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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

A Medium‐Sized Paleo‐Tsunami Reconstruction by a Deep Neural Network Processing Sedimentary Deposits

Abstract Reconstructing the magnitude and recurrence time of tsunamis, one of the most destructive and unpredictable natural hazards impacting coastal communities, is essential. While major tsunamis are the most studied due to their disastrous impact, small/medium tsunamis (SMTs) are much more frequent and can still significantly impact the coast. Therefore, SMTs potentially provide an extensive archive of information preserved in the geological record. Analyzing the deposits of small/medium paleo‐tsunamis (SMPTs) opens a window into when their direct observation was unavailable. However, deposits of SMPTs are often degraded, traditional sediment deposition inversion models might fail. Recent research has shown that Deep Neural Networks (DNN) can effectively reconstruct the flow conditions of major tsunamis from their deposits. We evaluate the effectiveness of this approach in reconstructing the characteristics of a recent medium size tsunami (2006 Java) and of a medium paleo‐tsunami (1929 Grand Banks). We successfully reconstruct the flow characteristics of the 2006 Java event and show that an inversion of comparable quality is possible for the 1929 Grand Banks tsunami, despite greater uncertainties due to the deposit degradation. Our research shows that Machine Learning has the potential to unseal the meaning of data of thousands SMPTs.

Batubo, P.↗
DOE OSTI2024

Prediction of the SYM-H Index Using a Bayesian Deep Learning Method With Uncertainty Quantification

We propose a novel deep learning framework, named SYMHnet, which employs a graph neural network and a bidirectional long short-term memory network to cooperatively learn patterns from solar wind and interplanetary magnetic field parameters for short-term forecasts of the SYM-H index based on 1- and 5-min resolution data. SYMHnet takes, as input, the time series of the parameters' values provided by NASA's Space Science Data Coordinated Archive and predicts, as output, the SYM-H index value at time point t + w hours for a given time point t where w is 1 or 2. By incorporating Bayesian inference into the learning framework, SYMHnet can quantify both aleatoric (data) uncertainty and epistemic (model) uncertainty when predicting future SYM-H indices. Experimental results show that SYMHnet works well at quiet time and storm time, for both 1- and 5-min resolution data. The results also show that SYMHnet generally performs better than related machine learning methods. For example, SYMHnet achieves a forecast skill score (FSS) of 0.343 compared to the FSS of 0.074 of a recent gradient boosting machine (GBM) method when predicting SYM-H indices (1 hr in advance) in a large storm (SYM-H = -393 nT) using 5-min resolution data. When predicting the SYM-H indices (2 hr in advance) in the large storm, SYMHnet achieves an FSS of 0.553 compared to the FSS of 0.087 of the GBM method. In addition, SYMHnet can provide results for both data and model uncertainty quantification, whereas the related methods cannot.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

The System for Classification of Low-Pressure Systems (SyCLoPS): An All-In-One Objective Framework for Large-Scale Data Sets

We propose the first unified objective framework (SyCLoPS) for detecting and classifying all types of low-pressure systems (LPSs) in a given data set. We use the state-of-the-art automated feature tracking software TempestExtremes (TE) to detect and track LPS features globally in ERA5 and compute 16 parameters from commonly found atmospheric variables for classification. A Python classifier is implemented to classify all LPSs at once. The framework assigns 16 different labels (classes) to each LPS data point and designates four different types of high-impact LPS tracks, including tracks of tropical cyclone (TC), monsoonal system, subtropical storm and polar low. The classification process involves disentangling high-altitude and drier LPSs, differentiating tropical and non-tropical LPSs using novel criteria, and optimizing for the detection of the four types of high-impact LPS. A comparison of our labels with those in the International Best Track Archive for Climate Stewardship (IBTrACS) revealed an overall accuracy of 95% in distinguishing between tropical systems, extratropical cyclones, and disturbances. SyCLoPS produces a better TC detection skill compared to the previous algorithms, highlighted by an approximately 6% reduction in the false alarm rate compared to the previous TE algorithm. The vertical cross section composite of the four types of high-impact LPS we detect each shows distinct structural characteristics. Finally, we demonstrate that SyCLoPS is valuable for investigating various aspects of LPSs in climate data, such as the evolution of a single LPS track, patterns of LPS frequencies, and precipitation or wind influence associated with a particular LPS class.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Distinct Fracture Mineralogy That is Out of Equilibrium With Modern Groundwaters Provides Important Context for Subsurface Life

