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At least 1,405 records · Page 78

Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes

Host-associated microbial communities (microbiomes) play critical roles in human, animal, and plant health and development. However, interactions between the host, members of the microbiome, and invading pathogens are in most cases still poorly understood. Such interactions are multidimensional and can alter the taxonomic composition and/or the functional metabolic activities of the microbiome in response to disease or treatment conditions. For example, after 2 days of antibiotic treatment, the mouse gut microbiome is altered and more susceptible to invasion by the pathogen Clostridioides difficile. Studies of these multidimensional interactions have been fueled by the ability to use high-throughput sequencing of phylogenetic marker genes to profile microbial community composition and shotgun metagenomics to profile functional potential. However, many protein-coding genes predicted from metagenomes are not necessarily expressed under a given condition, and thus, it is difficult to assess the activities and functional interactions in microbial communities based on DNA sequencing data alone. The physiological and pathological processes expressed in these communities under specific conditions are better reflected by the abundances of transcripts or proteins. In this Pearl, we provide a brief introduction to metaproteomics, which is a tool for the large-scale analysis of proteins in microbiomes that allows researchers to address a diversity of questions related to functions and interactions in microbiomes. The term “metaproteomics” was first used in 2004 for “the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time”, and since then, a large array of metaproteomics approaches have been developed. Our objective in this Pearl is to highlight what we feel are 5 essential elements to be considered for a metaproteomics research campaign and to introduce nonexpert readers to the topic without going into too much technical detail.

59 BASIC BIOLOGICAL SCIENCES↗

TX$^2$: Transformer eXplainability and eXploration

The Transformer eXplainability and eXploration (Martindale & Stewart, 2021), or TX 2 software package, is a library designed for artificial intelligence researchers to better understand the performance of transformer models (Vaswani et al., 2017) used for sequence classification. The tool is capable of integrating with a trained transformer model and a dataset split into training and testing populations to produce an ipywidget (Project Jupyter Contributors, 2021) dashboard with a number of visualizations to understand model performance with an emphasis on explainability and interpretability. The TX 2 package is primarily intended to integrate into a workflow centered around Jupyter Notebooks (Kluyver et al., 2016), and currently assumes the use of PyTorch (Paszke et al., 2019) and Hugging Face transformers library (Wolf et al., 2020). The dashboard includes visualization and data exploration features to aid researchers, including an interactive UMAP embedding graph (McInnes et al., 2018) to understand classification clusters, a word salience map that can be updated as researchers alter textual entries in near real time, a set of tools to understand word frequency and importance based on the clusters in the UMAP embedding graph, and a set of traditional confusion matrix analysis tools.

97 MATHEMATICS AND COMPUTING↗

gcamfaostat: An R package to prepare, process, and synthesize FAOSTAT data for global agroeconomic and multisector dynamic modeling

The gcamfaostat R package is designed for the preparation, processing, and synthesis of the Food and Agriculture Organization (FAO) Statistics (FAOSTAT) agroeconomic data. The primary purpose is to facilitate FAOSTAT data use in global economic and multisector dynamic models while ensuring transparency, traceability, and reproducibility. Here, we provide an overview of the development of gcamfaostat (v1.0) and demonstrate its capabilities in generating and maintaining agroeconomic data required for the Global Change Analysis Model (GCAM). Our initiative seeks to enhance the quality and accessibility of data for the global agroeconomic modeling community, with the aim of fostering more robust and harmonized outcomes in a collaborative, efficient, and open-source framework. One of the important features of the package is the possibility to construct the FAO Food Balance Sheets at the disaggregated commodity level (with over 500 commodities), which provides a comprehensive and detailed data input for a variety of analytical and modeling applications. The processed data and visualizations offered by gcamfaostat can also be valuable to a broader audience interested in gaining insights into the intricacies of global agriculture.

