type Journal Article
  Year (down) 2022 Publication Sensors Abbreviated Journal SENS  
  Volume 22 Issue 9 Pages 3193  
  Keywords Weather classification; synthetic data; dataset; autonomous car; computer vision; advanced driver assistance systems; deep learning; intelligent transportation systems  
  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.  
  Address 21 April 2022  
  Corporate Author Thesis  
  Publisher MDPI Place of Publication Editor  
  Language Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN ISBN Medium  
  Area Expedition Conference  
  Notes IAM; 600.139; 600.159; 600.166; 600.145; Approved no  
  Call Number Admin @ si @ MKE2022 Serial 3761  
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Author Sonia Baeza; Debora Gil; I.Garcia Olive; M.Salcedo; J.Deportos; Carles Sanchez; Guillermo Torres; G.Moragas; Antoni Rosell edit  doi
openurl 
  Title A novel intelligent radiomic analysis of perfusion SPECT/CT images to optimize pulmonary embolism diagnosis in COVID-19 patients Type Journal Article
  Year (down) 2022 Publication EJNMMI Physics Abbreviated Journal EJNMMI-PHYS  
  Volume 9 Issue 1, Article 84 Pages 1-17  
  Keywords  
  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.
 
  Address 5 dec 2022  
  Corporate Author Thesis  
  Publisher Springer Place of Publication Editor  
  Language Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN ISBN Medium  
  Area Expedition Conference  
  Notes IAM Approved no  
  Call Number Admin @ si @ BGG2022 Serial 3759  
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Author Debora Gil; Oriol Ramos Terrades; Raquel Perez edit  doi
openurl 
  Title Topological Radiomics (TOPiomics): Early Detection of Genetic Abnormalities in Cancer Treatment Evolution Type Book Chapter
  Year (down) 2021 Publication Extended Abstracts GEOMVAP 2019, Trends in Mathematics 15 Abbreviated Journal  
  Volume 15 Issue Pages 89–93  
  Keywords  
  Abstract Abnormalities in radiomic measures correlate to genomic alterations prone to alter the outcome of personalized anti-cancer treatments. TOPiomics is a new method for the early detection of variations in tumor imaging phenotype from a topological structure in multi-view radiomic spaces.  
  Address  
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  Publisher Springer Nature Place of Publication Editor  
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  Series Editor Series Title Abbreviated Series Title  
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  Notes IAM; DAG; 600.120; 600.145; 600.139 Approved no  
  Call Number Admin @ si @ GRP2021 Serial 3594  
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Author Jose Elias Yauri; Aura Hernandez-Sabate; Pau Folch; Debora Gil edit  doi
openurl 
  Title Mental Workload Detection Based on EEG Analysis Type Conference Article
  Year (down) 2021 Publication Artificial Intelligent Research and Development. Proceedings 23rd International Conference of the Catalan Association for Artificial Intelligence. Abbreviated Journal  
  Volume 339 Issue Pages 268-277  
  Keywords Cognitive states; Mental workload; EEG analysis; Neural Networks.  
  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.
 
  Address Virtual; October 20-22 2021  
  Corporate Author Thesis  
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  Language Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
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  ISSN ISBN Medium  
  Area Expedition Conference CCIA  
  Notes IAM; 600.139; 600.118; 600.145 Approved no  
  Call Number Admin @ si @ Serial 3723  
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Author Marta Ligero; Alonso Garcia Ruiz; Cristina Viaplana; Guillermo Villacampa; Maria V Raciti; Jaid Landa; Ignacio Matos; Juan Martin Liberal; Maria Ochoa de Olza; Cinta Hierro; Joaquin Mateo; Macarena Gonzalez; Rafael Morales Barrera; Cristina Suarez; Jordi Rodon; Elena Elez; Irene Braña; Eva Muñoz-Couselo; Ana Oaknin; Roberta Fasani; Paolo Nuciforo; Debora Gil; Carlota Rubio Perez; Joan Seoane; Enriqueta Felip; Manuel Escobar; Josep Tabernero; Joan Carles; Rodrigo Dienstmann; Elena Garralda; Raquel Perez Lopez edit  url
doi  openurl
  Title A CT-based radiomics signature is associated with response to immune checkpoint inhibitors in advanced solid tumors Type Journal Article
  Year (down) 2021 Publication Radiology Abbreviated Journal  
  Volume 299 Issue 1 Pages 109-119  
  Keywords  
  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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  Notes IAM; 600.145 Approved no  
  Call Number Admin @ si @ LGV2021 Serial 3593  
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Author Mireia Sole; Joan Blanco; Debora Gil; Oliver Valero; Alvaro Pascual; B. Cardenas; G. Fonseka; E. Anton; Richard Frodsham; Francesca Vidal; Zaida Sarrate edit  url
openurl 
  Title Chromosomal positioning in spermatogenic cells is influenced by chromosomal factors associated with gene activity, bouquet formation, and meiotic sex-chromosome inactivation Type Journal Article
  Year (down) 2021 Publication Chromosoma Abbreviated Journal  
  Volume 130 Issue Pages 163-175  
  Keywords  
  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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  Language Summary Language Original Title  
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  Area Expedition Conference  
  Notes IAM; 600.145 Approved no  
  Call Number Admin @ si @ SBG2021 Serial 3592  
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Author Sonia Baeza; R.Domingo; M.Salcedo; G.Moragas; J.Deportos; I.Garcia Olive; Carles Sanchez; Debora Gil; Antoni Rosell edit  url
openurl 
  Title Artificial Intelligence to Optimize Pulmonary Embolism Diagnosis During Covid-19 Pandemic by Perfusion SPECT/CT, a Pilot Study Type Journal Article
  Year (down) 2021 Publication American Journal of Respiratory and Critical Care Medicine Abbreviated Journal  
  Volume Issue Pages  
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  Abstract  
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  Notes IAM; 600.145 Approved no  
  Call Number Admin @ si @ BDS2021 Serial 3591  
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