A Jacobian-free Newton-Krylov method for time-implicit multidimensional hydrodynamics

This work is a continuation of our efforts to develop an efficient implicit solver for multidimensional hydrodynamics for the purpose of studying important physical processes in stellar interiors, such as turbulent convection and overshooting. We present an implicit solver that results from the combination of a Jacobian-Free Newton-Krylov method and a preconditioning technique tailored to the inviscid, compressible equations of stellar hydrodynamics. We assess the accuracy and performance of the solver for both 2D and 3D problems for Mach numbers down to $10^{-6}$. Although our applications concern flows in stellar interiors, the method can be applied to general advection and/or diffusion-dominated flows. The method presented in this paper opens up new avenues in 3D modeling of realistic stellar interiors allowing the study of important problems in stellar structure and evolution.Comment: Accepted for publication in A&

Interactive Medical Image Segmentation using Deep Learning with Image-specific Fine-tuning

Convolutional neural networks (CNNs) have achieved state-of-the-art performance for automatic medical image segmentation. However, they have not demonstrated sufficiently accurate and robust results for clinical use. In addition, they are limited by the lack of image-specific adaptation and the lack of generalizability to previously unseen object classes. To address these problems, we propose a novel deep learning-based framework for interactive segmentation by incorporating CNNs into a bounding box and scribble-based segmentation pipeline. We propose image-specific fine-tuning to make a CNN model adaptive to a specific test image, which can be either unsupervised (without additional user interactions) or supervised (with additional scribbles). We also propose a weighted loss function considering network and interaction-based uncertainty for the fine-tuning. We applied this framework to two applications: 2D segmentation of multiple organs from fetal MR slices, where only two types of these organs were annotated for training; and 3D segmentation of brain tumor core (excluding edema) and whole brain tumor (including edema) from different MR sequences, where only tumor cores in one MR sequence were annotated for training. Experimental results show that 1) our model is more robust to segment previously unseen objects than state-of-the-art CNNs; 2) image-specific fine-tuning with the proposed weighted loss function significantly improves segmentation accuracy; and 3) our method leads to accurate results with fewer user interactions and less user time than traditional interactive segmentation methods.Comment: 11 pages, 11 figure

Creative Economy Employment in the US, Canada and the UK

The US has the largest creative economy employment of the US, UK and Canada employing 14.2 million people. Canada had the largest creative economy employment as a percentage of the workforce at 12.9 per cent. Employment in the UK creative economy grew at 4.7 per cent per annum on average between 2011 and 2013, faster than the US between (3.1 per cent). A comparison with Canadian growth over this period was not possible with the data available. The largest centre of creative economy employment in the US in absolute terms is the New York-Newark-New Jersey Metro area employing 1.2 million people (12.7 per cent of the workforce) in 2013. The creative economy employment of this area in absolute and percentage terms is comparable to that of the Greater South East of England (London, the South East and Eastern regions). This employs 1.3 million people in the creative economy, 12.3 per cent of the workforce. This report provides consistent statistics on the US and Canadian creative economies in comparison to the UK. Creative economy employment being employment in creative industries and in creative occupations outside of these. Employment figures for creative industry groups are also provided. The report also analyses creative economy employment at a sub-national level for the US and UK, and the national level growth rates for these two countries between 2011 and 2013. The report applies the official UK creative industry classification to produce a best possible fit creative industries definition in the US and Canadian data. The report is based on analysing the US American Community Survey, the Canadian Household survey and the UK Annual Population Survey. A companion report that examines the creative industries employment in the 28 member states of the EU was published in December 2015

Image Analysis Applied to Slices of History

During the last 10 years, TASC has undertaken several digital image enhancement projects based on nondestructive evaluation (NDE) applications. Most of these projects involved analyzing NDE imagery to determine why a critical part failed to operate as expected, or trying to recover from a failure which degraded NDE imagery or made it difficult to obtain. Examples include our studies of the Inertial Upper Stage nozzle nosecap following the unsuccessful launch of a Tracking Data Relay Satellite in the summer of 1983 [1] and our development of a video data image processing system to enhance, in real time, unevenly lit, poor-contrast signals from within the contaminated Number 2 reactor vessel at Three Mile Island [2]

Anthrax lethal toxin induced lysosomal membrane permeabilization and cytosolic cathepsin release is Nlrp1b/Nalp1b-dependent.

NOD-like receptors (NLRs) are a group of cytoplasmic molecules that recognize microbial invasion or 'danger signals'. Activation of NLRs can induce rapid caspase-1 dependent cell death termed pyroptosis, or a caspase-1 independent cell death termed pyronecrosis. Bacillus anthracis lethal toxin (LT), is recognized by a subset of alleles of the NLR protein Nlrp1b, resulting in pyroptotic cell death of macrophages and dendritic cells. Here we show that LT induces lysosomal membrane permeabilization (LMP). The presentation of LMP requires expression of an LT-responsive allele of Nlrp1b, and is blocked by proteasome inhibitors and heat shock, both of which prevent LT-mediated pyroptosis. Further the lysosomal protease cathepsin B is released into the cell cytosol and cathepsin inhibitors block LT-mediated cell death. These data reveal a role for lysosomal membrane permeabilization in the cellular response to bacterial pathogens and demonstrate a shared requirement for cytosolic relocalization of cathepsins in pyroptosis and pyronecrosis

Merging biology and technology to achieve selective bi-directional fish passage

Selective, bi-directional fish passage can ease tensions between connectivity actions fish managers take to improve production of native and desirable fishes. Dam removal and fish passage can enhance fish production by increasing connectivity between tributaries and lakes or oceans. Conversely, in-stream barriers to movement can benefit native fishes by limiting the spread and reproduction of invasive species. To address the tensions, the Great Lakes Fishery Commission is leading a team of nearly 60 fisheries biologists, managers, and engineers in developing novel and effective tools to selectively pass desirable fishes while simultaneously blocking and removing invasive species. A uniquely designed facility (FishPass) is being planned for construction at the Boardman River’s Union Street Dam (Traverse City, MI) to stimulate research that integrates a suite of fish sorting, guidance, and passage technologies and techniques for selective bi-directional fish passage at conditions consistent with the scale and conditions of natural rivers. To be successful, selective fish passage solutions will require the integration and redundancy of automated technologies that both exploit and overcome sortable attributes of fish (i.e., phenology, behavior, physiology, and morphology). This presentation will discuss the status of the FishPass including conceptual designs, research agenda, and next steps