97 MATHEMATICS AND COMPUTING↗

Mobility Data and Models Informing Smart Cities

Using emerging data platforms, new mobility technologies, and travel demand models (TDMs), researchers, industry, and communities seek to improve the quality of transportation while maximizing the energy efficiency, equity, and safety of transportation services. As transportation may soon reach over 30% of U.S. energy consumption and with urban areas representing an increasing proportion of the U.S. population (>80% since 2010), a critical need exists to engage in urban data science-informed approaches to enhancing mobility. The objective of this study is to explore and document how aspiring Smart Cities are using data and models to inform mobility and energy initiatives within Smart City programs and in so doing identify gaps in knowledge and processes guiding Smart City mobility investment strategies, programs, projects, and pilots. A primary focus of the Smart Cities studied was the creation of an integrated data sharing environment approach. Most of these systems are being developed in parallel with multiple new data analysis tools, while regional metropolitan planning organizations continue to slowly evolve TDMs to take into account impacts of long-term strategies for emerging mobility technologies and services. Smart City initiatives in the United States have keen interests in leveraging knowledge and research on the mobility benefits and risks of automated, connected, efficient/electric, and shared on-demand mobility services; and understanding the related energy, environmental, economic, and societal impacts of these shifts. The results serve to identify key gaps in data, knowledge, and methods required to advance energy efficient urban mobility innovation, and to enable research and analysis collaboration between Smart Cities and the U.S. Department of Energy's efforts enabling new Systems and Modeling for Accelerated Research in Transportation (SMART) Mobility.

33 ADVANCED PROPULSION SYSTEMS↗

2019 Quantum Materials Young Investigators Workshop Report

The fourth edition of the workshop “Quantum Materials Young Investigators” was held June 6-7, 2019 at the Oak Ridge National Laboratory (ORNL). This workshop followed up on previous meetings that took place at ORNL starting in 2016. This important series of annual workshops, organized by Adam Aczel and Stuart Calder, ensures continuous engagement with the early career principal investigators (PIs) of the quantum materials neutron scattering community. Through a series of short scientific talks presented by the external PIs, members of the Neutron Scattering Division (NSD) learn about their scientific interests and needs. Presentations from ORNL staff members also help to inform the external PIs about the current state of ORNL’s quantum materials neutron scattering program. Topics covered include the current instrument suites, sample environment, data reduction, visualization, and analysis, and future neutron scattering and complementary capabilities. Feedback is solicited from the external PIs in all these key areas and communicated to NSD management in the form of a workshop report. This workshop series also helps to foster collaborations between NSD scientists and the research groups of the external PIs and plays an important role in attracting new neutron scattering users.

43 PARTICLE ACCELERATORS↗

GDSA Framework Development and Process Model Integration FY2022

The Spent Fuel and Waste Science and Technology (SFWST) Campaign of the U.S. Department of Energy (DOE) Office of Nuclear Energy (NE), Office of Spent Fuel & Waste Disposition (SFWD) is conducting research and development (R&D) on geologic disposal of spent nuclear fuel (SNF) and high-level nuclear waste (HLW). A high priority for SFWST disposal R&D is disposal system modeling (Sassani et al. 2021). The SFWST Geologic Disposal Safety Assessment (GDSA) work package is charged with developing a disposal system modeling and analysis capability for evaluating generic disposal system performance for nuclear waste in geologic media. This report describes fiscal year (FY) 2022 advances of the Geologic Disposal Safety Assessment (GDSA) performance assessment (PA) development groups of the SFWST Campaign. The common mission of these groups is to develop a geologic disposal system modeling capability for nuclear waste that can be used to assess probabilistically the performance of generic disposal options and generic sites. The modeling capability under development is called GDSA Framework (pa.sandia.gov). GDSA Framework is a coordinated set of codes and databases designed for probabilistically simulating the release and transport of disposed radionuclides from a repository to the biosphere for post-closure performance assessment. Primary components of GDSA Framework include PFLOTRAN to simulate the major features, events, and processes (FEPs) over time, Dakota to propagate uncertainty and analyze sensitivities, meshing codes to define the domain, and various other software for rendering properties, processing data, and visualizing results.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

