2D microstructure reconstruction for SEM via non-local patch-based image inpainting.
Abstract not provided.
Tran, Anh↗
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Simultaneous visualization of wall motion, drive beam propagation, and implosion symmetry by using hohlraums with thin-wall patches at the National Ignition Facility
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Physics - Plasma physics↗
Automated security patch and vulnerability remediation tool for electric utilities
A system and method for implementing a machine learningbased software for electric utilities that can automatically recommend a remediation action for a security vulnerability.
24 POWER TRANSMISSION AND DISTRIBUTION↗
Real-time patch-clamp sensing of transport across a barrier tissue
The present disclosure relates to methods, apparatuses, and systems to measure one or more electrical signals from a cultured cell layer. In some embodiments, such electrical signals can be indicative of transport or lack of transport of an agent through the cell layer.
Source record↗
Data-Driven Smoothers for Extreme-Scale Computing
Patch-based relaxation refers to a family of methods for solving linear systems which partitions the matrix into smaller pieces often corresponding to groups of adjacent degrees of freedom residing within patches of the computational domain. The two most common families of patch-based methods are block-Jacobi and Schwarz methods, where the former typically corresponds to non-overlapping domains and the later implies some overlap. We focus on cases where each patch consists of the degrees of freedom on a finite element method mesh cell. Patch methods often capture complex local physics much more effectively than simpler point-smoothers such as Jacobi; however, forming, inverting, and applying each patch can be prohibitively expensive in terms of both storage and computation time. To this end, we propose several approaches for performing analysis on these patches and constructing a reduced representation. The compression techniques rely on either matrix norm comparisons or unsupervised learning via a clustering approach. We illustrate how it is frequently possible to retain/factor less than 5% of all patches and still develop a method that converges only a little slower than when all patches are stored/factored.
97 MATHEMATICS AND COMPUTING↗
Habitat specialization and edge effects of soil microbial communities in a fragmented landscape
Abstract Soil microorganisms play outsized roles in nutrient cycling, plant health, and climate regulation. Despite their importance, we have a limited understanding of how soil microbes are affected by habitat fragmentation, including their responses to conditions at fragment edges, or “edge effects.” To understand the responses of soil communities to edge effects, we analyzed the distributions of soil bacteria, archaea, and fungi in an experimentally fragmented system of open patches embedded within a forest matrix. In addition, we identified taxa that consistently differed among patch, edge, or matrix habitats (“specialists”) and taxa that showed no habitat preference (“nonspecialists”). We hypothesized that microbial community turnover would be most pronounced at the edge between habitats. We also hypothesized that specialist fungi would be more likely to be mycorrhizal than nonspecialist fungi because mycorrhizae should be affected more by different plant hosts among habitats, whereas specialist prokaryotes would have smaller genomes (indicating reduced metabolic versatility) and be less likely to be able to sporulate than nonspecialist prokaryotes. Across all replicate sites, the matrix and patch soils harbored distinct microbial communities. However, sites where the contrasts in vegetation and pH between the patch and matrix were most pronounced exhibited larger differences between patch and matrix communities and tended to have edge communities that differed from those in the patch and forest. There were similar numbers of patch and matrix specialists, but very few edge specialist taxa. Acidobacteria and ectomycorrhizae were more likely to be forest specialists, while Chloroflexi, Ascomycota, and Glomeromycota (i.e., arbuscular mycorrhizae) were more likely to be patch specialists. Contrary to our hypotheses, nonspecialist bacteria were not more likely than specialist bacteria to have larger genomes or to be spore‐formers. We found partial support for our mycorrhizal hypothesis: arbuscular mycorrhizae, but not ectomycorrhizae, were more likely to be specialists. Overall, our results indicate that soil microbial communities are sensitive to edges, but not all taxa are equally affected, with arbuscular mycorrhizae in particular showing a strong response to habitat edges. In the context of increasing habitat fragmentation worldwide, our results can help inform efforts to maintain the structure and functioning of the soil microbiome.
