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At least 649 records · Page 36

Graph interpolating activation improves both natural and robust accuracies in data-efficient deep learning

Improving the accuracy and robustness of deep neural nets (DNNs) and adapting them to small training data are primary tasks in deep learning (DL) research. In this paper, we replace the output activation function of DNNs, typically the data-agnostic softmax function, with a graph Laplacian-based high-dimensional interpolating function which, in the continuum limit, converges to the solution of a Laplace–Beltrami equation on a high-dimensional manifold. Furthermore, we propose end-to-end training and testing algorithms for this new architecture. The proposed DNN with graph interpolating activation integrates the advantages of both deep learning and manifold learning. Compared to the conventional DNNs with the softmax function as output activation, the new framework demonstrates the following major advantages: First, it is better applicable to data-efficient learning in which we train high capacity DNNs without using a large number of training data. Second, it remarkably improves both natural accuracy on the clean images and robust accuracy on the adversarial images crafted by both white-box and black-box adversarial attacks. Third, it is a natural choice for semi-supervised learning. This paper is a significant extension of our earlier work published in NeurIPS, 2018. For reproducibility, the code is available at https://github.com/BaoWangMath/DNN-DataDependentActivation .

Mathematics↗

Negative Role of RIG-I Serine 8 Phosphorylation in the Regulatin of Interferon-beta Production

RIG-I (retinoic acid-inducible gene I) and TRIM25 (tripartite motif protein 25) have emerged as key regulatory factors to induce interferon (IFN)-mediated innate immune responses to limit viral replication. Upon recognition of viral RNA, TRIM25 E3 ligase binds the first caspase recruitment domain (CARD) of RIG-I and subsequently induces lysine 172 ubiquitination of the second CARD of RIG-I, which is essential for the interaction with downstream MAVS/IPS-1/CARDIF/VISA and, thereby, IFN-beta mRNA production. Although ubiquitination has emerged as a major factor involved in RIG-I activation, the potential contribution of other post-translational modifications, such as phosphorylation, to the regulation of RIG-I activity has not been addressed. Here, we report the identification of serine 8 phosphorylation at the first CARD of RIG-I as a negative regulatory mechanism of RIG-I-mediated IFN-beta production. Immunoblot analysis with a phosphospecific antibody showed that RIG-I serine 8 phosphorylation steady-state levels were decreased upon stimulation of cells with IFN-beta or virus infection. Substitution of serine 8 in the CARD RIG-I functional domain with phosphomimetic aspartate or glutamate results in decreased TRIM25 binding, RIG-I ubiquitination, MAVS binding, and downstream signaling. Finally, sequence comparison reveals that only primate species carry serine 8, whereas other animal species carry an asparagine, indicating that serine 8 phosphorylation may represent a primate-specific regulation of RIG-I activation. Collectively, these data suggest that the phosphorylation of RIG-I serine 8 operates as a negative switch of RIG-I activation by suppressing TRIM25 interaction, further underscoring the importance of RIG-I and TRIM25 connection in type I IFN signal transduction.

59 BASIC BIOLOGICAL SCIENCES↗

A Proposed Geospatial Data Preservation Strategy for DOE's Office of Legacy Management

Identifying and planning preservation and curation activities associated with geospatial data will improve the ability of the U.S. Department of Energy Office of Legacy Management (LM) to support their core mission of protecting human health and the environment. This report documents the development LM's strategy for preserving and curating geospatial data within the context of LM's data-lifecycle-management framework. The strategy consists of preservation and curation elements, specific activities, and key enabling factors that ensure LM's geospatial data is maintained. Preservation elements enable the effective preservation of LM's geospatial data and recognizes that strategies need to be flexible to adapt to ongoing changes in scale, technology, and standards. Key enabling factors are intended to highlight critical data management responsibilities that must be addressed by LM to meet its preservation and curation objectives. A summary of best practices for geospatial data preservation is provided as part of the strategy.