2022 Quantum Materials Young Investigators Workshop Report

The fifth edition of the workshop “Quantum Materials Young Investigators” was held August 18-19, 2022 at the Oak Ridge National Laboratory (ORNL). This workshop followed up on previous meetings that took place at ORNL starting in 2016. This important series of annual workshops, organized by Adam Aczel and Stuart Calder, ensures continuous engagement with the early career principal investigators (PIs) of the quantum materials neutron scattering community. Through a series of short scientific talks presented by the external PIs, members of the Neutron Scattering Division (NSD) learn about their scientific interests and needs. Presentations from ORNL staff members also help to inform the external PIs about the current state of ORNL’s quantum materials neutron scattering program. Topics covered include neutron scattering instruments, sample environment, neutron polarization, data reduction, visualization, and analysis, and future neutron scattering and complementary capabilities. Feedback is solicited from the external PIs in some or all of these key areas and communicated to NSD management in the form of a workshop report. This workshop series also helps to foster collaborations between NSD scientists and the research groups of the external PIs and plays an important role in attracting new neutron scattering users.

36 MATERIALS SCIENCE↗

Multi-Scale Characterization of Porosity and Cracks in Silicon Carbide Cladding after Transient Reactor Test Facility Irradiation

Silicon carbide (SiC) ceramic matrix composite (CMC) cladding is currently being pursued as one of the leading candidates for accident-tolerant fuel (ATF) cladding for light water reactor applications. The morphology of fabrication defects, including the size and shape of voids, is one of the key challenges that impacts cladding performance and guarantees reactor safety. Therefore, quantification of defects’ size, location, distribution, and leak paths is critical to determining SiC CMC in-core performance. This research aims to provide quantitative insight into the defect’s distribution under multi-scale characterization at different length scales before and after different Transient Reactor Test Facility (TREAT) irradiation tests. A non-destructive multi-scale evaluation of irradiated SiC will help to assess critical microstructural defects from production and/or experimental testing to better understand and predict overall cladding performance. X-ray computed tomography (XCT), a non-destructive, data-rich characterization technique, is combined with lower length scale electronic microscopic characterization, which provides microscale morphology and structural characterization. This paper discusses a fully automatic workflow to detect and analyze SiC-SiC defects using image processing techniques on 3D X-ray images. Following the XCT data analysis, advanced characterizations from focused ion beam (FIB) and transmission electron microscopy (TEM) were conducted to verify the findings from the XCT data, especially quantitative results from local nano-scale TEM 3D tomography data, which were utilized to complement the 3D XCT results. In this work, three SiC samples (two irradiated and one unirradiated) provided by General Atomics are investigated. The irradiated samples were irradiated in a way that was expected to induce cracking, and indeed, the automated workflow developed in this work was able to successfully identify and characterize the defects formation in the irradiated samples while detecting no observed cracking in the unirradiated sample. These results demonstrate the value of automated XCT tools to better understand the damage and damage propagation in SiC-SiC structures for nuclear applications.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Discovering New Strong Gravitational Lenses in the DESI Legacy Imaging Surveys

We have conducted a search for new strong gravitational lensing systems in the Dark Energy Spectroscopic Instrument Legacy Imaging Surveys' Data Release 8. We use deep residual neural networks, building on previous work presented by Huang et al. These surveys together cover approximately one-third of the sky visible from the Northern Hemisphere, reaching a z-band AB magnitude of ~22.5. We compile a training sample that consists of known lensing systems as well as non-lenses in the Legacy Surveys and the Dark Energy Survey. After applying our trained neural networks to the survey data, we visually inspect and rank images with probabilities above a threshold. In this work, we present 1210 new strong lens candidates.

