Journal: eLife

Article Title: Listeria monocytogenes cell-to-cell spread in epithelia is heterogeneous and dominated by rare pioneer bacteria

doi: 10.7554/eLife.40032

Figure Lengend Snippet: ( A ) On the left nine panels, micrographs show nuclei (Hoechst, blue) and intracellular bacteria (mTagRFP, red). Green lines, which serve as an approximation of host cell boundaries, depict the Voronoi tessellation of the centroids of the host nuclei. White arrows track a single pioneer and its two daughters through time. Start time (leftmost panel) refers to 1255 min post-infection. The right panel shows nuclei (Hoechst, blue) and the pioneer path throughout 180 min. Dots indicate the position of the pioneer at a given time point. Shades of red depict progression of time. Black arrow indicates start position. Orange arrows indicate the location and time of two bacterial replication events. ( B ) The left three panels depict three time steps of a stochastic simulation where D slow = 1, D fast = 100, P = 0.10, and k = 1. Each simulated bacterium is depicted by a data point. Green boundaries fully enclose all data points. On the fourth panel, boundaries (shades of green) depict the progression of a simulated focus boundaries at nine evenly-spaced time steps. ( C ) Images depicting 10 5 simulated bacteria at step 800 of stochastic simulations where D slow = 1, D fast = 100, k = 1, and probability of becoming a pioneer is depicted in cyan. Green boundaries fully enclose all data points. Circular dashed lines represent the smallest circles that fully enclose the green boundaries. ( D ) Data quantifying the circularity of experimental (red) and simulated (black) foci at step 800, which, normalized by the replication rate (0.006 min −1 ), is equivalent to approximately 1360 min of experimental time. For experimental data, each shape depicts an independent experiment. Dashed line at circularity of 0.58 refers to the mean of the experimental circularity. Horizontal bars indicate the mean for each condition. ( E ) Data quantifying circularity of simulated infection foci as a function of probability of becoming a pioneer. Each data point represents the average of 100 independent simulations. Vertical bars represent the standard deviation. Each color represents a different value of D fast /D slow ratio. Dashed line around 0.58 refers to the mean of the experimental circularity. For all simulations, replication rate k equals 1. 10.7554/eLife.40032.020 Figure 3—source data 1. This spreadsheet contains circularity data used to generate graphs in , in , and in . This spreadsheet also contains meansquared displacement data used to generate the graph in .

Article Snippet: The center of mass of each nucleus was calculated and used as the input for MATLAB’s Voronoi() function.

Techniques: Bacteria, Infection, Standard Deviation

Journal: Magnetic resonance in medicine

Article Title: Rapid Dynamic Contrast-Enhanced MRI for Small Animals at 7T using 3D Ultra-Short Echo Time and Golden-Angle Radial Sparse Parallel MRI

doi: 10.1002/mrm.27357

Figure Lengend Snippet: 3D golden angle sampling and parallel imaging. (a) modified 3D radial spokes in k-space with azimuth angle Φ = 2πmA and projection length (Z) in kz direction being the modules one of mB, for m = 1, 2, …, 102712 spokes with 2D golden angle means, A = 0.6823 and B = 0.4656. Distribution of 400 projection tips for the random (b), modified (c) and original (d) 3D golden angle sampling. The green areas are computed voronoi regions for k-space sampling density compensation. (e) Demonstration of images of individual channels of the receive coil and the coil sensitivity maps estimated from the temporal average of all spokes.

Article Snippet: Density compensation factors were computed using the 3D Voronoi diagram based method (implemented in Matlab with the function voronoin ), which implements a quick hull algorithm ( 29 ) to compute the volume of each sampling point in k -space.

Techniques: Sampling, Imaging, Modification