Rock fracture surfaces in the crust are essential habitat for microorganisms. Fracture‐groundwater interfaces provide physical substrates for biofilm growth and are sources of carbon, nutrients, and electron donors and acceptors. To better understand geochemical processes impacting fracture surfaces and the subsurface microbiome, we identified fractures in archived rock cores from the Soudan formation, which is known to host saline groundwaters and isolated microbial communities dependent on rock‐water interactions. Cores with open fractures were thin sectioned and studied via electron microprobe and synchrotron X‐ray fluorescence microprobe. Most fracture surfaces had mineralogy distinct from that of the bulk rock. Chlorite minerals were abundant on fracture surfaces and had elemental compositions suggesting deposition during late‐stage hydrothermal alteration. Fracture‐lining chlorites likely limit access to iron oxide and sulfide minerals that are active in subsurface biogeochemical cycles. Calcium‐rich rinds were also observed along fracture edges. These rinds were too thin and poorly ordered to be identified via light microscopy or X‐ray diffraction; however, Ca K‐edge micro‐X‐ray absorption near‐edge structure spectroscopy identified them as carbonates, minerals not observed in the bulk rock. Thermodynamic modeling shows that carbonate precipitation is largely unfavorable in Soudan groundwaters, indicating that fracture edge conditions differed from those in modern water samples. Because of the low carbon concentrations in Soudan groundwaters, carbonate rinds likely play an important role in subsurface carbon cycling and may mark fracture surfaces that once hosted biofilms. Overall, this study suggests that fracture alteration can both play an active role in and suppress rock‐water interactions essential to subsurface life.

36 MATERIALS SCIENCE↗
DOE OSTI2020

RCSB Protein Data Bank tools for 3D structure-guided cancer research: human papillomavirus (HPV) case study

Abstract Atomic-level three-dimensional (3D) structure data for biological macromolecules often prove critical to dissecting and understanding the precise mechanisms of action of cancer-related proteins and their diverse roles in oncogenic transformation, proliferation, and metastasis. They are also used extensively to identify potentially druggable targets and facilitate discovery and development of both small-molecule and biologic drugs that are today benefiting individuals diagnosed with cancer around the world. 3D structures of biomolecules (including proteins, DNA, RNA, and their complexes with one another, drugs, and other small molecules) are freely distributed by the open-access Protein Data Bank (PDB). This global data repository is used by millions of scientists and educators working in the areas of drug discovery, vaccine design, and biomedical and biotechnology research. The US Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) provides an integrated portal to the PDB archive that streamlines access for millions of worldwide PDB data consumers worldwide. Herein, we review online resources made available free of charge by the RCSB PDB to basic and applied researchers, healthcare providers, educators and their students, patients and their families, and the curious public. We exemplify the value of understanding cancer-related proteins in 3D with a case study focused on human papillomavirus.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Orbital stability analysis and photometric characterization of the second Earth Trojan asteroid 2020 XL5

Trojan asteroids are small bodies orbiting around the L 4 or L 5 Lagrangian points of a Sun-planet system. Due to their peculiar orbits, they provide key constraints to the Solar System evolution models. Despite numerous dedicated observational efforts in the last decade, asteroid 2010 TK 7 has been the only known Earth Trojan thus far. Here we confirm that the recently discovered 2020 XL 5 is the second transient Earth Trojan known. To study its orbit, we used archival data from 2012 to 2019 and observed the object in 2021 from three ground-based observatories. Our study of its orbital stability shows that 2020 XL 5 will remain in L 4 for at least 4 000 years. With a photometric analysis we estimate its absolute magnitude to be ${H}_{r}=18.5{8}_{-0.15}^{+0.16}$, and color indices suggestive of a C-complex taxonomy. Assuming an albedo of 0.06 ± 0.03, we obtain a diameter of 1.18 ± 0.08 km, larger than the first known Earth Trojan asteroid.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Evaluating the risk of data loss due to particle radiation damage in a DNA data storage system

