ScaleTrotter: Illustrative Visual Travels Across Negative Scales

We present ScaleTrotter, a conceptual framework for an interactive, multi-scale visualization of biological mesoscale data and, specifically, genome data. ScaleTrotter allows viewers to smoothly transition from the nucleus of a cell to the atomistic composition of the DNA, while bridging several orders of magnitude in scale. The challenges in creating an interactive visualization of genome data are fundamentally different in several ways from those in other domains like astronomy that require a multi-scale representation as well. First, genome data has intertwined scale levels---the DNA is an extremely long, connected molecule that manifests itself at all scale levels. Second, elements of the DNA do not disappear as one zooms out---instead the scale levels at which they are observed group these elements differently. Third, we have detailed information and thus geometry for the entire dataset and for all scale levels, posing a challenge for interactive visual exploration. Finally, the conceptual scale levels for genome data are close in scale space, requiring us to find ways to visually embed a smaller scale into a coarser one. We address these challenges by creating a new multi-scale visualization concept. We use a scale-dependent camera model that controls the visual embedding of the scales into their respective parents, the rendering of a subset of the scale hierarchy, and the location, size, and scope of the view. In traversing the scales, ScaleTrotter is roaming between 2D and 3D visual representations that are depicted in integrated visuals. We discuss, specifically, how this form of multi-scale visualization follows from the specific characteristics of the genome data and describe its implementation. Finally, we discuss the implications of our work to the general illustrative depiction of multi-scale data

Radical-induced hetero-nuclear mixing and low-field 13^{13}C relaxation in solid pyruvic acid

Radicals serve as a source of polarization in dynamic nuclear polarization, but may also act as polarization sink, in particular at low field. Additionally, if the couplings between the electron spins and different nuclear reservoirs are stronger than any of the reservoirs’ couplings to the lattice, radicals can mediate hetero-nuclear polarization transfer. Here, we report radical-enhanced $^{13}$C relaxation in pyruvic acid doped with trityl. Up to 40 K, we find a linear carbon $T_{1}$ field dependence between 5 mT and 2 T. We model the dependence quantitatively, and find that the presence of trityl accelerates direct hetero-nuclear polarization transfer at low fields, while at higher fields $^{13}$C relaxation is diffusion limited. Measurements of hetero-nuclear polarization transfer up to 600 mT confirm the predicted radical-mediated proton–carbon mixing

Radical-Induced Low-Field 1H Relaxation in Solid Pyruvic Acid Doped with Trityl-OX063

In dynamic nuclear polarization (DNP), radicals such as trityl provide a source for high nuclear spin polarization. Conversely, during the low-field transfer of hyperpolarized solids, the radicals’ dipolar or Non-Zeeman reservoir may act as a powerful nuclear polarization sink. Here, we report the low-temperature proton spin relaxation in pyruvic acid doped with trityl, for fields from 5 mT to 2 T. We estimate the heat capacity of the radical Non-Zeeman reservoir experimentally and show that a recent formalism by Wenckebach yields a parameter-free, yet quantitative model for the entire field range

Case report: Susac syndrome—two ends of the spectrum, single center case reports and review of the literature

Susac syndrome is a rare and enigmatic complex neurological disorder primarily affecting small blood vessels in the brain, retina, and inner ear. Diagnosing Susac syndrome may be extremely challenging not only due to its rarity, but also due to the variability of its clinical presentation. This paper describes two vastly different cases—one with mild symptoms and good response to therapy, the other with severe, complicated course, relapses and long-term sequelae despite multiple therapeutic interventions. Building upon the available guidelines, we highlight the utility of black blood MRI in this disease and provide a comprehensive review of available clinical experience in clinical presentation, diagnosis and therapy of this disease. Despite its rarity, the awareness of Susac syndrome may be of uttermost importance since it ultimately is a treatable condition. If diagnosed in a timely manner, early intervention can substantially improve the outcomes of our patients

