Quantification of Nematic Cell Polarity in Three-dimensional Tissues

How epithelial cells coordinate their polarity to form functional tissues is an open question in cell biology. Here, we characterize a unique type of polarity found in liver tissue, nematic cell polarity, which is different from vectorial cell polarity in simple, sheet-like epithelia. We propose a conceptual and algorithmic framework to characterize complex patterns of polarity proteins on the surface of a cell in terms of a multipole expansion. To rigorously quantify previously observed tissue-level patterns of nematic cell polarity (Morales-Navarette et al., eLife 8:e44860, 2019), we introduce the concept of co-orientational order parameters, which generalize the known biaxial order parameters of the theory of liquid crystals. Applying these concepts to three-dimensional reconstructions of single cells from high-resolution imaging data of mouse liver tissue, we show that the axes of nematic cell polarity of hepatocytes exhibit local coordination and are aligned with the biaxially anisotropic sinusoidal network for blood transport. Our study characterizes liver tissue as a biological example of a biaxial liquid crystal. The general methodology developed here could be applied to other tissues or in-vitro organoids.Comment: 27 pages, 9 color figure

Relación entre la altura del salto vertical y la capacidad de recuperación posterior a un protocolo de esfuerzo y recuperación física

Tesis (Profesor de Educación Física para la Enseñanza Básica, Licenciado en Educación)Objetivo: El objetivo de este estudio es determinar si existe alguna correlación significativa entre las variables altura del salto contramovimiento con brazos (Abalakov) y el porcentaje de pérdida de este. Metodología: Se apeló a interpretaciones de datos, que involucran principalmente la altura de diversos saltos y el nivel de recuperación presentado, al correlacionar estas dos variables se valoró el grado de relación. Se midió a la población la cual comprendió un total de 154 jugadores de basquetbol pertenecientes al club Universidad Católica, de los cuales la muestra estuvo compuesta por un total de 58 jugadores de las categorías sub-13, sub-15 y sub-17 respectivamente. Por lo tanto, nuestra muestra corresponde a una no probabilística o dirigida. Los datos presentados fueron procesados a través del software IBM SPSS y Excel, con la finalidad de determinar la existencia o no de relaciones, comparaciones y descripciones entre las variables de la investigación. Resultados: Se obtuvo una correlación negativa débil, por lo que se acepta la hipótesis nula de trabajo, indicando que no hay una correlación en la altura del salto vertical y la recuperación posterior a un estímulo fatigante y un minuto en la posición decúbito supino con pies en altura

Uncovering developmental time and tempo using deep learning

During animal development, embryos undergo complex morphological changes over time. Differences in developmental tempo between species are emerging as principal drivers of evolutionary novelty, but accurate description of these processes is very challenging. To address this challenge, we present here an automated and unbiased deep learning approach to analyze the similarity between embryos of different timepoints. Calculation of similarities across stages resulted in complex phenotypic fingerprints, which carry characteristic information about developmental time and tempo. Using this approach, we were able to accurately stage embryos, quantitatively determine temperature-dependent developmental tempo, detect naturally occurring and induced changes in the developmental progression of individual embryos, and derive staging atlases for several species de novo in an unsupervised manner. Our approach allows us to quantify developmental time and tempo objectively and provides a standardized way to analyze early embryogenesis.publishe

EmbryoNet : using deep learning to link embryonic phenotypes to signaling pathways

Evolutionarily conserved signaling pathways are essential for early embryogenesis, and reducing or abolishing their activity leads to characteristic developmental defects. Classification of phenotypic defects can identify the underlying signaling mechanisms, but this requires expert knowledge and the classification schemes have not been standardized. Here we use a machine learning approach for automated phenotyping to train a deep convolutional neural network, EmbryoNet, to accurately identify zebrafish signaling mutants in an unbiased manner. Combined with a model of time-dependent developmental trajectories, this approach identifies and classifies with high precision phenotypic defects caused by loss of function of the seven major signaling pathways relevant for vertebrate development. Our classification algorithms have wide applications in developmental biology and robustly identify signaling defects in evolutionarily distant species. Furthermore, using automated phenotyping in high-throughput drug screens, we show that EmbryoNet can resolve the mechanism of action of pharmaceutical substances. As part of this work, we freely provide more than 2 million images that were used to train and test EmbryoNet.publishe