97 MATHEMATICS AND COMPUTING↗

A GATE evaluation of the sources of error in quantitative {sup 90}Y PET

Purpose: Accurate reconstruction of the dose delivered by {sup 90}Y microspheres using a postembolization PET scan would permit the establishment of more accurate dose–response relationships for treatment of hepatocellular carcinoma with {sup 90}Y. However, the quality of the PET data obtained is compromised by several factors, including poor count statistics and a very high random fraction. This work uses Monte Carlo simulations to investigate what impact factors other than low count statistics have on the quantification of {sup 90}Y PET. Methods: PET acquisitions of two phantoms—a NEMA PET phantom and the NEMA IEC PET body phantom-containing either {sup 90}Y or {sup 18}F were simulated using GATE. Simulated projections were created with subsets of the simulation data allowing the contributions of random, scatter, and LSO background to be independently evaluated. The simulated projections were reconstructed using the commercial software for the simulated scanner, and the quantitative accuracy of the reconstruction and the contrast recovery of the reconstructed images were evaluated. Results: The quantitative accuracy of the {sup 90}Y reconstructions were not strongly influenced by the high random fraction present in the projection data, and the activity concentration was recovered to within 5% of the known value. The contrast recovery measured for simulated {sup 90}Y data was slightly poorer than that for simulated {sup 18}F data with similar count statistics. However, the degradation was not strongly linked to any particular factor. Using a more restricted energy range to reduce the random fraction in the projections had no significant effect. Conclusions: Simulations of {sup 90}Y PET confirm that quantitative {sup 90}Y is achievable with the same approach as that used for {sup 18}F, and that there is likely very little margin for improvement by attempting to model aspects unique to {sup 90}Y, such as the much higher random fraction or the presence of bremsstrahlung in the singles data.

61 RADIATION PROTECTION AND DOSIMETRY↗

Replication Data for: Single Nickel Atoms Anchored on Nitrogen-Doped Graphene as a Highly Active Cocatalyst for Photocatalytic H2 Evolution

The data underlying this published work have been made publicly available in this repository as part of the IMASC Data Management Plan. This work was supported as part of the Integrated Mesoscale Architectures for Sustainable Catalysis (IMASC), an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under Award # DE-SC0012573.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

SU-E-CAMPUS-I-03: Dosimetric Comparison of the Hypoxia Agent Iodoazomycin Arabinoside (IAZA) Labeled with the Radioisotopes I-123, I-131 and I-124

Purpose: To compare the radiation dose to normal organs from the radio-iodinated, hypoxia-binding radiosensitizer iodoazomycin arabinoside (IAZA) for three different isotopes of iodine. Methods: Dosimety studies with normal volunteers had been carried out with [{sup 123}I]IAZA, a drug binding selectively to hypoxic sites. Two other isotopes of iodine, {sup 131}I and {sup 124}I, offer the opportunity to use IAZA as an agent for radioisotope therapy and as an imaging tracer for Positron Emission Tomography. Radioisotope dosimetry for {sup 131}I and {sup 124}I was performed by first deriving from the [{sup 123}I]IAZA studies biological uptake and excretion data. The cumulated activities for {sup 131}I or {sup 124}I where obtained by including their half-lives when integrating the biological data and then extrapolating to infinite time points considering a) physical decay only or b) physical and biological excretion. Doses were calculated using the Medical Internal Radiation Dose (MIRD) schema (OLINDA1.1 code, Vanderbilt 2007). Results: Compared to {sup 123}I, organ doses were elevated on average by a factor 6 and 9 for {sup 131}I and {sup 124}I, respectively, if both physical decay and biological excretion were modeled. If only physical decay is considered, doses increase by a factor 18 ({sup 131}I) and 19 ({sup 124}I). Highest organ doses were observed in intestinal walls, urinary bladder and thyroid. Effective doses increased by a factor 11 and 14 for {sup 131}I and {sup 124}I, respectively, if biological and physical decay are present. Purely physical decay yields a 23-fold increase over {sup 123}I for both, {sup 131}I and {sup 124}I. Conclusion: Owing to the significant dose increase, caused by their longer half life and the approximately 10 times larger electronic dose deposited in tissue per nuclear decay, normal tissue doses of IAZA labeled with {sup 131}I and {sup 124}I need to be carefully considered when designing imaging and therapy protocols for clinical trials. Effective blocking of iodine uptake in the thyroid is essential. Alberta Innovates - Health Solutions (AIHS) and Canadian Institutes of Health Research (CIHR)

