Quantitative measurements in 3-dimensional datasets of mouse lymph nodes resolve organ-wide functional dependencies

Deep tissue imaging has become state of the art in biology, but now the problem is to quantify spatial information in a global, organ-wide context. Although access to the raw data is no longer a limitation, the computational tools to extract biologically useful information out of these large data sets is still catching up. In many cases, to understand the mechanism behind a biological process, where molecules or cells interact with each other, it is mandatory to know their mutual positions. We illustrate this principle here with the immune system. Although the general functions of lymph nodes as immune sentinels are well described, many cellular and molecular details governing the interactions of lymphocytes and dendritic cells remain unclear to date and prevent an in-depth mechanistic understanding of the immune system. We imaged ex vivo lymph nodes isolated from both wild-type and transgenic mice lacking key factors for dendritic cell positioning and used software written in MATLAB to determine the spatial distances between the dendritic cells and the internal high endothelial vascular network. This allowed us to quantify the spatial localization of the dendritic cells in the lymph node, which is a critical parameter determining the effectiveness of an adaptive immune response.

Visualization Techniques For The Analysis Of Network Simulation Results

The Simulation Automation Framework for Experiments (SAFE) streamlines the de- sign and execution of experiments with the ns-3 network simulator. SAFE ensures that best practices are followed throughout the workflow a network simulation study, guaranteeing that results are both credible and reproducible by third parties. Data analysis is a crucial part of this workflow, where mistakes are often made. Even when appearing in highly regarded venues, scientific graphics in numerous network simulation publications fail to include graphic titles, units, legends, and confidence intervals. After studying the literature in network simulation methodology and in- formation graphics visualization, I developed a visualization component for SAFE to help users avoid these errors in their scientific workflow. The functionality of this new component includes support for interactive visualization through a web-based interface and for the generation of high-quality, static plots that can be included in publications. The overarching goal of my contribution is to help users create graphics that follow best practices in visualization and thereby succeed in conveying the right information about simulation results.

Centennial mineral dust variability in high-resolution ice core data from Dome C, Antarctica

Ice core data from Antarctica provide detailed insights into the characteristics of past climate, atmospheric circulation, as well as changes in the aerosol load of the atmosphere. We present high-resolution records of soluble calcium (Ca2+), non-sea-salt soluble calcium (nssCa2+), and particulate mineral dust aerosol from the East Antarctic Plateau at a depth resolution of 1 cm, spanning the past 800 000 years. Despite the fact that all three parameters are largely dust-derived, the ratio of nssCa2+ to particulate dust is dependent on the particulate dust concentration itself. We used principal component analysis to extract the joint climatic signal and produce a common high-resolution record of dust flux. This new record is used to identify Antarctic warming events during the past eight glacial periods. The phasing of dust flux and CO2 changes during glacial-interglacial transitions reveals that iron fertilization of the Southern Ocean during the past nine glacial terminations was not the dominant factor in the deglacial rise of CO2 concentrations. Rapid changes in dust flux during glacial terminations and Antarctic warming events point to a rapid response of the southern westerly wind belt in the region of southern South American dust sources on changing climate conditions. The clear lead of these dust changes on temperature rise suggests that an atmospheric reorganization occurred in the Southern Hemisphere before the Southern Ocean warmed significantly.

3D documentation of footwear impressions and tyre tracks in snow with high resolution optical surface scanning

The three-dimensional documentation of footwear and tyre impressions in snow offers an opportunity to capture additional fine detail for the identification as present photographs. For this approach, up to now, different casting methods have been used. Casting of footwear impressions in snow has always been a difficult assignment. This work demonstrates that for the three-dimensional documentation of impressions in snow the non-destructive method of 3D optical surface scanning is suitable. The new method delivers more detailed results of higher accuracy than the conventional casting techniques. The results of this easy to use and mobile 3D optical surface scanner were very satisfactory in different meteorological and snow conditions. The method is also suitable for impressions in soil, sand or other materials. In addition to the side by side comparison, the automatic comparison of the 3D models and the computation of deviations and accuracy of the data simplify the examination and delivers objective and secure results. The results can be visualized efficiently. Data exchange between investigating authorities at a national or an international level can be achieved easily with electronic data carriers.

Visualizing Genomic Data

The advent of experimental techniques capable of probing biomolecules and cells at high levels of resolution has led to a rapid change in the methods used for the analysis of experimental molecular biology data. In this article we give an overview over visualization techniques and methods that can be used to assess various aspects of genomic data.