Winfrey, Claire C. [Department of Ecology and Evol↗
A Scalable Pipeline for Gigapixel Whole Slide Imaging Analysis on Leadership Class HPC Systems
Whole Slide Imaging (WSI) captures microscopic details of a patient's histopathological features at multiple res-olutions organized across different levels. Images produced by WSI are gigapixel-sized, and saving a single image in memory requires a few gigabytes which is scarce since a complicated model occupies tens of gigabytes. Performing a simple met-ric operation on these large images is also expensive. High-performance computing (HPC) can help us quickly analyze such large images using distributed training of complex deep learning models. One popular approach in analyzing these images is to divide a WSI image into smaller tiles (patches) and then train a simpler model with these reduced-sized but large numbers of patches. However, we need to solve three pre-processing challenges efficiently for pursuing this patch-based approach. 1) Creating small patches from a high-resolution image can result in a high number (hundreds of thousands per image) of patches. Storing and processing these images can be challenging due to a large number of I/O and arithmetic operations. To reduce I/Oand memory accesses, an optimal balance between the size and number of patches must exist to reduce I/O and memory accesses. 2) WSI images may have tiny annotated regions for cancer tissue and a significant portion with normal and fatty tissues; correct patch sampling should avoid dataset imbalance. 3) storing and retrieving many patches to and from disk storage might incur I/O latency while training a deep learning model. An efficient distributed data loader should reduce I/O latency during the training and inference steps. This paper explores these three challenges and provides empirical and algorithmic solutions deployed on the Summit supercomputer hosted at the Oak Ridge Leadership Computing Facility.
Dash, Sajal↗
Classification of Wetland Vegetation Based on NDVI Time Series from the HLS Dataset
Natural wetlands are intrinsically heterogeneous and typically composed of a mosaic of ecosystem patches with different vegetation types. Hydrological and biogeochemical processes in wetlands vary strongly among these ecosystem patches. To date, most remote sensing classification approaches for wetland vegetation either rely on coarse images that cannot capture the spatial variability of wetland vegetation or rely on very-high-resolution multi-spectral images that are detailed but very sporadic in time (less than once per year). This study aimed to use NDVI time series, generated from NASA’s HLS dataset, to classify vegetation patches. We demonstrate our approach at a temperate, coastal lake, estuarine marsh. To classify vegetation patches, a standard time series library of the four land-cover patch types was built from referencing specific locations that were identified as “pure” pixels. These were identified using a single-time high-resolution image. We calculated the distance between the HLS-NDVI time series at each pixel and the “pure”-pixel standards for each land-cover type. The resulting true-positive classified rate was >73% for all patch types other than water lily. The classification accuracy was higher in pixels of a more uniform composition. A set of vegetation maps was created for the years 2016 to 2020 at our research site to identify the vegetation changes at the site as it is affected by rapid water elevation increases in Lake Erie. Our results reveal how changes in water elevation have changed the patch distribution in significant ways, leading to the local extinction of cattail by 2019 and a continuous increase in the area cover of water lily patches.
