DFFOCT As a Tool to Detect Cellular Activity

The discrete element method is well suited for simulating the cracks and subsequent large displacements of catastrophic landslides or rock avalanches, and is therefore a useful tool for analysing their complicated dynamic processes and hypermobility mechanisms. In this study, particle flow code was used to investigate the dynamic processes and hypermobility mechanisms of the Wenjiagou rock avalanche triggered by the 2008 Wenchuan earthquake. Characterization of the avalanche dynamics was achieved using a model comprising four stages: failure rupture, projectile motion, granular debris flow, and debris mass accumulation. The results show that collision on the valley floor was the main factor causing the fragmentation of the Wenjiagou rock avalanche. The upper and front edge of the landslide body were the most likely to move over a long distance. The results also show that friction was the main source of energy dissipation during the entirety of the avalanche movement. The high gravitational potential energy of the avalanche was the basis of the high mobility. In addition, because of their effects on energy dissipation, the low basal friction coefficient, favourable block movement, and topographical conditions played key roles in the rapid, long-runout Wenjiagou avalanche process.

Embodying complex multi-user agendas in rehabilitation trials through dynamic visualisations and co-creation processes

Brief description of methods of parallelizing of dynamic 3D scenes visualization process is given. Performance analysis of experimental implementation of such system on the basis of multicomputer network was done. Theoretical estimation of performance of the system versus network bandwidth, image size, and graphics performance are done. The dependences obtained are confirmed experimentally.

Microtubules, polymers of α, β-tubulin heterodimers, are organized into multi-microtubule arrays for diverse cellular functions. The dynamic properties of microtubule arrays govern their structural and functional properties. While numerous insights into the biophysical mechanisms underlying microtubule organization have been gleaned from in vitro reconstitution studies, the assays are largely restricted to visualization of single or pairs of microtubules. Thus, the dynamic processes underlying the remodeling of multi-microtubule arrays remain poorly understood. Recent work shows that Atomic Force Microscopy (AFM) enables the visualization of nanoscale dynamics within multi-microtubule 2D arrays. In this assay, electrostatic interactions permit the non-specific adsorption of microtubule arrays to mica. AFM imaging in tapping mode, a gentle method of imaging, allows the visualization of microtubules and protofilaments without sample damage. The height information captured by AFM imaging enables the tracking of structural changes in microtubules and protofilaments within multi-microtubule arrays over time. The experimental data from the method described here reveal previously unseen modes of nanoscale dynamics in microtubule bundles formed by the microtubule-crosslinking protein PRC1 in the presence of the depolymerase MCAK. The observations demonstrate the potential of AFM imaging in transforming our understanding of the fundamental cellular process by which multi-microtubule arrays are dynamically assembled and disassembled. © 2023 Wiley Periodicals LLC. Basic Protocol: Sample preparation and real-time visualization of microtubule arrays by atomic force microscopy Alternate Protocol: Protocol for coating surface with poly-L-lysine and immobilizing microtubules.

This paper proposes a dynamic analytical processing (DAP) visualization tool based on the Bubble-Wall Plot. It can be handily used to develop visual warning systems for visualizing the dynamic analytical processes of hazard data. Comparative analysis and case study methods are used in this research. Based on a literature review of Q1 publications since 2017, 23 types of data visualization approaches/tools are identified, including seven anomaly data visualization tools. This study presents three significant findings by comparing existing data visualization approaches. The primary finding is that no single visualization tool can fully satisfy industry requirements. This finding motivates academics to develop new DAP visualization tools. The second finding is that there are different views of Line Charts and various perspectives on Scatter Plots. The other one is that different researchers may perceive an existing data visualization tool differently, such as arguments between Scatter Plots and Line Charts and diverse opinions about Parallel Coordinate Plots and Scatter Plots. Users' awareness rises when they choose data visualization tools that satisfy their requirements. By conducting a comparative analysis based on five categories (Style, Value, Change, Correlation, and Others) with 26 subcategories of metric features, results show that this new tool can effectively solve the limitations of existing visualization tools as it appears to have three remarkable characteristics: the simplest cartographic tool, the most straightforward visual result, and the most intuitive tool. Furthermore, this paper illustrates how the Bubble-Wall Plot can be effectively applied to develop a warning system for presenting dynamic analytical processes of hazard data in the coal mine. Lastly, this paper provides two recommendations, one implication, six research limitations, and eleven further study topics.