60 APPLIED LIFE SCIENCES↗

Structure and Dynamics of FosA-Mediated Fosfomycin Resistance in Klebsiella pneumoniae and Escherichia coli

ABSTRACT Fosfomycin exhibits broad-spectrum antibacterial activity and is being reevaluated for the treatment of extensively drug-resistant pathogens. Its activity in Gram-negative organisms, however, can be compromised by expression of FosA, a metal-dependent transferase that catalyzes the conjugation of glutathione to fosfomycin, rendering the antibiotic inactive. In this study, we solved the crystal structures of two of the most clinically relevant FosA enzymes: plasmid-encoded FosA3 from Escherichia coli and chromosomally encoded FosA from Klebsiella pneumoniae (FosA KP ). The structure, molecular dynamics, catalytic activity, and fosfomycin resistance of FosA3 and FosA KP were also compared to those of FosA from Pseudomonas aeruginosa (FosA PA ), for which prior crystal structures exist. E. coli TOP10 transformants expressing FosA3 and FosA KP conferred significantly greater fosfomycin resistance (MIC, >1,024 μg/ml) than those expressing FosA PA (MIC, 16 μg/ml), which could be explained in part by the higher catalytic efficiencies of the FosA3 and FosA KP enzymes. Interestingly, these differences in enzyme activity could not be attributed to structural differences at their active sites. Instead, molecular dynamics simulations and hydrogen-deuterium exchange experiments with FosA KP revealed dynamic interconnectivity between its active sites and a loop structure that extends from the active site of each monomer and traverses the dimer interface. This dimer interface loop is longer and more extended in FosA KP and FosA3 than in FosA PA , and kinetic analyses of FosA KP and FosA PA loop-swapped chimeric enzymes highlighted its importance in FosA activity. Collectively, these data yield novel insights into fosfomycin resistance that could be leveraged to develop new strategies to inhibit FosA and potentiate fosfomycin activity.

Klontz, Erik H.↗

Spatially Explicit Modeling of Criteria Air Pollutants from Agricultural and Forestry Feedstock Production

The Feedstock Production Emissions to Air Model (FPEAM) is a spatially explicit supply chain model that quantifies criteria air pollutants and precursors generated by biomass production, harvest and transportation to biorefineries. FPEAM was most recently used for the 2016 Billion Ton Study (BTS) published by the U.S. Department of Energy Bioenergy Technologies Office. This presentation describes several use cases for the model, and provides an overview of recent restructuring that increases FPEAM's usability and functionality. FPEAM currently estimates emissions of volatile organic compounds, particulate matter, nitrogen oxides, sulfur oxides, and carbon monoxide from on-farm equipment operation, on-farm fugitive dust, on-farm chemical (fertilizer, herbicide and insecticide) application, and biomass transportation. These calculations are implemented within FPEAM as modules, which independently perform calculations for each emissions category. This structure allows users to include or exclude emissions categories according to the goal and scope of their analysis. Each module's input data defines the activities taking place with information including fuel combusted, chemicals applied, and equipment used. Users can replace or augment the default input data to quantify additional pollutant types, emissions categories, farming practices and biomass types. Emissions from biomass transportation and on-farm equipment operation are by default calculated by the U.S. Environmental Protection Agency's Motor Vehicle Emission Simulator (MOVES) and NONROAD model, respectively. These models - which are computationally intensive but provide detailed results - can optionally be replaced with user-provided emissions factors for fuel combustion and vehicle operation. This approach reduces FPEAM's runtime and allows users to run sensitivity analyses around biomass production and transportation scenarios. Other enhancements currently under development are the use of farm-to-biorefinery route information to increase the spatial resolution of transportation emissions, and a module to connect FPEAM and the Intervention Model for Air Pollution (InMAP), which will enable the quantification of human health impacts.

