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At least 613 records · Page 34

The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data

The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

X-ray Thomson scattering absolute intensity from the f-sum rule in the imaginary-time domain

We present a formally exact and simulation-free approach for the normalization of X-ray Thomson scattering (XRTS) spectra based on the f-sum rule of the imaginary-time correlation function (ITCF). Our method works for any degree of collectivity, over a broad range of temperatures, and is applicable even in nonequilibrium situations. In addition to giving us model-free access to electronic correlations, this new approach opens up the intriguing possibility to extract a plethora of physical properties from the ITCF based on XRTS experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Computation of the expectation value of the spin operator S^ 2 for the spin-flip Bethe–Salpeter equation

Spin-flip (SF) methods applied to excited-state approaches like the Bethe–Salpeter equation allow access to the excitation energies of open-shell systems, such as molecules and defects in solids. The eigenstates of these solutions, however, are generally not eigenstates of the spin operator S^ 2 . Even for simple cases where the excitation vector is expected to be, for example, a triplet state, the value of S^ 2 may be found to differ from 2.00; this difference is called 'spin contamination'. The expectation values S^ 2 must be computed for each excitation vector, to assist with the characterization of the particular excitation and to determine the amount of spin contamination of the state. Here, our aim is to provide for the first time in the SF methods literature a comprehensive resource on the derivation of the formulas for S^ 2 as well as its computational implementation. After a brief discussion of the theory of the SF Bethe–Salpeter equation (BSE) and some examples further illustrating the need for calculating S^ 2 , we present the derivation for the general equation for computing S^ 2 with the eigenvectors from an SF-BSE calculation, how it is implemented in a Python script, and timing information on how this calculation scales with the size of the SF-BSE Hamiltonian.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Quantum Monte Carlo studies of a trimer scaling function with microscopic two- and three-body interactions

Here, we present an energy scaling function to predict, in a specific range, the energy of bosonic trimers with large scattering lengths and finite range interactions, which is validated by quantum Monte Carlo calculations using microscopic Hamiltonians with two- and three-body potentials. The proposed scaling function depends on the scattering length, effective range, and a reference energy, which we chose as the trimer energy at unitarity. We obtained the scaling function as a limit cycle from the solution of the renormalized zero-range model with effective range corrections. We proposed a simple parametrization of the energy scaling function. Besides the intrinsic interest in theoretical and experimental investigations, this scaling function allows one to probe Efimov physics with only the trimer ground states, which may open opportunities to identify Efimov trimers whenever access to excited states is limited.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Demonstrating SolarPILOT’s Python API Through Heliostat Optimal Aimpoint Strategy Use Case

SolarPILOT is a software package that generates solar field layouts and characterizes the optical performance of concentrating solar power (CSP) tower systems. SolarPILOT was developed by the National Renewable Energy Laboratory (NREL) as a stand-alone desktop application but has also been incorporated into NREL’s1 System Advisor Model (SAM) in a simplified format. Prior means for user interaction with SolarPILOT have included the application’s graphical interface, the SAM routines with limited configurability, and through a built-in scripting language called “LK.” This paper presents a new, full-featured, Python-based application programmable interface (API) for SolarPILOT, which we hereafter refer to as CoPylot. CoPylot provides access to all SolarPILOT’s capabilities to generate and characterize power tower CSP systems seamlessly through Python. Supported capabilities include (i) creating and destroying a model instance with message reporting tools; (ii) accessing and setting any SolarPILOT variable including custom land boundaries for field layouts; (iii) programmatically managing receiver and heliostat objects with varied attributes for systems with multiple receiver or heliostat types; (iv) generating, assigning, and modifying solar field layouts including the ability to set individual heliostat locations, aimpoints, soiling rates, and reflectivity levels; (v) simulating solar field performance; (vi) returning detailed results describing performance of individual heliostats, the aggregate field, and receiver flux distribution; and, (vii) exporting Python-based model instances to multiple file formats. CoPylot enables Python users to perform detailed CSP tower analysis utilizing either the Hermite expansion technique (analytical) or the SolTrace ray-tracing engine. In addition to CoPylot’s functionality, Python users have access to the over 100,000 open-source libraries to develop, analyze, optimize, and visualize power tower CSP research. This enables CSP researchers to perform analysis that was previously not possible through SolarPILOT’s existing interfaces. This paper discusses the capabilities of CoPylot and presents a use case wherein we demonstrate optimal solar field aiming strategies.