DNA data storage is a potential alternative to magnetic tape for archival storage purposes, promising substantial gains in information density. Critical to the success of DNA as a storage media is an understanding of the role of environmental factors on the longevity of the stored information. In this paper, we evaluate the effect of exposure to ionizing particle radiation, a cause of data loss in traditional magnetic media, on the longevity of data in DNA data storage pools. We develop a mass action kinetics model to estimate the rate of damage accumulation in DNA strands due to neutron interactions with both nucleotides and residual water molecules, then utilize the model to evaluate the effect several design parameters of a typical DNA data storage scheme have on expected data longevity. Finally, we experimentally validate our model by exposing dried DNA samples to different levels of neutron irradiation and analyzing the resulting error profile. Our results show that particle radiation is not a significant contributor to data loss in DNA data storage pools under typical storage conditions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Robust collection and processing for label-free single voxel proteomics

With advanced mass spectrometry (MS)-based proteomics, genome-scale proteome coverage can be achieved from bulk tissues. However, such bulk measurement lacks spatial resolution and obscures tissue heterogeneity, precluding proteome mapping of tissue microenvironment. Here we report an integrated $\underline{w}et$ $\underline{c}ollection$ of single microscale tissue voxels and $\underline{S}urfactant$$-assisted$ $\underline{O}ne$-$\underline{P}ot$ voxel processing method termed wcSOP for robust label-free single voxel proteomics. wcSOP capitalizes on buffer droplet-assisted wet collection of a single voxel dissected by LCM into the PCR tube cap and MS-compatible surfactant-assisted one-pot voxel processing in the collection cap. This convenient method allows reproducible label-free quantification of ~900 and ~4,600 proteins for single voxels at 20 µm × 20 µm × 10 µm (close to single cells) and 200 µm × 200 µm × 10 µm (~100 cells) from fresh frozen human spleen tissue, respectively. 100s-1000s of protein signatures were spatially resolved between spleen red and white pulp regions depending on the voxel size. Region-specific signaling pathways were enriched from single voxel proteomics data. To evaluate its broad applicability, we applied wcSOP-MS to two commonly accessible, OCT-embedded and FFPE, human archived tissues. It enabled to identify spatially resolved proteome changes and enriched pathways between diseased (breast cancer tumor or AD amyloid plaque) and adjacent normal regions. Antibody-based CODEX and IHC imaging validated label-free MS quantitation for single voxel analysis. The wcSOP-MS method paves the way for routine robust single voxel proteomics and spatial proteomics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology

Bioimaging data have significant potential for reuse, but unlocking this potential requires systematic archiving of data and metadata in public databases. Here, we propose draft metadata guidelines to begin addressing the needs of diverse communities within light and electron microscopy. We hope this publication and the proposed Recommended Metadata for Biological Images (REMBI) will stimulate discussions about their implementation and future extension.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A harmonized global nighttime light dataset 1992–2018

Nighttime light (NTL) data from the Defense Meteorological Satellite Program (DMSP)/Operational Linescan System (OLS) and the Visible Infrared Imaging Radiometer Suite (VIIRS) on the Suomi National Polar-orbiting Partnership satellite provide a great opportunity for monitoring human activities from regional to global scales. Despite the valuable records of nightscape from DMSP (1992–2013) and VIIRS (2012–2018), the potential of the historical archive of NTL observations has not been fully explored because of the severe inconsistency between DMSP and VIIRS. In this study, we generated an integrated and consistent NTL dataset at the global scale by harmonizing the inter-calibrated NTL observations from the DMSP data and the simulated DMSP-like NTL observations from the VIIRS data. The generated global DMSP NTL time-series data (1992–2018) show consistent temporal trends. This temporally extended DMSP NTL dataset provides valuable support for various studies related to human activities such as electricity consumption and urban extent dynamics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Enabling FAIR data in Earth and environmental science with community-centric (meta)data reporting formats

Abstract Research can be more transparent and collaborative by using Findable, Accessible, Interoperable, and Reusable (FAIR) principles to publish Earth and environmental science data. Reporting formats—instructions, templates, and tools for consistently formatting data within a discipline—can help make data more accessible and reusable. However, the immense diversity of data types across Earth science disciplines makes development and adoption challenging. Here, we describe 11 community reporting formats for a diverse set of Earth science (meta)data including cross-domain metadata (dataset metadata, location metadata, sample metadata), file-formatting guidelines (file-level metadata, CSV files, terrestrial model data archiving), and domain-specific reporting formats for some biological, geochemical, and hydrological data (amplicon abundance tables, leaf-level gas exchange, soil respiration, water and sediment chemistry, sensor-based hydrologic measurements). More broadly, we provide guidelines that communities can use to create new (meta)data formats that integrate with their scientific workflows. Such reporting formats have the potential to accelerate scientific discovery and predictions by making it easier for data contributors to provide (meta)data that are more interoperable and reusable.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