79 ASTRONOMY AND ASTROPHYSICS↗

New Strong Gravitational Lenses from the DESI Legacy Imaging Surveys Data Release 9

We have conducted a search for strong gravitational lensing systems in the Dark Energy Spectroscopic Instrument (DESI) Legacy Imaging Surveys Data Release 9. This is the third paper in a series. These surveys together cover ~19,000 deg 2 visible from the Northern Hemisphere, reaching a z-band AB magnitude of ~22.5. We use a deep residual neural network, trained on a compilation of known lensing systems and high-grade candidates as well as nonlenses in the same footprint. After applying our trained neural network to the survey data, we visually inspect and rank images with probabilities above a threshold which has been chosen to balance precision and recall. We have found 1895 lens candidates, of which 1512 are identified for the first time. Combining the discoveries from this work with those from Papers I (335) and II (1210), we have discovered a total of 3057 new candidates in the Legacy Surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

Realized ecological forecast through an interactive Ecological Platform for Assimilating Data (EcoPAD, v1.0) into models

Abstract. Predicting future changes in ecosystem services is not only highly desirable but is also becoming feasible as several forces (e.g., available big data, developed data assimilation (DA) techniques, and advanced cyber-infrastructure) are converging to transform ecological research into quantitative forecasting. To realize ecological forecasting, we have developed an Ecological Platform for Assimilating Data (EcoPAD, v1.0) into models. EcoPAD (v1.0) is a web-based software system that automates data transfer and processing from sensor networks to ecological forecasting through data management, model simulation, data assimilation, forecasting, and visualization. It facilitates interactive data–model integration from which the model is recursively improved through updated data while data are systematically refined under the guidance of model. EcoPAD (v1.0) relies on data from observations, process-oriented models, DA techniques, and the web-based workflow. We applied EcoPAD (v1.0) to the Spruce and Peatland Responses Under Climatic and Environmental change (SPRUCE) experiment in northern Minnesota. The EcoPAD-SPRUCE realizes fully automated data transfer, feeds meteorological data to drive model simulations, assimilates both manually measured and automated sensor data into the Terrestrial ECOsystem (TECO) model, and recursively forecasts the responses of various biophysical and biogeochemical processes to five temperature and two CO 2 treatments in near-real time (weekly). Forecasting with EcoPAD-SPRUCE has revealed that mismatches in forecasting carbon pool dynamics are more related to model (e.g., model structure, parameter, and initial value) than forcing variables, opposite to forecasting flux variables. EcoPAD-SPRUCE quantified acclimations of methane production in response to warming treatments through shifted posterior distributions of the CH 4 :CO 2 ratio and the temperature sensitivity ( Q 10 ) of methane production towards lower values. Different case studies indicated that realistic forecasting of carbon dynamics relies on appropriate model structure, correct parameterization, and accurate external forcing. Moreover, EcoPAD-SPRUCE stimulated active feedbacks between experimenters and modelers to identify model components to be improved and additional measurements to be taken. It has become an interactive model–experiment (ModEx) system and opens a novel avenue for interactive dialogue between modelers and experimenters. Altogether, EcoPAD (v1.0) acts to integrate multiple sources of information and knowledge to best inform ecological forecasting.

54 ENVIRONMENTAL SCIENCES↗

Battery inverter experimental data

The increase in power electronic based generation sources require accurate modeling of inverters. Accurate modeling requires experimental data over wider operation range. We used 30 kW off-the-shelf grid following battery inverter in the experiments. We used controllable AC supply and controllable DC supply to emulate AC and DC side characteristics. The experiments were performed at NREL's Energy Systems Integration Facility. Inverter is tested under 100%, 75%, 50%, 25% load conditions. In the first dataset, for each operating condition, controllable AC source voltage is varied from 0.9 to 1.1 per unit (p.u) with a step value of 0.025 p.u while keeping the frequency at 60 Hz. In the second dataset, under similar load conditions (100%, 75%, 50%, 25% ), the frequency of the controllable AC source voltage was varied from 59 Hz to 61 Hz with a step value of 0.2 Hz. Voltage and frequency range is chosen based on inverter protection. Voltages and currents on DC and AC side are included in the dataset.