41 EE - Solar Energy Technologies Office (EE-4S)↗

Targeting the Spike Receptor Binding Domain Class V Cryptic Epitope by an Antibody with Pan-Sarbecovirus Activity

Novel therapeutic monoclonal antibodies (MAbs) must accommodate comprehensive breadth of activity against diverse sarbecoviruses and high neutralization potency to overcome emerging variants. Here, in this study, we report the crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor binding domain (RBD) in complex with MAb WRAIR-2063, a moderate-potency neutralizing antibody with exceptional sarbecovirus breadth, that targets the highly conserved cryptic class V epitope. This epitope overlaps substantially with the spike protein N-terminal domain (NTD) -interacting region and is exposed only when the spike is in the open conformation, with one or more RBDs accessible. WRAIR-2063 binds the RBD of SARS-CoV-2 WA-1, all variants of concern (VoCs), and clade 1 to 4 sarbecoviruses with high affinity, demonstrating the conservation of this epitope and potential resiliency against variation. We compare structural features of additional class V antibodies with their reported neutralization capacity to further explore the utility of the class V epitope as a pan-sarbecovirus vaccine and therapeutic target.

60 APPLIED LIFE SCIENCES↗

A Small, Low Cost Event-Driven Architecture for Spiking Neural Networks on FPGAs

Currently, there is a lack of availability of low cost, low power neuromorphic hardware. In this work, we introduce the μCaspian architecture along with an associated development PCB design which provides a low cost and SWaP (size, weight, and power) optimized neuromorphic hardware platform. Further, our proposed system only uses commercial off the shelf components and an open source FPGA workflow to maximize the accessibility of μCaspian to all researchers.

Mitchell, Parker↗

UNNT: A novel Utility for comparing Neural Net and Tree-based models

The use of deep learning (DL) is steadily gaining traction in scientific challenges such as cancer research. Advances in enhanced data generation, machine learning algorithms, and compute infrastructure have led to an acceleration in the use of deep learning in various domains of cancer research such as drug response problems. In our study, we explored tree-based models to improve the accuracy of a single drug response model and demonstrate that tree-based models such as XGBoost (eXtreme Gradient Boosting) have advantages over deep learning models, such as a convolutional neural network (CNN), for single drug response problems. However, comparing models is not a trivial task. To make training and comparing CNNs and XGBoost more accessible to users, we developed an open-source library called UNNT (A novel Utility for comparing Neural Net and Tree-based models). The case studies, in this manuscript, focus on cancer drug response datasets however the application can be used on datasets from other domains, such as chemistry.

59 BASIC BIOLOGICAL SCIENCES↗

The Center for Integrated Nanotechnologies (CINT)

The Center for Integrated Nanotechnologies (CINT) offers world-leading scientific expertise and specialized capabilities to create, characterize, and integrate nanostructured materials at a range of length scales, from nano- to meso-scale. CINT helps scientists perform cutting-edge research in the areas of nanoscience and nanotechnology, providing FREE ACCESS for nonproprietary research. CINT facilities are open to the international research community, including government, academic, and industry researchers. One of CINT's core research areas is in-situ S/TEM experiments. Early capabilities focused on electrical and electrochemical property measurements of materials during high-resolution imaging. More recently, the staff has expanded the available techniques to include gaseous environments (ETEM), liquid-cell, mechanics, ion irradiation, laser ablation, cryogenic, heating, and air-free transfer. In-situ investigations have focused on coupled structure-property measurements on real materials, with the CINT user community expanding many of the in-situ method developments.