54 ENVIRONMENTAL SCIENCES↗
Thermal-Hydraulics Modeling and Simulations of Hot Pool Using the SAS-CFD Coupled Code
The main goal of this activity is to test the dynamic coupling of the SAS4A/SASSYS-1 (SAS) and CFD models, using a recently patched version of the SAS code intended to address an undocumented limitation that hindered the Versatile Test Reactor (VTR) simulation efforts in FY21. As described in previous VTR calculation reports, the undocumented limitation in SAS v5.4 does not allow the user to activate the CFD coupling option during restart calculations. Since the analysts were unaware of this limitation, prior SAS-CFD simulation results for the protected station blackout (PSBO) transient were erroneous. Root-cause analysis was performed to determine the cause of this undocumented limitation in SAS v5.4, the SAS software was updated in a new patch, and the SAS-CFD simulations were repeated with this patched software. The results of the SAS-CFD simulations documented in this report show that the software patch does address the cited issue, and that the patched software indeed supports the activation of the CFD coupling model in restart calculations. The SAS development team will determine the schedule for implementing the patch in an official software release. This report documents updated SAS-CFD simulations of the PSBO transient response in the VTR. The hot pool is modeled with the CFD code STAR-CCM+, which is coupled at the flow boundaries to the SAS model of the primary heat transport system. SAS computes the mass flow rate and temperature at each core subassembly outlet, the thermal insulation cavity bypass, and the IHX inlet windows. CFD in turn computes the absolute pressure and temperature at each of these boundaries. The SAS code will ignore the temperature data at flow boundaries where flow is directed into the hot pool, i.e., at the core subassembly outlets unless flow reversal occurs. Similarly, CFD will ignore temperature data at boundaries where the flow is directed out of the hot pool, i.e., at the IHX inlets except under flow reversal. The focus of this work is to ensure that the SAS software patch addresses the undocumented limitation described in prior VTR calculation reports, rather than the accurate assessment of thermal stratification in the VTR during protected transients. This motivates the development of a new, simplified CFD model with a coarser mesh to accelerate the testing process. The updated model, and simplifying assumptions, are documented in this report. In future work, the thermal stratification assessment should be performed in more detail. The simplified CFD model can be improved by performing grid convergence studies sensitivity studies of turbulence parameters (e.g., Prandtl number, turbulence production and dissipation parameters) on temperature distributions and thermal stratification.
22 GENERAL STUDIES OF NUCLEAR REACTORS↗
Composing preconditioners for multiphysics PDE systems with applications to Generalized MHD
New patch smoothers or relaxation techniques are developed for solving linear matrix equations coming from systems of discretized partial differential equations (PDEs). One key linear solver challenge for many PDE systems arises when the resulting discretization matrix has a near null space that has a large dimension, which can occur in generalized magnetohydrodynamic (GMHD) systems. Patch-based relaxation is highly effective for problems when the null space can be spanned by a basis of locally supported vectors. The patch-based relaxation methods that we develop can be used either within an algebraic multigrid (AMG) hierarchy or as stand-alone preconditioners. These patch-based relaxation techniques are a form of well-known overlapping Schwarz methods where the computational domain is covered with a series of overlapping sub-domains (or patches). Patch relaxation then corresponds to solving a set of independent linear systems associated with each patch. In the context of GMHD, we also reformulate the underlying discrete representation used to generate a suitable set of matrix equations. In general, deriving a discretization that accurately approximates the curl operator and the Hall term while also producing linear systems with physically meaningful near null space properties can be challenging. Unfortunately, many natural discretization choices lead to a near null space that includes non-physical oscillatory modes and where it is not possible to span the near null space with a minimal set of locally supported basis vectors. Further discretization research is needed to understand the resulting trade-offs between accuracy, stability, and ease in solving the associated linear systems.
97 MATHEMATICS AND COMPUTING↗
Climate change and invasion may synergistically affect native plant reproduction
Global change drivers can interact in synergistic ways, yet the interactive effect of global change drivers, such as climatic warming and species invasions, on plant pollination are poorly represented in experimental studies. We paired manipulative experiments to probe two mechanistic pathways through which plant invasion and warming may alter phenology and reproduction of native plant species. In the first, we tested how experimental warming (+1.7°C) modulated flowering phenology and how this affected flowering overlap between a native plant (Dracophyllum subulatum) and an invasive plant (Calluna vulgaris L.). In the second experiment, we explored how variation in the ratio of native to invasive flowers, and the overall quantity of resources in a floral patch, affected the reproduction of the native species. We hypothesized that the flowering overlap of native and invasive plants would be altered by warming, given that invading plants typically exhibit greater phenological plasticity than native plants. Further, we hypothesized that pollination of native plant flowers would decrease in floral patches dominated by invasive plant flowers, but that this effect would depend on total floral density in the patch. As predicted, the invasive plant had a stronger phenological response to experimental warming than the native plant, resulting in increased flowering overlap between the native the invasive plants. There was a four-fold increase in the number of native flowers co-flowering with high densities of invasive flowers suggesting native plant competition for pollinators with invasive plants under a warmed climate. In the second experiment, we found depressed seed masses of the native species in high density floral patches that were dominated by invasive flowers relative to high density floral patches dominated by native flowers. At low floral densities, seed mass of native plants was unaffected by invasion. Together, these results demonstrate that by increasing their phenological overlap, warming may enhance the magnitude of existing competition for pollination exerted by an invasive plant on a native plant, particularly in plant patches with high floral density. Finally, our results illustrate a novel pathway through which global change drivers can operate synergistically to alter an important ecosystem service: pollination.