Data from: A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture

A prerequisite for the systems biology analysis of tissues is an accurate digital three-dimensional reconstruction of tissue structure based on images of markers covering multiple scales. Here, we designed a flexible pipeline for the multi-scale reconstruction and quantitative morphological analysis of tissue architecture from microscopy images. Our pipeline includes newly developed algorithms that address specific challenges of thick dense tissue reconstruction. Our implementation allows for a flexible workflow, scalable to high-throughput analysis and applicable to various mammalian tissues. We applied it to the analysis of liver tissue and extracted quantitative parameters of sinusoids, bile canaliculi and cell shapes, recognizing different liver cell types with high accuracy. Using our platform, we uncovered an unexpected zonation pattern of hepatocytes with different size, nuclei and DNA content, thus revealing new features of liver tissue organization. The pipeline also proved effective to analyse lung and kidney tissue, demonstrating its generality and robustness

Phenotypic characterization of liver tissue heterogeneity through a next-generation 3D single-cell atlas

Abstract Three-dimensional (3D) geometrical models are potent tools for quantifying complex tissue features and exploring structure–function relationships. However, these models are generally incomplete due to experimental limitations in acquiring multiple (> 4) fluorescent channels in thick tissue sections simultaneously. Indeed, predictive geometrical and functional models of the liver have been restricted to few tissue and cellular components, excluding important cellular populations such as hepatic stellate cells (HSCs) and Kupffer cells (KCs). Here, we combined deep-tissue immunostaining, multiphoton microscopy, deep-learning techniques, and 3D image processing to computationally expand the number of simultaneously reconstructed tissue structures. We then generated a spatial single-cell atlas of hepatic architecture (Hep3D), including all main tissue and cellular components at different stages of post-natal development in mice. We used Hep3D to quantitatively study 1) hepatic morphodynamics from early post-natal development to adulthood, and 2) the effect on the liver's overall structure when changing the hepatic environment after removing KCs. In addition to a complete description of bile canaliculi and sinusoidal network remodeling, our analysis uncovered unexpected spatiotemporal patterns of non-parenchymal cells and hepatocytes differing in size, number of nuclei, and DNA content. Surprisingly, we found that the specific depletion of KCs results in morphological changes in hepatocytes and HSCs. These findings reveal novel characteristics of liver heterogeneity and have important implications for both the structural organization of liver tissue and its function. Our next-gen 3D single-cell atlas is a powerful tool to understand liver tissue architecture, opening up avenues for in-depth investigations into tissue structure across both normal and pathological conditions

3D ground truth models of liver tissue

3D ‘ground truth’ images of idealized models of liver tissue ( 0.3 um x 0.3 um x 0.3u m per voxel

3D simulated microscopy images of liver tissue

3D simulated microscopy images of liver tissue models with 10:1, 4:1 and 2:1 signal-to-noise ratios

Scripts to generate 3D models and simulated images

MotionTracking scripts to generate 3D ‘ground truth’ voxelated models and simulated microscopy images of mouse liver tissue. A test example is included

Confluences: traditions, music and contexts

Las prácticas artísticas en nuestro país y los movimientos y ciclos del mercado trasnacional, han venido determinado algunas formas y modos de ejercer el oficio de la música, sea desde las propuestas individuales o grupales así como desde lo particular y global que éstas puedan ser. La reincidencia y los motores de transformación de esta praxis musical se ha ido ejerciendo como una mezcla entre los procesos interpretativos y compositivos que integran la manera como las músicas populares regionales, conocidas como de ´tradición oral´, se hacen en su cotidianidad y los lenguajes urbanos que revelan múltiples modos de estructurar propuestas sonoras donde lo escrito, lo oído y lo interpretativo se conjugan a manera de un sincretismo performativo.Artistic practices in our country and the movements and cycles of the transnational market have determined some ways and means of exercising the trade of music, be it from individual or group proposals as well as from how particular and global they may be. The recidivism and transformation engines of this musical praxis has been exercised as a mixture between the interpretive and compositional processes that integrate the way in which regional popular music, known as "oral tradition", is made in its daily life and the languages urban that reveal multiple ways of structuring sound proposals where the written, the heard and the interpretative are conjugated in the manner of a performative syncretism