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DOE OSTI2026

Causes and consequences of experimental variation in Nicotiana benthamiana transient expression

Infiltration of Agrobacterium tumefaciens into Nicotiana benthamiana has become a foundational technique in plant biology, enabling efficient delivery of transgenes in planta with technical ease, robust signal, and relatively high throughput. Despite transient expression’s prevalence in disciplines such as synthetic biology, little work has been done to describe and address the variability inherent in this system, a concern for experiments that rely on highly quantitative readouts. In a comprehensive analysis of N. benthamiana agroinfiltration experiments, we model sources of variability that affect transient expression. Our findings emphasize the need to validate normalization methods under the specific conditions of each study, as distinct normalization schemes do not always reduce variation either within or between experiments. Using a dataset of 1915 plants collected over three years, we develop a model of variation in N. benthamiana transient expression, using power analysis to determine the number of individual plants required for a given effect size. Drawing on our longitudinal data, these findings inform practical guidelines for minimizing variability through strategic experimental design and power analysis, providing a foundation for more robust and reproducible use of N. benthamiana in quantitative plant biology and synthetic biology applications.

Tang, Sophia N. [Joint BioEnergy Institute (JBEI),↗

DOE OSTI2024

Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures

The advent of single-particle cryo-electron microscopy (cryo-EM) has brought forth a new era of structural biology, enabling the routine determination of large biological molecules and their complexes at atomic resolution. The high-resolution structures of biological macromolecules and their complexes significantly expedite biomedical research and drug discovery. However, automatically and accurately building atomic models from high-resolution cryo-EM density maps is still time-consuming and challenging when template-based models are unavailable. Artificial intelligence (AI) methods such as deep learning trained on limited amount of labeled cryo-EM density maps generate inaccurate atomic models. To address this issue, we created a dataset called Cryo2StructData consisting of 7,600 preprocessed cryo-EM density maps whose voxels are labelled according to their corresponding known atomic structures for training and testing AI methods to build atomic models from cryo-EM density maps. Cryo2StructData is larger than existing, publicly available datasets for training AI methods to build atomic protein structures from cryo-EM density maps. We trained and tested deep learning models on Cryo2StructData to validate its quality showing that it is ready for being used to train and test AI methods for building atomic models.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Applying MALDI-TOF MS to resolve morphologic and genetic similarities between two Dermacentor tick species of public health importance

Abstract Hard ticks (Acari: Ixodidae) have been historically identified by morphological methods which require highly specialized expertise and more recently by DNA-based molecular assays that involve high costs. Although both approaches provide complementary data for tick identification, each method has limitations which restrict their use on large-scale settings such as regional or national tick surveillance programs. To overcome those obstacles, the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been introduced as a cost-efficient method for the identification of various organisms, as it balances performance, speed, and high data output. Here we describe the use of this technology to validate the distinction of two closely relatedDermacentortick species based on the development of the first nationwide MALDI-TOF MS reference database described to date. The dataset obtained from this protein-based approach confirms that tick specimens collected from United States regions west of the Rocky Mountains and identified previously asDermacentor variabilisare the recently described species,Dermacentor similis. Therefore, we propose that this integrative taxonomic tool can facilitate vector and vector-borne pathogen surveillance programs in the United States and elsewhere.

Science & Technology - Other Topics↗

DOE OSTI2026

Monthly Mean In Situ Surface Flux Observations Paired with Satellite-Derived and Reanalysis-Based Flux Data for the Great Lakes Region, 2001–2020