54 ENVIRONMENTAL SCIENCES↗
Delta size and plant patchiness as controls on channel network organization in experimental deltas
Understanding the feedbacks between water, sediment, and vegetation in deltas is an important part of understanding deltas as ecomorphodynamic systems. Here, we conducted a set of laboratory experiments using alfalfa (Medicago sativa) as a proxy for delta vegetation to investigate (1) the effects of plants on delta growth and channel network formation and (2) the timescales controlling delta evolution in the presence of plants. Experiments were conducted with fluctuating discharge (i.e. flood and base flow periods) and variable seeding densities. We found that when deltas were small, channels had no memory across flood cycles, as floods could completely fill the incised channel network. When deltas were large, the larger channel volume could remain underfilled to keep channel memory. Plant patches also helped to increase the number of channels and make a more distributive network. Patchiness increased over time to continually aid in bifurcation, but as vegetation cover and patch sizes increased, patches began to merge. Larger patches blocked the flow to enhance topset deposition and channel filling, even for the case of large deltas with a high channel volume. We conclude that both plant patchiness and delta size affect the development of the channel network, and we hypothesize that their influences are manifested through two competing timescales. The first timescale, T v , defines the time when the delta is large enough for channels to have memory (i.e., remain underfilled), and the second, T p , defines the time when vegetation patches merge, amplifying deposition and blocking channels. Finally, when run time is between these two timescales, the delta can develop a persistent distributary network of channels aided by bifurcation around plant patches, but once T p is reached, the channel network can again be destroyed by vegetation.
58 GEOSCIENCES↗
Liquid metasurface‐based periodically stacked radome design
Abstract We present liquid metasurface‐based periodically stacked radome design. Radome is a layer placed above the antenna to protect it from weather disturbances. The layer protects the antenna but reduces its gain. Periodic stacking of liquid metasurface based radome improve the antenna parameters like gain and bandwidth. Microstrip patch antenna is used as basic antenna to check the improvement in gain. The comparison of microstrip patch antenna, patch antenna with simple multilayer radome, patch antenna with liquid metasurface multilayer radome and patch antenna with liquid metasurface periodically stacked multilayer radome is presented in the manuscript. The improvement in terms of gain is clearly visible from the comparison of results for all the designs. Efficiency is also increasing by adding liquid metasurface periodically stacked multilayer radome to patch antenna.
Patel, Shobhit K.↗
Transdermal Delivery of Nicotine Using Pectin Isolated from Durian Fruit-Hulls-Based Polymer Blends as a Matrix Layer
Many natural polymers with various chemical structures are used to prepare transdermal patches. Pectin is a one interesting type of polymer because it can control drug release when used in transdermal patches. In Thailand, the waste from durian fruit-hulls is a major problem for the environment. However, the pectin from it can be isolated under acid conditions and used to prepare transdermal patches for nicotine delivery which has not yet been reported. As the isolated pectin is a natural polymer, the film made from isolated pectin is a brittle; therefore, adding a low protein natural rubber latex (LPNRL) polymer was needed to increase its flexibility. The transdermal patches were amorphous and had T{sub g} values ranging from 81.0 to 93.3 °C. Moisture uptake, swelling ratio, and erosion values of the patches were significantly decreased after addition of LPNRL, which resulted in low hydrophilicity. The in vitro release and permeation of nicotine depends on the hydrophilicity of the patches. The kinetic models for in vitro release and permeation of nicotine were Higuchi model and zero order, respectively. In conclusion, pectin isolated from fruit-hulls of Mon Thong durians is an effective polymer to control the release of nicotine. It also is an option that could solve the environmental problems caused by durian fruit-hulls waste.