36 MATERIALS SCIENCE↗

Exploring Electrocatalysis of Methane on Transition Metal Surfaces

Methane is a potent greenhouse gas because it has a heat-absorbing ability that is 20 times stronger than the better-known carbon dioxide. It is also the dominant component of nature gas (>70%). Its current greenhouse effect is only second to carbon dioxide largely because of its relatively low atmospheric concentration. Alarmingly, however, the latter has seen a 1.5-time increase since 1750, mainly due to anthropogenic livestock farming, coal and natural gas mining, and organic matter decomposing in waste landfills. Mitigating such a trend effectively and efficiently is therefore highly desirable and intensely sought for. This final technical report describes some exciting research progresses made over the last three years supported financially by the aforementioned award. The research conducted focused on exploring electrochemical direct methane to methanol (DMTM) conversion under mild conditions. The goal of research was to explore the possibility of developing potentially game-changing electrocatalysts and electrocatalysis that can convert methane directly to methanol in a most sustainable way for curbing its effect on global warming. Progress has been made in the following three directions. First, by adapting a hydrogen fuel-cell configuration that enables gaseous methane to be transported directly to the electrocatalyst surface, we have overcome the perennial difficulty in measuring activity of methane electro-oxidation at low temperature and ambient pressure that has prevented any meaningful studies of electrocatalysis of methane conversion thus far. Second, we have developed a novel and operational in situ electrochemical infrared (IR) spectral cell for studying electrocatalysis of direct methane to methanol conversion. This novel cell is also expected to alleviate the measuring difficulty caused by low solubility of methane in aqueous electrolyte and low sticking coefficient for methane adsorption onto transition metal surface. It will improve significantly the IR’s signal to noise ratio. Third, we have successfully synthesized nano-sizing copper (Cu) exchanged zeolite mordenite (Cu-ZMOR) and coated it with carbon that enabled electrochemical access to the encaged Cu ions. This opens a door to unravel the chemistry of Cu ions in catalyzing direct methane to methanol conversion under mild experimental conditions. Altogether, these progresses achieved have laid a solid foundation for further exploring electrocatalysis of direct methane to methanol conversion in general where there exists “a plenty of room” for new discoveries and developments.

03 NATURAL GAS↗

Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research

Introduction The agriculture genomics community has numerous data submission standards available, but the standards for describing and storing single-cell (SC, e.g., scRNA- seq) data are comparatively underdeveloped. Methods To bridge this gap, we leveraged recent advancements in human genomics infrastructure, such as the integration of the Human Cell Atlas Data Portal with Terra, a secure, scalable, open-source platform for biomedical researchers to access data, run analysis tools, and collaborate. In parallel, the Single Cell Expression Atlas at EMBL-EBI offers a comprehensive data ingestion portal for high-throughput sequencing datasets, including plants, protists, and animals (including humans). Developing data tools connecting these resources would offer significant advantages to the agricultural genomics community. The FAANG data portal at EMBL-EBI emphasizes delivering rich metadata and highly accurate and reliable annotation of farmed animals but is not computationally linked to either of these resources. Results Herein, we describe a pilot-scale project that determines whether the current FAANG metadata standards for livestock can be used to ingest scRNA-seq datasets into Terra in a manner consistent with HCA Data Portal standards. Importantly, rich scRNA-seq metadata can now be brokered through the FAANG data portal using a semi-automated process, thereby avoiding the need for substantial expert curation. We have further extended the functionality of this tool so that validated and ingested SC files within the HCA Data Portal are transferred to Terra for further analysis. In addition, we verified data ingestion into Terra, hosted on Azure, and demonstrated the use of a workflow to analyze the first ingested porcine scRNA-seq dataset. Additionally, we have also developed prototype tools to visualize the output of scRNA-seq analyses on genome browsers to compare gene expression patterns across tissues and cell populations. This JBrowse tool now features distinct tracks, showcasing PBMC scRNA-seq alongside two bulk RNA-seq experiments. Discussion We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem based on Findable, Accessible, Interoperable, and Reusable (FAIR) SC principles to facilitate SC-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species.