09 BIOMASS FUELS↗

The Fourth Catalog of Active Galactic Nuclei Detected by the Fermi Large Area Telescope: Data Release 3

Abstract An incremental version of the fourth catalog of active galactic nuclei (AGNs) detected by the Fermi Large Area Telescope is presented. This version (4LAC-DR3) derives from the third data release of the 4FGL catalog based on 12 yr of E > 50 MeV gamma-ray data, where the spectral parameters, spectral energy distributions (SEDs), yearly light curves, and associations have been updated for all sources. The new reported AGNs include 587 blazar candidates and four radio galaxies. We describe the properties of the new sample and outline changes affecting the previously published one. We also introduce two new parameters in this release, namely the peak energy of the SED high-energy component and the corresponding flux. These parameters allow an assessment of the Compton dominance, the ratio of the inverse-Compton to the synchrotron-peak luminosities, without relying on X-ray data.

79 ASTRONOMY AND ASTROPHYSICS↗

IDENTIFICATION OF 1.4 MILLION ACTIVE GALACTIC NUCLEI IN THE MID-INFRARED USING WISE DATA

We present an all-sky sample of ≈1.4 million active galactic nuclei (AGNs) meeting a two-color infrared photometric selection criteria for AGNs as applied to sources from the Wide-field Infrared Survey Explorer final catalog release (AllWISE). We assess the spatial distribution and optical properties of our sample and find that the results are consistent with expectations for AGNs. These sources have a mean density of ≈38 AGNs per square degree on the sky, and their apparent magnitude distribution peaks at g ≈ 20, extending to objects as faint as g ≈ 26. We test the AGN selection criteria against a large sample of optically identified stars and determine the “leakage” (that is, the probability that a star detected in an optical survey will be misidentified as a quasi-stellar object (QSO) in our sample) rate to be ≤4.0 × 10{sup −5}. We conclude that our sample contains almost no optically identified stars (≤0.041%), making this sample highly promising for future celestial reference frame work as it significantly increases the number of all-sky, compact extragalactic objects. We further compare our sample to catalogs of known AGNs/QSOs and find a completeness value of ≳84% (that is, the probability of correctly identifying a known AGN/QSO is at least 84%) for AGNs brighter than a limiting magnitude of R ≲ 19. Our sample includes approximately 1.1 million previously uncataloged AGNs.

79 ASTRONOMY AND ASTROPHYSICS↗

Comparison Of 252 Cf Time Correlated Induced Fisssion With AmLi Induced Fission On Fresh MTR Research Reactor Fuel

The effective application of international safeguards to research reactors requires verification of spent fuel as well as fresh fuel. To accomplish this goal various nondestructive and destructive assay techniques have been developed in the US and around the world. The Advanced Experimental Fuel Counter (AEFC) is a nondestructive assay (NDA) system developed at Los Alamos National Laboratory (LANL) combining both neutron and gamma measurement capabilities. Since spent fuel assemblies are stored in water, the system was designed to be watertight to facilitate underwater measurements by inspectors. The AEFC is comprised of six 3 He detectors as well as a shielded and collimated ion chamber. The 3 He detectors are used for active and passive neutron coincidence counting while the ion chamber is used for gross gamma counting. Active coincidence measurement data is used to measure residual fissile mass, whereas the passive coincidence measurement data along with passive gamma measurement can provide information about burnup, cooling time, and initial enrichment. In the past, most of the active interrogation systems along with the AEFC used an AmLi neutron interrogation source. Owing to the difficulty in obtaining an AmLi source, a 252 Cf spontaneous fission (SF) source was used during a 2014 field trail in Uzbekistan as an alternative. In this study, experiments were performed to calibrate the AEFC instrument and compare use of the 252 Cf spontaneous fission source and the AmLi (α,n) neutron emission source. The 252 Cf source spontaneously emits bursts of time-correlated prompt fission neutrons that thermalize in the water and induce fission in the fuel assembly. The induced fission (IF) neutrons are also time correlated resulting in more correlated neutron detections inside the 3 He detector, which helps reduce the statistical errors in doubles when using the 252 Cf interrogation source instead of the AmLi source. In this work, two MTR fuel assemblies varying both in size and number of fuel plates were measured using 252 Cf and AmLi active interrogation sources. This paper analyzes time correlated induced fission (TCIF) from fresh MTR fuel assemblies due to 252 Cf and AmLi active interrogation sources.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Hanford Site Ecological Monitoring Report for Calendar Year 2017