A large expert-curated cryo-EM image dataset for machine learning protein particle picking

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of biological macromolecular complexes. Picking single-protein particles from cryo-EM micrographs is a crucial step in reconstructing protein structures. However, the widely used template-based particle picking process is labor-intensive and time-consuming. Though machine learning and artificial intelligence (AI) based particle picking can potentially automate the process, its development is hindered by lack of large, high-quality labelled training data. To address this bottleneck, we present CryoPPP, a large, diverse, expert-curated cryo-EM image dataset for protein particle picking and analysis. It consists of labelled cryo-EM micrographs (images) of 34 representative protein datasets selected from the Electron Microscopy Public Image Archive (EMPIAR). The dataset is 2.6 terabytes and includes 9,893 high-resolution micrographs with labelled protein particle coordinates. The labelling process was rigorously validated through 2D particle class validation and 3D density map validation with the gold standard. The dataset is expected to greatly facilitate the development of both AI and classical methods for automated cryo-EM protein particle picking.

42 ENGINEERING↗
DOE OSTI2023

Proof of principle study: synchrotron X-ray fluorescence microscopy for identification of previously radioactive microparticles and elemental mapping of FFPE tissues

Biobanks containing formalin-fixed, paraffin-embedded (FFPE) tissues from animals and human atomic-bomb survivors exposed to radioactive particulates remain a vital resource for understanding the molecular effects of radiation exposure. These samples are often decades old and prepared using harsh fixation processes which limit sample imaging options. Optical imaging of hematoxylin and eosin (H&E) stained tissues may be the only feasible processing option, however, H&E images provide no information about radioactive microparticles or radioactive history. Synchrotron X-ray fluorescence microscopy (XFM) is a robust, non-destructive, semi-quantitative technique for elemental mapping and identifying candidate chemical element biomarkers in FFPE tissues. Still, XFM has never been used to uncover distribution of formerly radioactive micro-particulates in FFPE canine specimens collected more than 30 years ago. In this work, we demonstrate the first use of low-, medium-, and high-resolution XFM to generate 2D elemental maps of ~ 35-year-old, canine FFPE lung and lymph node specimens stored in the Northwestern University Radiobiology Archive documenting distribution of formerly radioactive micro-particulates. Additionally, we use XFM to identify individual microparticles and detect daughter products of radioactive decay. The results of this proof-of-principle study support the use of XFM to map chemical element composition in historic FFPE specimens and conduct radioactive micro-particulate forensics.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2023

Mapping canopy traits over Québec using airborne and spaceborne imaging spectroscopy

Abstract The advent of new spaceborne imaging spectrometers offers new opportunities for ecologists to map vegetation traits at global scales. However, to date most imaging spectroscopy studies exploiting satellite spectrometers have been constrained to the landscape scale. In this paper we present a new method to map vegetation traits at the landscape scale and upscale trait maps to the continental level, using historical spaceborne imaging spectroscopy (Hyperion) to derive estimates of leaf mass per area, nitrogen, and carbon concentrations of forests in Québec, Canada. We compare estimates for each species with reference field values and obtain good agreement both at the landscape and continental scales, with patterns consistent with the leaf economic spectrum. By exploiting the Hyperion satellite archive to map these traits and successfully upscale the estimates to the continental scale, we demonstrate the great potential of recent and upcoming spaceborne spectrometers to benefit plant biodiversity monitoring and conservation efforts.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Planck intermediate results