Genetics & Heredity↗

Retainer for laboratory animals

Bio-retainer holds laboratory animals in fixed position for research and clinical experiments. Retainer allows full access to animals and can be rapidly opened and closed to admit and release specimens.

Lee, R. W.↗

Airborne Sunphotometer Studies of Aerosol Properties and Effects, Including Closure Among Satellite, Suborbital Remote, and In situ Measurements

Airborne sunphotometry has been used to measure aerosols from North America, Europe, and Africa in coordination with satellite and in situ measurements in TARFOX (1996), ACE-2 (1997), PRIDE (2000), and SAFARI 2000. Similar coordinated measurements of Asian aerosols are being conducted this spring in ACE-Asia and are planned for North American aerosols this summer in CLAMS. This paper summarizes the approaches used, key results, and implications for aerosol properties and effects, such as single scattering albedo and regional radiative forcing. The approaches exploit the three-dimensional mobility of airborne sunphotometry to access satellite scenes over diverse surfaces (including open ocean with and without sunglint) and to match exactly the atmospheric layers sampled by airborne in situ measurements and other radiometers. These measurements permit tests of the consistency, or closure, among such diverse measurements as aerosol size-resolved chemical composition; number or mass concentration; light extinction, absorption, and scattering (total, hemispheric back and 180 deg.); and radiative fluxes. In this way the airborne sunphotometer measurements provide a key link between satellite and in situ measurements that helps to understand any discrepancies that are found. These comparisons have led to several characteristic results. Typically these include: (1) Better agreement among different types of remote measurements than between remote and in situ measurements. (2) More extinction derived from transmission measurements than from in situ measurements. (3) Larger aerosol absorption inferred from flux radiometry than from in situ measurements. Aerosol intensive properties derived from these closure studies have been combined with satellite-retrieved fields of optical depth to produce fields of regional radiative forcing. We show results for the North Atlantic derived from AVHRR optical depths and aerosol intensive properties from TARFOX and ACE-2. Companion papers show analogous, preliminary results for Asian-Pacific aerosols and results of SAFARI-2000 closure studies on African aerosols.

Russlee, Philip B.↗

Goddard Space Flight Center Spacecraft Magnetic Test Facility Restoration Project

The Goddard Space Flight Center Spacecraft Magnetic Test Facility (SMTF) was constructed in the 1960's for the purpose of simulating geomagnetic and interplanetary magnetic field environments. The facility includes a three axis Braunbek coil system consisting of 12 loops, 4 loops on each of the three orthogonal axes; a remote earth field sensing magnetometer and servo control building; and a remote power control and instrumentation building. The inner coils are 42-foot in diameter and a 10-foot by 10-foot opening through the outer coils accommodates spacecraft access to the test volume. The physical size and precision of the facility are matched by only two other such facilities in the world. The facility was used extensively from the late 1960's until the early 1990's when the requirement for spacecraft level testing diminished. New NASA missions planned under the Living with a Star, Solar Terrestrial Probes, Explorer, and New Millennium Programs include precision, high-resolution magnetometers to obtain magnetic field data that is critical to fulfilling their scientific mission. It is highly likely that future Lunar and Martian exploration missions will also use precision magnetometers to conduct geophysical magnetic surveys. To ensure the success of these missions ground testing using a magnetic test facility such as the GSFC SMTF will be required. This paper describes the history of the facility, the future mission requirements that have renewed the need for spacecraft level magnetic testing, and the plans for restoring the facility to be capable of performing to its original design specifications.

Vernier, Robert↗

NASA's Earth Science Data Systems Standards Process Experiences

NASA has impaneled several internal working groups to provide recommendations to NASA management on ways to evolve and improve Earth Science Data Systems. One of these working groups is the Standards Process Group (SPC). The SPG is drawn from NASA-funded Earth Science Data Systems stakeholders, and it directs a process of community review and evaluation of proposed NASA standards. The working group's goal is to promote interoperability and interuse of NASA Earth Science data through broader use of standards that have proven implementation and operational benefit to NASA Earth science by facilitating the NASA management endorsement of proposed standards. The SPC now has two years of experience with this approach to identification of standards. We will discuss real examples of the different types of candidate standards that have been proposed to NASA's Standards Process Group such as OPeNDAP's Data Access Protocol, the Hierarchical Data Format, and Open Geospatial Consortium's Web Map Server. Each of the three types of proposals requires a different sort of criteria for understanding the broad concepts of "proven implementation" and "operational benefit" in the context of NASA Earth Science data systems. We will discuss how our Standards Process has evolved with our experiences with the three candidate standards.