The U.S. Department of Energy, Richland Operations Office (DOE-RL) conducts ecological monitoring on the Hanford Site to collect and track data needed to ensure compliance with an array of environmental laws, regulations, and policies governing the U.S. Department of Energy’s (DOE) activities. Ecological monitoring data provide baseline information about the plants, animals, and habitats under DOE-RL stewardship at the Hanford Site required for decision making under the National Environmental Policy Act and Comprehensive Environmental Response, Compensation, and Liability Act. DOE/EIS-0222-FU, Final Hanford Comprehensive Land Use Plan Environmental Impact Statement, (CLUP) evaluates potential environmental impacts associated with implementing a comprehensive land use plan for the Hanford Site over the next 50 years. The vision for the DOE-RL-managed portion of the Hanford Site focuses not only on the cleanup of nuclear facilities and waste sites but on the protection of groundwater, the Columbia River, and the restoration of the land for access and use. To reach these goals DOE-RL is working closely with partners, such as the U. S. Fish and Wildlife Service (FWS) and National Park Service, to enable use of the Hanford land consistent with the CLUP. As DOE-RL moves toward accomplishing this vision, monitoring the ecological resources present to determine whether there is a need for conservation and/or protection of any resources will be critical for making informed decisions for responsible site stewardship.

54 ENVIRONMENTAL SCIENCES↗

A Parallel Graph Environment for Real-World Data Analytics Workflows

Economic competitiveness and national security depend increasingly on the insightful analysis of large data sets. The diversity of real-world data sources and analytic workflows impose challenging hardware and software requirements for parallel graph platforms. The irregular nature of graph methods is not supported well by the deep memory hierarchies of conventional distributed systems, requiring new processor and runtime system designs to tolerate memory and synchronization latencies. Moreover, the efficiency of relational table operations and matrix computations are not attainable when data is stored in common graph data structures. In this paper, we present HAGGLE, a high-performance, scalable data analytics platform. The platform’s hybrid data model supports a variety of distributed, thread-safe data structures, parallel programming constructs, and persistent and streaming data. An abstract runtime layer enables us to map the stack to conventional, distributed computer systems with accelerators. The runtime uses multithreading, active messages, and data aggregation to hide memory and synchronization latencies on large-scale systems.

Graph Analytics↗

Discovering hydrothermalism from Afar: In Situ methane instrumentation and change-point detection for decision-making

Seafloor hydrothermalism plays a critical role in fundamental interactions between geochemical and biological processes in the deep ocean. A significant number of hydrothermal vents are hypothesized to exist, but many of these remain undiscovered due in part to the difficulty of detecting hydrothermalism using standard sensors on rosettes towed in the water column or robotic platforms performing surveys. Here, we use in situ methane sensors to complement standard sensing technology for hydrothermalism discovery and compare sensors on a towed rosette and an autonomous underwater vehicle (AUV) during a 17 km long transect in the Northern Guaymas Basin in the Gulf of California. This transect spatially intersected with a known hydrothermally active venting site. These data show that methane signalled possible hydrothermal-activity 1.5–3 km laterally (100–150 m vertically) from a known vent. Methane as a signal for hydrothermalism performed similarly to standard turbidity sensors (plume detection 2.2–3.3 km from reference source), and more sensitively and clearly than temperature, salinity, and oxygen instruments which readily respond to physical mixing in background seawater. We additionally introduce change-point detection algorithms—streaming cross-correlation and regime identification—as a means of real-time hydrothermalism discovery and discuss related data supervision technologies that could be used in planning, executing, and monitoring explorative surveys for hydrothermalism.