Surface radiative and turbulent heat fluxes over the Great Lakes strongly influence regional hydrological and meteorological processes, and their accurate representation is critical for numerical weather prediction and coupled atmosphere–lake modeling. However, direct flux observations are spatially sparse across the region, so gridded reanalysis and satellite-derived products are often used for climatological analyses and model evaluation despite differences in their flux representations. This dataset provides processed, quality-controlled, monthly mean surface flux observations from the Great Lakes Evaporation Network (GLEN), AmeriFlux, and the National Data Buoy Center, paired with spatiotemporally matched flux estimates from two reanalysis products, the fifth generation European Centre for Medium-Range Weather Forecasts (ECMWF) reanalysis dataset (ERA5) and the Modern Era Reanalysis for Research and Applications, version 2 (MERRA-2), and two satellite-derived products, the Clouds and Earth's Radiant Energy Systems Energy Balanced and Filled (CERES-EBAF) and the Cloud, Albedo and Surface Radiation dataset from AVHRR data - Edition 3 (CLARA-A3). The dataset includes sixteen observational stations with variable temporal coverage within 2001–2020. For each station, a CSV file contains monthly time series of available flux variables, including surface downwelling shortwave radiation (SW), surface downwelling longwave radiation (LW), sensible heat (SH) flux, and latent heat flux (LH), alongside matched gridded product values where available. Columns in the CSV file correspond to different variables sourced from each dataset, with column titles structured as "{dataset}_{variable}". Columns with relevant metadata are also provided in each CSV file, including station latitude and longitude, monthly timestamps, and the name of the sourced observational data. These files are structured for direct use in common analysis tools, including Microsoft Excel, Python pandas, and Python matplotlib. This dataset supports climatological analysis of the Great Lakes regional surface energy budget, evaluation of satellite-derived and reanalysis-based flux products, and development or validation of flux representations in numerical weather prediction and coupled atmosphere–lake models.

Great Lakes↗

DOE OSTI2026

NW-BRaVE T3 Hydroplane Project Close: Project Close-out for T3 Hydroplane Analysis

Thrust 3 of the Northwest Biopreparedness Research in a Virtual Environment was an expansive project including method development, sample collection and sequence analysis. The sampling occurred over a multi-year period to generate metagenomic datasets that inform cyanophage-picocyanobacterial interactions in the Salish Sea across a moderate timeframe and geographical range. Part of the thrust’s aim was to validate how much experimental structural and multiomics work in a model organism (Prochlorococcus Marinus, str. MED4) from thrusts 1 and 2 would carry over into a broader range of related organisms in the natural world, to address a fundamental question in scientific preparation for epidemics: whether and how much experimental information from known and experimentally tractable species can translate to actionable biological information in unknown species. In other words, thrust 3 aimed to find out whether the model organism experiments matter in terms of how organisms interact. This report updates work described in Johnson and Pollock 2025 (1).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Bifacial Vertical Testbed and Ground Irradiance Data in Golden, Colorado

This data was collected for Tonita et al., “Vertical bifacial photovoltaic system model validation: study with field data, various orientations, and latitudes,” for validation of optical models for vertically-oriented photovoltaics under high albedo. Ground irradiance data for vertical PV arrays modeling in agrivoltaics is also provided. The dataset is provided for further use or study as open source. For any questions on the dataset, email silvana.ovaitt@nlr.gov.

14 SOLAR ENERGY↗

NASA NTRS2014

Profiling the SO2 Plume from Volcan Turrialba: Ticosonde Balloon Measurements Compared with OMI and OMPS Retrievals

The summit of Volcan Turrialba (elev. 3340 m) lies less than 50 km upstream in the prevailing easterlies from the Ticosonde balloon launch site at San Jose, Costa Rica, where ECC ozone sondes have been launched regularly since 2005. In 2006 we began to see telltale notches in the ozone profiles in the altitude range between 2 and 6 km. Given the proximity of Turrialba, it seemed likely that SO2 in the volcano's plume was interfering in the chemical reaction in the ECC ozone sonde used to detect ozone. In early 2010, fumarolic activity in the Turrialba crater increased strongly, and the profile notches in our soundings increased in frequency as well, consistent with this hypothesis. In February 2012 we tested a dual ECC sonde system, where an additional sonde is flown on the same payload using a selective SO2 filter. The difference of the measurements in the dual sonde is a direct measure of the amount of SO2 encountered. This first dual sonde passed through the plume, and the data indicated a tropospheric SO2 column of 1.4 DU, comparing favorably with a total column of 1.7 DU in the OMI 3-km linear fit (LF) product at the sonde profile location and at nearly the same time. We are now launching dual sondes on a regular basis with 18 launches in the first 12 months through July 2014; 11 of these have detectable SO2 signals. These soundings have great potential for validation of the Aura OMI and the Suomi-NPP OMPS retrievals of SO2. Here we present the sonde measurements and compare them with two satellite datasets: the Aura OMI Linear Fit (LF) product and the Suomi-NPP OMPS Principal Components Analysis (PCA) boundary layer product. The PCA algorithm reduces retrieval noise and artifacts by more accurately accounting for various interferences in SO2 retrievals such as O3 absorption and rotational Raman scattering. The comparisons with the in situ observations indicate a significant improvement of the PCA algorithm in capturing relatively weak volcanic SO2 signals.

