A convolutional autoencoder approach for mining features in cellular electron cryo-tomograms and weakly supervised coarse segmentation

Cellular electron cryo-tomography enables the 3D visualization of cellular organization in the near-native state and at submolecular resolution. However, the contents of cellular tomograms are often complex, making it difficult to automatically isolate different in situ cellular components. In this paper, we propose a convolutional autoencoder-based unsupervised approach to provide a coarse grouping of 3D small subvolumes extracted from tomograms. We demonstrate that the autoencoder can be used for efficient and coarse characterization of features of macromolecular complexes and surfaces, such as membranes. In addition, the autoencoder can be used to detect non-cellular features related to sample preparation and data collection, such as carbon edges from the grid and tomogram boundaries. The autoencoder is also able to detect patterns that may indicate spatial interactions between cellular components. Furthermore, we demonstrate that our autoencoder can be used for weakly supervised semantic segmentation of cellular components, requiring a very small amount of manual annotation.Comment: Accepted by Journal of Structural Biolog

High-resolution truncated plurigaussian simulations for the characterization of heterogeneous formations

Integrating geological concepts, such as relative positions and proportions of the different lithofacies, is of highest importance in order to render realistic geological patterns. The truncated plurigaussian simulation method provides a way of using both local and conceptual geological information to infer the distributions of the facies and then those of hydraulic parameters. The method (Le Loc'h and Galli 1994) is based on the idea of truncating at least two underlying multi-Gaussian simulations in order to create maps of categorical variable. In this manuscript we show how this technique can be used to assess contaminant migration in highly heterogeneous media. We illustrate its application on the biggest contaminated site of Switzerland. It consists of a contaminant plume located in the lower fresh water Molasse on the western Swiss Plateau. The highly heterogeneous character of this formation calls for efficient stochastic methods in order to characterize transport processes.Comment: 12 pages, 9 figure

Review of the Synergies Between Computational Modeling and Experimental Characterization of Materials Across Length Scales

With the increasing interplay between experimental and computational approaches at multiple length scales, new research directions are emerging in materials science and computational mechanics. Such cooperative interactions find many applications in the development, characterization and design of complex material systems. This manuscript provides a broad and comprehensive overview of recent trends where predictive modeling capabilities are developed in conjunction with experiments and advanced characterization to gain a greater insight into structure-properties relationships and study various physical phenomena and mechanisms. The focus of this review is on the intersections of multiscale materials experiments and modeling relevant to the materials mechanics community. After a general discussion on the perspective from various communities, the article focuses on the latest experimental and theoretical opportunities. Emphasis is given to the role of experiments in multiscale models, including insights into how computations can be used as discovery tools for materials engineering, rather than to "simply" support experimental work. This is illustrated by examples from several application areas on structural materials. This manuscript ends with a discussion on some problems and open scientific questions that are being explored in order to advance this relatively new field of research.Comment: 25 pages, 11 figures, review article accepted for publication in J. Mater. Sc

Pathways to clinical CLARITY: volumetric analysis of irregular, soft, and heterogeneous tissues in development and disease

AbstractThree-dimensional tissue-structural relationships are not well captured by typical thin-section histology, posing challenges for the study of tissue physiology and pathology. Moreover, while recent progress has been made with intact methods for clearing, labeling, and imaging whole organs such as the mature brain, these approaches are generally unsuitable for soft, irregular, and heterogeneous tissues that account for the vast majority of clinical samples and biopsies. Here we develop a biphasic hydrogel methodology, which along with automated analysis, provides for high-throughput quantitative volumetric interrogation of spatially-irregular and friable tissue structures. We validate and apply this approach in the examination of a variety of developing and diseased tissues, with specific focus on the dynamics of normal and pathological pancreatic innervation and development, including in clinical samples. Quantitative advantages of the intact-tissue approach were demonstrated compared to conventional thin-section histology, pointing to broad applications in both research and clinical settings.</jats:p

Characterization of nuclear polyadenylated RNA-binding proteins in Saccharomyces cerevisiae.

To study the functions of heterogeneous nuclear ribonucleoproteins (hnRNPs), we have characterized nuclear polyadenylated RNA-binding (Nab) proteins from Saccharomyces cerevisiae. Nab1p, Nab2p, and Nab3p were isolated by a method which uses UV light to cross-link proteins directly bound to poly(A)+ RNA in vivo. We have previously characterized Nab2p, and demonstrated that it is structurally related to human hnRNPs. Here we report that Nab1p is identical to the Np13p/Nop3p protein recently implicated in both nucleocytoplasmic protein shuttling and pre-rRNA processing, and characterize a new nuclear polyadenylated RNA-binding protein, Nab3p. The intranuclear distributions of the Nab proteins were analyzed by three-dimensional immunofluorescence optical microscopy. All three Nab proteins are predominantly localized within the nucleoplasm in a pattern similar to the distribution of hnRNPs in human cells. The NAB3 gene is essential for cell viability and encodes an acidic ribonucleoprotein. Loss of Nab3p by growth of a GAL::nab3 mutant strain in glucose results in a decrease in the amount of mature ACT1, CYH2, and TPI1 mRNAs, a concomitant accumulation of unspliced ACT1 pre-mRNA, and an increase in the ratio of unspliced CYH2 pre-mRNA to mRNA. These results suggest that the Nab proteins may be required for packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing

Quantitative characterization of pore structure of several biochars with 3D imaging

Pore space characteristics of biochars may vary depending on the used raw material and processing technology. Pore structure has significant effects on the water retention properties of biochar amended soils. In this work, several biochars were characterized with three-dimensional imaging and image analysis. X-ray computed microtomography was used to image biochars at resolution of 1.14 $\mu$m and the obtained images were analysed for porosity, pore-size distribution, specific surface area and structural anisotropy. In addition, random walk simulations were used to relate structural anisotropy to diffusive transport. Image analysis showed that considerable part of the biochar volume consist of pores in size range relevant to hydrological processes and storage of plant available water. Porosity and pore-size distribution were found to depend on the biochar type and the structural anisotopy analysis showed that used raw material considerably affects the pore characteristics at micrometre scale. Therefore attention should be paid to raw material selection and quality in applications requiring optimized pore structure.Comment: 16 pages, 4 figures. The final publication is available at Springer via http://dx.doi.org/10.1007/s11356-017-8823-

Imaging of a fluid injection process using geophysical data - A didactic example

In many subsurface industrial applications, fluids are injected into or withdrawn from a geologic formation. It is of practical interest to quantify precisely where, when, and by how much the injected fluid alters the state of the subsurface. Routine geophysical monitoring of such processes attempts to image the way that geophysical properties, such as seismic velocities or electrical conductivity, change through time and space and to then make qualitative inferences as to where the injected fluid has migrated. The more rigorous formulation of the time-lapse geophysical inverse problem forecasts how the subsurface evolves during the course of a fluid-injection application. Using time-lapse geophysical signals as the data to be matched, the model unknowns to be estimated are the multiphysics forward-modeling parameters controlling the fluid-injection process. Properly reproducing the geophysical signature of the flow process, subsequent simulations can predict the fluid migration and alteration in the subsurface. The dynamic nature of fluid-injection processes renders imaging problems more complex than conventional geophysical imaging for static targets. This work intents to clarify the related hydrogeophysical parameter estimation concepts