Ullman, Richard E.↗

Provenance in Data Interoperability for Multi-Sensor Intercomparison

As our inventory of Earth science data sets grows, the ability to compare, merge and fuse multiple datasets grows in importance. This requires a deeper data interoperability than we have now. Efforts such as Open Geospatial Consortium and OPeNDAP (Open-source Project for a Network Data Access Protocol) have broken down format barriers to interoperability; the next challenge is the semantic aspects of the data. Consider the issues when satellite data are merged, cross-calibrated, validated, inter-compared and fused. We must match up data sets that are related, yet different in significant ways: the phenomenon being measured, measurement technique, location in space-time or quality of the measurements. If subtle distinctions between similar measurements are not clear to the user, results can be meaningless or lead to an incorrect interpretation of the data. Most of these distinctions trace to how the data came to be: sensors, processing and quality assessment. For example, monthly averages of satellite-based aerosol measurements often show significant discrepancies, which might be due to differences in spatio- temporal aggregation, sampling issues, sensor biases, algorithm differences or calibration issues. Provenance information must be captured in a semantic framework that allows data inter-use tools to incorporate it and aid in the intervention of comparison or merged products. Semantic web technology allows us to encode our knowledge of measurement characteristics, phenomena measured, space-time representation, and data quality attributes in a well-structured, machine-readable ontology and rulesets. An analysis tool can use this knowledge to show users the provenance-related distrintions between two variables, advising on options for further data processing and analysis. An additional problem for workflows distributed across heterogeneous systems is retrieval and transport of provenance. Provenance may be either embedded within the data payload, or transmitted from server to client in an out-of-band mechanism. The out of band mechanism is more flexible in the richness of provenance information that can be accomodated, but it relies on a persistent framework and can be difficult for legacy clients to use. We are prototyping the embedded model, incorporating provenance within metadata objects in the data payload. Thus, it always remains with the data. The downside is a limit to the size of provenance metadata that we can include, an issue that will eventually need resolution to encompass the richness of provenance information required for daata intercomparison and merging.

Lynnes, Chris↗

Predicting the Sunspot Cycle

The 11-year sunspot cycle was discovered by an amateur astronomer in 1844. Visual and photographic observations of sunspots have been made by both amateurs and professionals over the last 400 years. These observations provide key statistical information about the sunspot cycle that do allow for predictions of future activity. However, sunspots and the sunspot cycle are magnetic in nature. For the last 100 years these magnetic measurements have been acquired and used exclusively by professional astronomers to gain new information about the nature of the solar activity cycle. Recently, magnetic dynamo models have evolved to the stage where they can assimilate past data and provide predictions. With the advent of the Internet and open data policies, amateurs now have equal access to the same data used by professionals and equal opportunities to contribute (but, alas, without pay). This talk will describe some of the more useful prediction techniques and reveal what they say about the intensity of the upcoming sunspot cycle.

Hathaway, David H.↗

A New Look at Data Usage by Using Metadata Attributes as Indicators of Data Quality

This study reviews the key metrics (users, distributed volume, and files) in multiple ways to gain an understanding of the significance of the metadata. Characterizing the usability of data by key metadata elements, such as discipline and study area, will assist in understanding how the user needs have evolved over time. The data usage pattern based on product level provides insight into the level of data quality. In addition, the data metrics by various services, such as the Open-source Project for a Network Data Access Protocol (OPeNDAP) and subsets, address how these services have extended the usage of data. Over-all, this study presents the usage of data and metadata by metrics analyses, which may assist data centers in better supporting the needs of the users.

metadata↗