The dynamic behavior of the polypeptide backbone of a recombinant antidigoxin antibody VL domain has been characterized by measurements of 15NT1 and T2 relaxation times, 1H-15N NOE values, and 1H-2H exchange rates. These data were acquired with 2D inverse detected heteronuclear 1H-15N NMR methods. The relaxation data are interpreted in terms of model free spectral density functions and exchange contributions to transverse relaxation rates R2 (= 1/T2). All characterized residues display low-amplitude picosecond time-scale librational motions. Fifteen residues undergo conformational changes on the nanosecond timescale, and 24 residues have significant R2 exchange contributions, which reflect motions on the microsecond to millisecond time-scale. For several residues, microsecond to millisecond motions of nearby aromatic rings are postulated to account for some or all of their observed R2 exchange contributions. The measured 1H-2H exchange rates are correlated with hydrogen bonding patterns and distances from the solvent accessible surface. The degree of local flexibility indicated by the NMR measurements is compared to crystallographic B-factors derived from X-ray analyses of the native Fab and the Fab/digoxin complex. In general, both the NMR and X-ray data indicate enhanced flexibility in the turns, hypervariable loops, and portions of beta-strands A, B, and G. However, on a residue-specific level, correlations among the various NMR data, and between the NMR and X-ray data, are often absent. This is attributed to the different dynamic processes and environments that influence the various observables. The combined data indicate that certain regions of the VL domain, including the three hypervariable loops, undergo dynamic changes upon VL:VH association and/or complexation with digoxin. Overall, the 26-10 VL domain exhibits relatively low flexibility on the ps-ns timescale. The possible functional consequences of this result are considered.

NMR characterization of structure and moisture sorption dynamics of damaged starch granules

The study of complex networks, especially temporal networks, increased over the last years. Understanding patterns, trends, and anomalies in these networks, as well as simulating and analyzing dynamic processes (e.g., infection spread dynamics in social networks), are not trivial tasks. Information Visualization techniques offer significant potential to assist the user in these analyses. This paper presents an extended version of Dynamic Network Visualization (DyNetVis), a freely available and open-source interactive software to perform visual analysis of temporal networks. It provides four visualization techniques, structural, temporal, matrix, and community layouts, and a number of state-of-the-art methods to interact with each of these layouts. DyNetVis also implements dynamic processes, including standard epidemic models. It is a computational tool to study and explore networks in diverse domains.

Tomography is a non-invasive, non-intrusive imaging technique allowing the visualization of phase dynamics in industrial and biological processes. This article reviews progress in Electrical Capacitance Volume Tomography (ECVT). ECVT is a direct 3D visualizing technique, unlike three-dimensional imaging, which is based on stacking 2D images to obtain an interpolated 3D image. ECVT has recently matured for real time, non-invasive 3-D monitoring of processes involving materials with strong contrast in dielectric permittivity. In this article, ECVT sensor design, optimization and performance of various sensors seen in literature are summarized. Qualitative Analysis of ECVT image reconstruction techniques has also been presented.

Characterization of fungal community and dynamics during the traditional brewing of Wuyi Hong Qu glutinous rice wine by means of multiple culture-independent methods

We investigate the relative merit of different linear and nonlinear synchronization measures for a characterization of the spatio-temporal dynamics of the epileptic process. Analyzing long-lasting multichannel electroencephalographic recordings from more than 20 epilepsy patients we show that all measures are able to identify brain regions of pathological synchronization associated with epilepsy, even during the seizure-free interval, and are able to detect a long-lasting transitional preseizure state. These findings render synchronization measures attractive for future prospective studies on seizure prediction.

We made fluorescence multi‐scale imager including 1P, 2P, light‐sheet, microscope, and on‐chip sensors for visualization of XYZT single cell dynamics in vivo. We integrated five microscope for systematic evaluation of living animals. First visualization system is super‐resolution imaging based on non‐linear optics, with X‐ (resonance), Y‐(galvano), and Z‐(piezo) axis scanning. Real‐time, multi‐color XYZT multi‐photon imaging enabled us to visualize single blood cell behavior in vessels and stroma. Spatial and time resolution was improved by pattern illumination. We analyzed thrombus formation, and inflammatory responses under microscope. We developed thrombus formation animal models, and elucidated cellular mechanisms of cardiovascular diseases. We directly manipulated cells by photo‐chemical reactions, and two photon lasers to induce and observe thrombotic reactions. Using this system, we elucidated contribution of endothelial injuries to thrombus formation. Second, high‐resolutions and broad‐imaging field was simultaneously enabled using 8K CMOS technologies, and 1P spinning disk confocal. We visualized whole organs and single cell in one image, and revealed complicated cell‐cell interactions networks in single view. 8K, 60fps, and multi‐color imaging visualized single platelet dynamics and tissue structural changes in single image. Third, we performed light‐sheet imaging for living mice, and enabled high‐speed observation of living animals. Fourth, macro imaging system for awake mice, pigs and humans was also developed, and free behavior monitoring revealed the tight association between metabolism and vascular reactions during daily life. Bioluminescent and fluorescent imaging from body surface using CMOS camera, image intensifier, and macro‐lens enabled us to visualize cellular dynamics without anesthesia. Last, wearable, implantable, and minimized devices for non‐invasive recording were also developed using lens‐less and on‐chip technologies. We utilized SCMOS, micro‐lens array, and LED illumination technologies. In sum, we developed multi‐scale imaging system which can evaluate cellular networks dysregulations in diseased conditions.

