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  1. The motility mechanisms of microorganisms are critical virulence factors, enabling their spread and survival during infection. Motility is frequently characterized by qualitative analysis of macroscopic colonies, yet the standard quantification method has mainly been limited to manual measurement. Recent studies have applied deep learning for classification and segmentation of specific microbial species in microscopic images, but less work has focused on macroscopic colony analysis. Here, we advance computational tools for analyzing colonies of Proteus mirabilis, a bacterium that produces a macroscopic bullseye-like pattern via periodic swarming, a process implicated in its virulence. We present a dual-task pipeline for segmenting (1) the macroscopic colony including faint outer swarm rings, and (2) internal ring boundaries, unique features of oscillatory swarming. Our convolutional neural network for patch-based colony segmentation and U-Net with a VGG-11 encoder for ring boundary segmentation achieved test Dice scores of 93.28% and 83.24%, respectively. The predicted masks at times improved on the ground truths from our automated annotation algorithms. We demonstrate how application of our pipeline to a typical swarming assay enables ease of colony analysis and precise measurements of more complex pattern features than those which have been historically quantified. An implementation of our work can be foundmore »on https://github.com/daninolab/proteus-mirabilis.« less
    Free, publicly-accessible full text available April 1, 2023
  2. Abstract We report on optical spectroscopic study of the Sr 3 (Ir 1- x Ru x ) 2 O 7 system over a wide doping regime. We find that the changes in the electronic structure occur in the limited range of the concentration of Ru ions where the insulator–metal transition occurs. In the insulating regime, the electronic structure associated with the effective total angular momentum J eff  = 1/2 Mott state remains robust against Ru doping, indicating the localization of the doped holes. Upon entering the metallic regime, the Mott gap collapses and the Drude-like peak with strange metallic character appears. The evolution of the electronic structure registered in the optical data can be explained in terms of a percolative insulator–metal transition. The phonon spectra display anomalous doping evolution of the lineshapes. While the phonon modes of the compounds deep in the insulating and metallic regimes are almost symmetric, those of the semiconducting compound with x  = 0.34 in close proximity to the doping-driven insulator–metal transition show a pronounced asymmetry. The temperature evolution of the phonon modes of the x  = 0.34 compound reveals the asymmetry is enhanced in the antiferromagnetic state. We discuss roles of the S  = 1 spins of the Rumore »ions and charge excitations for the conspicuous lineshape asymmetry of the x  = 0.34 compound.« less
  3. Elastic scaling is a central promise of NFV but has been hard to realize in practice. The difficulty arises because most Network Functions (NFs) are stateful and this state need to be shared across NF instances. Implementing state sharing while meeting the throughput and latency requirements placed on NFs is challenging and, to date, no solution exists that meets NFV’s performance goals for the full spectrum of NFs. S6 is a new framework that supports elastic scaling of NFs without compromising performance. Its design builds on the insight that a distributed shared state abstraction is well-suited to the NFV context. We organize state as a distributed shared object (DSO) space and extend the DSO concept with techniques designed to meet the need for elasticity and high-performance in NFV workloads. S6 simplifies development: NF writers program with no awareness of how state is distributed and shared. Instead, S6 transparently migrates state and handles accesses to shared state. In our evaluation, compared to recent solutions for dynamic scaling of NFs, S6 improves performance by 100x during scaling events [25], and by 2-5x under normal operation