In this work, we describe an extension of the most recent version of the Planck Catalogue of Compact Sources (PCCS2), produced using a new multi-band Bayesian Extraction and Estimation Package (BeeP). BeeP assumes that the compact sources present in PCCS2 at 857 GHz have a dust-like spectral energy distribution (SED), which leads to emission at both lower and higher frequencies, and adjusts the parameters of the source and its SED to fit the emission observed in Planck’s three highest frequency channels at 353, 545, and 857 GHz, as well as the IRIS map at 3000 GHz. In order to reduce confusion regarding diffuse cirrus emission, BeeP’s data model includes a description of the background emission surrounding each source, and it adjusts the confidence in the source parameter extraction based on the statistical properties of the spatial distribution of the background emission. BeeP produces the following three new sets of parameters for each source: (a) fits to a modified blackbody (MBB) thermal emission model of the source; (b) SED-independent source flux densities at each frequency considered; and (c) fits to an MBB model of the background in which the source is embedded. BeeP also calculates, for each source, a reliability parameter, which takes into account confusion due to the surrounding cirrus. This parameter can be used to extract sub-samples of high-frequency sources with statistically well-understood properties. We define a high-reliability subset (BeeP/base), containing 26 083 sources (54.1% of the total PCCS2 catalogue), the majority of which have no information on reliability in the PCCS2. We describe the characteristics of this specific high-quality subset of PCCS2 and its validation against other data sets, specifically for: the sub-sample of PCCS2 located in low-cirrus areas; the Planck Catalogue of Galactic Cold Clumps; the Herschel GAMA15-field catalogue; and the temperature- and spectral-index-reconstructed dust maps obtained with Planck’s Generalized Needlet Internal Linear Combination method. The results of the BeeP extension of PCCS2, which are made publicly available via the Planck Legacy Archive, will enable the study of the thermal properties of well-defined samples of compact Galactic and extragalactic dusty sources.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Velocity dispersion and dynamical masses for 388 galaxy clusters and groups

The second catalogue of Planck Sunyaev-Zeldovich (SZ) sources, hereafter PSZ2, represents the largest galaxy cluster sample selected by means of their SZ signature in a full-sky survey. For this work, using telescopes at the Canary Island observatories, we conducted the long-term observational program 128- MULTIPLE-16/15B (hereafter LP15), a large and complete optical follow-up campaign of all the unidentified PSZ2 sources in the northern sky, with declinations above –15° and no correspondence in the first Planck catalogue PSZ1. This paper is the third and last in the series of LP15 results, after Streblyanska et al. (2019, A&A, 628, A13) and Aguado-Barahona et al. (2019, A&A, 631, A148), and presents all the spectroscopic observations of the full program. We complement these LP15 spectroscopic results with Sloan Digital Sky Survey archival data and other observations from a previous program (ITP13-08), and present a catalogue of 388 clusters and groups of galaxies including estimates of their velocity dispersion. The majority of them (356) are optical counterparts of PSZ2 sources. A subset of 297 of those clusters are used to construct the M SZ – M dyn scaling relation based on the estimated SZ mass from Planck measurements and our dynamical mass estimates. We discuss and correct for different statistical and physical biases in the estimation of the masses, such as the Eddington bias when estimating M SZ and the aperture and the number of galaxies used to calculate M dyn . The SZ-to-dynamical mass ratio for those 297 PSZ2 clusters is (1 – B) = 0.80 ± 0.04 (stat) ± 0.05 (sys), with only marginal evidence for a possible mass dependence for this factor. Our value is consistent with previous results in the literature, but is associated with a significantly smaller uncertainty due to the use of the largest sample size for this type of study.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Velocity dispersion and dynamical mass for 270 galaxy clusters in the Planck PSZ1 catalogue

Here, we present the velocity dispersion and dynamical mass estimates for 270 galaxy clusters included in the first Planck Sunyaev-Zeldovich (SZ) source catalogue, the PSZ1. Part of the results presented here were achieved during a two-year observational program, the ITP, developed at the Roque de los Muchachos Observatory (La Palma, Spain). In the ITP we carried out a systematic optical follow-up campaign of all the 212 unidentified PSZ1 sources in the northern sky that have a declination above –15° and are without known counterparts at the time of the publication of the catalogue. We present for the first time the velocity dispersion and dynamical mass of 58 of these ITP PSZ1 clusters, plus 35 newly discovered clusters that are not associated with the PSZ1 catalogue. Using Sloan Digital Sky Survey archival data, we extend this sample, including 212 already confirmed PSZ1 clusters in the northern sky. Using a subset of 207 of these galaxy clusters, we constrained the M SZ –M dyn scaling relation, finding a mass bias of (1 – B) = 0.83 ± 0.07(stat) ± 0.02(sys). We show that this value is consistent with other results in the literature that were obtained with different methods (X-ray, dynamical masses, or weak-lensing mass proxies). This result cannot dissolve the tension between primordial cosmic microwave background anisotropies and cluster number counts in the Ω M –σ 8 plane.

79 ASTRONOMY AND ASTROPHYSICS↗