One of the critical microstructures in directional solidification of alloys is the cellular/dendritic pattern that governs the properties and reliability of the solidified material. Our quantitative understanding of the solid–liquid interface pattern has come mainly from experiments in thin samples where the microstructure selection is shown to occur during the dynamical growth process. A more realistic configuration is to examine the evolution of microstructure in three-dimensions, which is not possible terrestrially since convection effects dominate in bulk samples and prevent precise characterization of microstructure dynamics. Recently, experiments under low gravity conditions have been carried out jointly by NASA and CNES in the model transparent system succinonitrile–camphor on board the International Space Station using the Directional Solidification Insert in the DECLIC facility. After a brief description of the experimental setup and methods, the first results on dynamics of interface pattern formation obtained in microgravity will be presented and the information extracted from their quantitative analysis will be discussed.

Optimizing and benchmarking data reduction methods for dynamic or spatial visualization and interpretation (DSVI) face challenges due to many factors, including data complexity, lack of ground truth, time-dependent metrics, dimensionality bias and different visual mappings of the same data. Current studies often focus on independent static visualization or interpretability metrics that require ground truth. To overcome this limitation, we propose the MIBCOVIS framework, a comprehensive and interpretable benchmarking and computational approach. MIBCOVIS enhances the visualization and interpretability of high-dimensional data without relying on ground truth by integrating five robust metrics, including a novel time-ordered Markov-based structural metric, into a semi-supervised hierarchical Bayesian model. The framework assesses method accuracy and considers interaction effects among metric features. We apply MIBCOVIS using linear and nonlinear dimensionality reduction methods to evaluate optimal DSVI for four distinct dynamic and spatial biological processes captured by three single-cell data modalities: CyTOF, scRNA-seq and CODEX. These data vary in complexity based on feature dimensionality, unknown cell types and dynamic or spatial differences. Unlike traditional single-summary score approaches, MIBCOVIS compares accuracy distributions across methods. Our findings underscore the joint evaluation of visualization and interpretability, rather than relying on separate metrics. We reveal that prioritizing average performance can obscure method feature performance. Additionally, we explore the impact of data complexity on visualization and interpretability. Specifically, we provide optimal parameters and features and recommend methods, like the optimized variational contractive autoencoder, for targeted DSVI for various data complexities. MIBCOVIS shows promise for evaluating dynamic single-cell atlases and spatiotemporal data reduction models.

Abstract. Landslides exhibit themselves in different mass movement processes and are considered among the most complex natural hazards occurring on the earth surface. Making landslide database available online via WWW (World Wide Web) promotes the spreading and reaching out of the landslide information to all the stakeholders. The aim of this research is to present a comprehensive database for generating landslide hazard scenario with the help of available historic records of landslides and geo-environmental factors and make them available over the Web using geospatial Free & Open Source Software (FOSS). FOSS reduces the cost of the project drastically as proprietary software's are very costly. Landslide data generated for the period 1982 to 2009 were compiled along the national highway road corridor in Indian Himalayas. All the geo-environmental datasets along with the landslide susceptibility map were served through WEBGIS client interface. Open source University of Minnesota (UMN) mapserver was used as GIS server software for developing web enabled landslide geospatial database. PHP/Mapscript server-side application serve as a front-end application and PostgreSQL with PostGIS extension serve as a backend application for the web enabled landslide spatio-temporal databases. This dynamic virtual visualization process through a web platform brings an insight into the understanding of the landslides and the resulting damage closer to the affected people and user community. The landslide susceptibility dataset is also made available as an Open Geospatial Consortium (OGC) Web Feature Service (WFS) which can be accessed through any OGC compliant open source or proprietary GIS Software.