24 POWER TRANSMISSION AND DISTRIBUTION↗

PV inverter experimental data

The increase in power electronic based generation sources require accurate modeling of inverters. Accurate modeling requires experimental data over wider operation range. We used 20 kW off-the-shelf grid following PV inverter in the experiments. We used controllable AC supply and controllable DC supply to emulate AC and DC side characteristics. The experiments were performed at NREL's Energy Systems Integration Facility. Due to the limitations of the DC supply used, inverter is tested under 75%, 50%, 25% load conditions (This dataset does not contain 100% load condition). In the first dataset, for each operating condition, controllable AC source voltage is varied from 0.88 to 1.09 per unit (p.u) with a step value of 0.025 p.u while keeping the frequency at 60 Hz. In the second dataset, under similar load conditions (75%, 50%, 25% ), the frequency of the controllable AC source voltage was varied from 59.4 Hz to 60.45 Hz with a step value of 0.2 Hz. Voltage and frequency range is chosen based on inverter protection. Voltages and currents on DC and AC side are included in the dataset.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Split phase inverter data

The increase in power electronic based generation sources require accurate modeling of inverters. Accurate modeling requires experimental data over wider operation range. We used 8.35 kW off-the-shelf grid following split phase PV inverter in the experiments. We used controllable AC supply and controllable DC supply to emulate AC and DC side characteristics. The experiments were performed at NREL's Energy Systems Integration Facility. Inverter is tested under 100%, 75%, 50%, 25% load conditions. In the first dataset, for each operating condition, controllable AC source voltage is varied from 0.9 to 1.1 per unit (p.u) with a step value of 0.025 p.u while keeping the frequency at 60 Hz. In the second dataset, under similar load conditions (100%, 75%, 50%, 25% ), the frequency of the controllable AC source voltage was varied from 59 Hz to 61 Hz with a step value of 0.2 Hz. Voltage and frequency range is chosen based on inverter protection. Voltages and currents on DC and AC side are included in the dataset.

24 POWER TRANSMISSION AND DISTRIBUTION↗

PV Inverter Experimental Dataset Version 2 with 100 Percent Power

The increase in power electronic based generation sources require accurate modeling of inverters. Accurate modeling requires experimental data over wider operation range. We used 20 kW off-the-shelf grid following PV inverter in the experiments. We used controllable AC supply and controllable DC supply to emulate AC and DC side characteristics. The experiments were performed at NREL's Energy Systems Integration Facility. The PV inverter is tested under 100%, 75%, 50%, 25% load conditions. In the first dataset, for each operating condition, controllable AC source voltage is varied from 0.88 to 1.09 per unit (p.u) with a step value of 0.025 p.u while keeping the frequency at 60 Hz. In the second dataset, under similar load conditions (100%, 75%, 50%, 25% ), the frequency of the controllable AC source voltage was varied from 59.4 Hz to 60.45 Hz with a step value of 0.2 Hz. Voltage and frequency range is chosen based on inverter protection. Voltages and currents on DC and AC side are included in the dataset.

14 SOLAR ENERGY↗

Computerized image processing at JPL.

Digital imaging techniques used in sinusoidal frequency response modification with or without computer control and display on operator console

IMAGING TECHNIQUE↗

NASTRAN data generation and management using interactive graphics

A method of using an interactive graphics device to generate a large portion of the input bulk data with visual checks of the structure and the card images is described. The generation starts from GRID and PBAR cards. The visual checks result from a three-dimensional display of the model in any rotated position. By detailing the steps, the time saving and cost effectiveness of this method may be judged, and its potential as a useful tool for the structural analyst may be established.

Smootkatow, M.↗

Fixed base simulator study of an externally blown flap STOL transport airplane during approach and landing

A fixed-base simulator study was conducted to determine the flight characteristics of a representative STOL transport having a high wing and equipped with an external-flow jet flap in combination with four high-bypass-ratio fan-jet engines during the approach and landing. Real-time digital simulation techniques were used. The computer was programed with equations of motion for six degrees of freedom and the aerodynamic inputs were based on measured wind-tunnel data. A visual display of a STOL airport was provided for simulation of the flare and touchdown characteristics. The primary piloting task was an instrument approach to a breakout at a 200-ft ceiling with a visual landing.

Grantham, W. D.↗