36 MATERIALS SCIENCE↗
On behaviour and scaling of small repeating earthquakes in rate and state fault models
With abundant seismic data for small repeating earthquakes, it is important to construct a dynamic model that can explain various aspects of related observations. We report on small repeating earthquakes on a fault governed by rate- and state-dependent friction laws. The earthquakes occur on a velocity-weakening patch surrounded by a much larger velocity-strengthening region. The whole fault is subject to long-term tectonic loading. The model with a circular patch and the aging form of rate- and state-dependent friction laws has been shown to reproduce the scaling of recurrence time versus seismic moment for small repeating earthquakes in a previous study. In this work we investigate the behaviour of small repeating earthquakes in related models under different scenarios, including several forms of the state evolution equations in rate- and state-dependent friction laws, rectangular velocity-weakening patch geometries, quasi-dynamic versus fully dynamic representation of inertial effects and 2-D versus 3-D simulations. We discover that the simulated scalings between the recurrence time and seismic moment for these different scenarios is similar while differences do exist. We propose a theoretical consideration for the scaling between the recurrence time and seismic moment of small repeating earthquakes. For patch radii smaller than or comparable to the full nucleation size, the scaling is explained by the increase of seismic to aseismic slip ratio with magnitude. For patch radii larger than the full nucleation size, the scaling is explained by the model in which the recurrence time is determined by the earthquake nucleation time, which is in turn determined by the time for aseismic slip to penetrate the distance of the full nucleation size into the patch. The obtained theoretical insight is used to find the combinations of fault properties that allow the model to fit the observed scaling and range of the seismic moment and recurrence time.
58 GEOSCIENCES↗
Deer Vigilance and Movement Behavior Are Affected by Edge Density and Connectivity
ABSTRACT Animal behavior is an important component of individual, population, and community responses to anthropogenic habitat alteration. For example, antipredator behavior (e.g., vigilance) and animal movement behavior may both be important behavioral responses to the increased density of habitat edges and changes in patch connectivity that characterize highly modified habitats. Importantly, edge density and connectivity might interact, and this interaction is likely to mediate animal behavior: linear, edge‐rich landscape features often provide structural connectivity between patches, but the functional connectedness of patches for animal use could depend upon how edge density modifies animal vigilance and movement. Using remote cameras in large‐scale experimental landscapes that manipulate edge density (high‐ vs. low‐density edges) and patch connectivity (isolated or connected patches), we examined the effects of edge density and connectivity on the antipredator behavior and movement behavior of white‐tailed deer ( Odocoileus virginianus ). Deer vigilance was 1.38 times greater near high‐density edges compared to low‐density edges, regardless of whether patches were connected or isolated. Deer were also more likely to move parallel to connected high‐density edges than all other edge types, suggesting that connectivity promotes movement along high‐density edges. These results suggest that increases in edge density that accompany human fragmentation of existing habitats may give rise to large‐scale changes in the antipredator behavior of deer. These results also suggest that conservation strategies that simultaneously manipulate edge density and connectivity (i.e., habitat corridors) may have multiple effects on different aspects of deer behavior: linear habitat corridors were areas of high vigilance, but also areas where deer movement behavior implied increased movement along the habitat edge.
Bartel, Savannah L. [University of Wisconsin‐Madis↗