Interactive visualization of dense and multi-scale data for science outreach

This thesis focuses on the problem of navigating complex 3D models composed of large numbers of molecular instances packed densely in the three-dimensional space. Due to the large environment encompassing several magnitudes of scale, the traditional navigational paradigms applied in real-time computer graphics are becoming insufficient when applied to biological environments. In the first part of the thesis, I analyze navigation challenges presented by such a use case and recognize several modes of navigation that can be employed when interfacing a complex 3D visualization system with the end-user. We discuss three such modes of navigation: augmentive, declarative, and automative. First, in augmentive navigation, the user is given fully manual control over all aspects of navigation, such as controlling the camera's position and rotation, or the visibility of the individual model's parts. Their manual exploration is, however, augmented by automatically deployed annotation to help make sense of the environment. In declarative navigation, the user interaction is simplified to declaring their target. The visualization system then takes over the low-level controls of the visualization, e.g., camera path animation and scene visibility transition, which are computed to navigate the user directly to their declared target. The third stage, automative navigation, relieves the user from even this responsibility and places the choice of what gets shown to an algorithmic solution. In this case, such automated fly-through can then be guided by a specific storyline. In the second part of the thesis, I present specific methods addressing technical gaps and contributing to realizing the navigational stages presented in the first part. I start by introducing an approach for textual labeling of multi-scale molecular models inspired by the level-of-detail concept. That way, a scenario of augmentive navigation is provided. Second, I propose a navigational method for traversing a dense molecular model with a hierarchical organization, implementing the declarative navigation concept. The presented method uses textual labels for browsing the three-dimensional model, essentially providing a way of traversing the hierarchical organization and exploring the spatial characteristics of the model. Finally, I propose a pipeline for producing automated tours of molecular models, demonstrating the automative navigation mode.12

Strategie stavební firmy Unistav s.r.o.

Import 20/04/2006Prezenční výpůjčkaVŠB - Technická univerzita Ostrava. Ekonomická fakulta. Katedra (152) podnikohospodářsk

GeneDBase – Genetic Database of Selected Species of Mammals in the Czech Republic

Part 8: Information Systems and ApplicationsInternational audienceGeneDBase is a part of a research project titled “Creating a genetic database of selected species of mammals in the Czech Republic to be used for sustainable transport development”. The aim of the research project is to assess the impact of roads on the fragmentation of animal populations and their genetic variability. Further, the objective is to create a genetic database of mammals comprising the data from collected samples of selected wild animals which could be used widely, not only for road planning, but also in other fields (agriculture, environmental protection, land-use planning)

Multiscale Unfolding: Illustratively Visualizing the Whole Genome at a Glance

International audienceWe present Multiscale Unfolding, an interactive technique for illustratively visualizing multiple hierarchical scales of DNA in a single view, showing the genome at different scales and demonstrating how one scale spatially folds into the next. The DNA's extremely long sequential structure---arranged differently on several distinct scale levels---is often lost in traditional 3D depictions, mainly due to its multiple levels of dense spatial packing and the resulting occlusion. Furthermore, interactive exploration of this complex structure is cumbersome, requiring visibility management like cutaways. In contrast to existing temporally controlled multiscale data exploration, we allow viewers to always see and interact with any of the involved scales. For this purpose we separate the depiction into constant-scale and scale transition zones. Constant-scale zones maintain a single-scale representation, while still linearly unfolding the DNA. Inspired by illustration, scale transition zones connect adjacent constant-scale zones via level unfolding, scaling, and transparency. We thus represent the spatial structure of the whole DNA macro-molecule, maintain its local organizational characteristics, linearize its higher-level organization, and use spatially controlled, understandable interpolation between neighboring scales. We also contribute interaction techniques that provide viewers with a coarse-to-fine control for navigating within our all-scales-in-one-view representations and visual aids to illustrate the size differences. Overall, Multiscale Unfolding allows viewers to grasp the DNA's structural composition from chromosomes to the atoms, with increasing levels of "unfoldedness," and can be applied in data-driven illustration and communication