58 GEOSCIENCES↗

182 W (𝑛,2⁢𝑛)⁢ 181 W cross-section data from threshold to 15 MeV

Measurements of the 182 W(n, 2n) 181 W cross section have been performed in the neutron energy range between 8 and 15 MeV using the activation technique. Such data are needed to help interpret results of laser shots at the National Ignition Facility using a new DT capsule design, featuring a high-Z inner shell, with tungsten as the favored material, and an outer shell made of a low-Z material. Our data are in very good agreement with the previous data of Frehaut et al., which are based on a different technique, and in fair agreement with the ENDF/B-VIII.0 and the JEFF-3.3 evaluations.

150 ≤ A ≤ 189↗

Toward a Multimodal-Deep Learning Retrieval System for Monitoring Nuclear Proliferation Activities

As the amount of available data increases, the human ability to locate, process, and analyze it is strained and eventually overwhelmed. To address this challenge for nonproliferation analysts, the authors have been creating a large-scale multimodal retrieval system to help analysts triage and search open source science, technology, and news data for indicators of nuclear proliferation capabilities and activities. The system relies on a set of deep neural networks (DNNs) trained to evaluate conceptual similarities across data modalities, such as text, image, and video. These DNNs can be used to search and prioritize data, according to a nuclear fuel cycle (NFC) process template, that are conceptually closest to the seed query items regardless of data modality. The DNNs have been trained to map conceptually related words, sentences, and images to nearby points in a multimodal feature space, enabling intra- and intermodal retrieval via nearest-neighbor calculations to seed query points. The authors evaluate the system’s ability to retrieve NFC-related data that have been purposely hidden in collections of unrelated background data. They demonstrate quantitative and qualitative results for text-to-image, image-to-image, and image-to-video retrievals. This paper discusses data challenges confronting nonproliferation analysts, describes the DNNs designed to retrieve multimodal data that are proximal in the semantic space, and demonstrates their effectiveness by applying the DNNs to nonproliferation-specific multimodal data sets.

97 MATHEMATICS AND COMPUTING↗

On the Operando Structure of Ruthenium Oxides during the Oxygen Evolution Reaction in Acidic Media

In the search for rational design strategies for oxygen evolution reaction (OER) catalysts, linking the catalyst structure to activity and stability is key. However, highly active catalysts such as IrO x and RuO x undergo structural changes under OER conditions, and hence, structure–activity–stability relationships need to take into account the operando structure of the catalyst. Under the highly anodic conditions of the oxygen evolution reaction (OER), electrocatalysts are often converted into an active form. Here, we studied this activation for amorphous and crystalline ruthenium oxide using X-ray absorption spectroscopy (XAS) and electrochemical scanning electron microscopy (EC-SEM). We tracked the evolution of surface oxygen species in ruthenium oxides while in parallel mapping the oxidation state of the Ru atoms to draw a complete picture of the oxidation events that lead to the OER active structure. Our data show that a large fraction of the OH groups in the oxide are deprotonated under OER conditions, leading to a highly oxidized active material. The oxidation is centered not only on the Ru atoms but also on the oxygen lattice. This oxygen lattice activation is particularly strong for amorphous RuO x . We propose that this property is key for the high activity and low stability observed for amorphous ruthenium oxide.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Utah FORGE: Wells 16A(78)-32 and 16B(78)-32 Stimulation Program Report - May 2024

This dataset consists of a comprehensive report documenting the stimulation program conducted in May 2024 on Utah FORGE wells 16A(78)-32 and 16B(78)-32. It includes detailed accounts of operational and scientific objectives, stimulation methodologies, and testing outcomes. The report describes the hydraulic fracturing activities, equipment setups, proppant and fluid usage, and the execution of a nine-hour circulation test. It also includes observations from seismic and fiber optic monitoring systems, providing data on microseismic activity and fracture propagation. Detailed parameters for each stimulation stage are provided, alongside operational challenges and solutions. The dataset includes analyses of injection and production rates, well temperatures, and pressure data, supported by graphical illustrations and logs.

15 GEOTHERMAL ENERGY↗