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Carles Sanchez, Jorge Bernal, F. Javier Sanchez, Antoni Rosell, Marta Diez-Ferrer, & Debora Gil. (2015). "Towards On-line Quantification of Tracheal Stenosis from Videobronchoscopy " . International Journal of Computer Assisted Radiology and Surgery, 10(6), 935–945.
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Mireia Sole, Joan Blanco, Debora Gil, Oliver Valero, B. Cardenas, G. Fonseka, et al. (2022). "Time to match; when do homologous chromosomes become closer? " Chromosoma, .
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.
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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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Mireia Sole, Joan Blanco, Debora Gil, G. Fonseka, Richard Frodsham, Oliver Valero, et al. (2017)." Análisis 3d de la territorialidad cromosómica en células espermatogénicas: explorando la infertilidad desde un nuevo prisma" . Revista Asociación para el Estudio de la Biología de la Reproducción, 22(2), 105.
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Mireia Sole, Joan Blanco, Debora Gil, G. Fonseka, Richard Frodsham, Francesca Vidal, et al. (2017). "Noves perspectives en l estudi de la territorialitat cromosomica de cel·lules germinals masculines: estudis tridimensionals " . Biologia de la Reproduccio, 15, 73–78.
Abstract: In somatic cells, chromosomes occupy specific nuclear regions called chromosome territories which are involved in the
maintenance and regulation of the genome. Preliminary data in male germ cells also suggest the importance of chromosome
territoriality in cell functionality. Nevertheless, the specific characteristics of testicular tissue (presence of different
cell types with different morphological characteristics, in different stages of development and with different ploidy)
makes difficult to achieve conclusive results. In this study we have developed a methodology to approach the threedimensional
study of all chromosome territories in male germ cells from C57BL/6J mice (Mus musculus). The method
includes the following steps: i) Optimized cell fixation to obtain an optimal preservation of the three-dimensionality cell
morphology, ii) Chromosome identification by FISH (Chromoprobe Multiprobe® OctoChrome™ Murine System; Cytocell)
and confocal microscopy (TCS-SP5, Leica Microsystems), iii) Cell type identification by immunofluorescence
iv) Image analysis using Matlab scripts, v) Numerical data extraction related to chromosome features, chromosome
radial position and chromosome relative position. This methodology allows the unequivocally identification and the
analysis of the chromosome territories of all spermatogenic stages. Results will provide information about the features
that determine chromosomal position, preferred associations between chromosomes, and the relationship between chromosome
positioning and genome regulation.
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Mireia Sole, Joan Blanco, Debora Gil, G. Fonseka, Richard Frodsham, Oliver Valero, et al. (2017)." Unraveling the enigmas of chromosome territoriality during spermatogenesis" In IX Jornada del Departament de Biologia Cel•lular, Fisiologia i Immunologia.
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Mireia Sole, Joan Blanco, Debora Gil, Oliver Valero, G. Fonseka, M. Lawrie, et al. (2017). "Chromosome Territories in Mice Spermatogenesis: A new three-dimensional methodology of study " In 11th European CytoGenesis Conference.
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Carles Sanchez, Jorge Bernal, Debora Gil, & F. Javier Sanchez. (2013). "On-line lumen centre detection in gastrointestinal and respiratory endoscopy " In Klaus Miguel Angel and Drechsler Stefan and González Ballester Raj and Wesarg Cristina and Shekhar Marius George and Oyarzun Laura M. and L. Erdt (Ed.), Second International Workshop Clinical Image-Based Procedures (Vol. 8361, pp. 31–38). Springer International Publishing.
Abstract: We present in this paper a novel lumen centre detection for gastrointestinal and respiratory endoscopic images. The proposed method is based on the appearance and geometry of the lumen, which we defined as the darkest image region which centre is a hub of image gradients. Experimental results validated on the first public annotated gastro-respiratory database prove the reliability of the method for a wide range of images (with precision over 95 %).
Keywords: Lumen centre detection; Bronchoscopy; Colonoscopy
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Carles Sanchez. (2014)." Tracheal Structure Characterization using Geometric and Appearance Models for Efficient Assessment of Stenosis in Videobronchoscopy" (F. Javier Sanchez, Debora Gil, & Jorge Bernal, Eds.). Ph.D. thesis, Ediciones Graficas Rey, .
Abstract: Recent advances in endoscopic devices have increased their use for minimal invasive diagnostic and intervention procedures. Among all endoscopic modalities, bronchoscopy is one of the most frequent with around 261 millions of procedures per year. Although the use of bronchoscopy is spread among clinical facilities it presents some drawbacks, being the visual inspection for the assessment of anatomical measurements the most prevalent of them. In
particular, inaccuracies in the estimation of the degree of stenosis (the percentage of obstructed airway) decreases its diagnostic yield and might lead to erroneous treatments. An objective computation of tracheal stenosis in bronchoscopy videos would constitute a breakthrough for this non-invasive technique and a reduction in treatment cost.
This thesis settles the first steps towards on-line reliable extraction of anatomical information from videobronchoscopy for computation of objective measures. In particular, we focus on the computation of the degree of stenosis, which is obtained by comparing the area delimited by a healthy tracheal ring and the stenosed lumen. Reliable extraction of airway structures in interventional videobronchoscopy is a challenging task. This is mainly due to the large variety of acquisition conditions (positions and illumination), devices (different digitalizations) and in videos acquired at the operating room the unpredicted presence of surgical devices (such as probe ends). This thesis contributes to on-line stenosis assessment in several ways. We
propose a parametric strategy for the extraction of lumen and tracheal rings regions based on the characterization of their geometry and appearance that guide a deformable model. The geometric and appearance characterization is based on a physical model describing the way bronchoscopy images are obtained and includes local and global descriptions. In order to ensure a systematic applicability we present a statistical framework to select the optimal
parameters of our method. Experiments perform on the first public annotated database, show that the performance of our method is comparable to the one provided by clinicians and its computation time allows for a on-line implementation in the operating room.
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Esmitt Ramirez, Carles Sanchez, & Debora Gil. (2019). "Localizing Pulmonary Lesions Using Fuzzy Deep Learning " In 21st International Symposium on Symbolic and Numeric Algorithms for Scientific Computing (pp. 290–294).
Abstract: The usage of medical images is part of the clinical daily in several healthcare centers around the world. Particularly, Computer Tomography (CT) images are an important key in the early detection of suspicious lung lesions. The CT image exploration allows the detection of lung lesions before any invasive procedure (e.g. bronchoscopy, biopsy). The effective localization of lesions is performed using different image processing and computer vision techniques. Lately, the usage of deep learning models into medical imaging from detection to prediction shown that is a powerful tool for Computer-aided software. In this paper, we present an approach to localize pulmonary lung lesion using fuzzy deep learning. Our approach uses a simple convolutional neural network based using the LIDC-IDRI dataset. Each image is divided into patches associated a probability vector (fuzzy) according their belonging to anatomical structures on a CT. We showcase our approach as part of a full CAD system to exploration, planning, guiding and detection of pulmonary lesions.
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