sondes↗

NASA NTRS2019

Local and Downstream Relationships Between Labrador Sea Water Volume and North Atlantic Meridional Overturning Circulation Variability

While it has generally been understood that the production of Labrador Sea Water (LSW) impacts the Atlantic meridional overturning circulation (MOC), this relationship has not been explored extensively nor validated against observations. To explore this relationship, a suite of global ocean and ocean–sea-ice models forced by the same interannually-varying atmospheric dataset, varying in resolution from non-eddy permitting to eddy-permitting (1°–1/4°), is analyzed to investigate the local and downstream relationships between LSW formation and the MOC on interannual to decadal time scales. While all models display a strong relationship between changes in the LSW volume and the MOC in the Labrador Sea, this relationship degrades considerably downstream of the Labrador Sea. In particular, there is no consistent pattern among the models in the North Atlantic subtropical basin over interannual to decadal time scales. Furthermore, the strong response of the MOC in the Labrador Sea to LSW volume changes in that basin may be biased by the overproduction of LSW in many models compared to observations. This analysis shows that changes in LSW volume in the Labrador Sea cannot be clearly and consistently linked to a coherent MOC response across latitudes over interannual to decadal time scales in ocean hindcast simulations of the last half-century. Similarly, no coherent relationships are identified between the MOC and the Labrador Sea mixed layer depth or the density of newly formed LSW across latitudes or across models over interannual to decadal time scales.

Feili Li↗

NASA NTRS2020

Detecting Seasonal Ice Dynamics in Satellite Images

Fully understanding how glaciers respond to environmental change will require new methods to help us identify the onset of ice acceleration events and observe how dynamic signals propagate within glaciers. In particular, observations of ice dynamics on seasonal timescales may offer insights into how a glacier interacts with various forcing mechanisms throughout the year. The task of generating continuous ice velocity time series that resolve seasonal variability is made more difficult by a spotty satellite record that contains no optical observations throughout the dark, polar winters. Furthermore, velocities obtained by feature tracking are marked by high noise when image pairs are separated by short time intervals and contain no direct insights into variability that occurs between images separated by long time intervals. In this paper, we describe a method of analyzing optical or SAR-derived feature-tracked velocities to characterize the magnitude and timing of seasonal ice dynamic variability. Our method is agnostic to data gaps and is able to recover climatological average winter velocities regardless of the availability of direct observations during winter. Using characteristic image acquisition times and error distributions from Antarctic image pairs in the ITS_LIVE dataset, we generate synthetic ice velocity time series, then apply our method to recover imposed magnitudes of seasonal variability within ±1.4 m yr−1. We then validate the techniques by comparing our results to GPS data collected on Russell Glacier in Greenland. The methods presented here may be applied to better understand how ice dynamic signals propagate on seasonal timescales, and what mechanisms control the flow of the world’s ice.

Chad A. Greene↗

NASA NTRS2020

Radiometric approach for the detection of picophytoplankton assemblages across oceanic fronts

Cell abundances of Prochlorococcus, Synechococcus, and autotrophic picoeukaryotes were estimated in surface waters using principal component analysis (PCA) of hyperspectral and multispectral remote-sensing reflectance data. This involved the development of models that employed multilinear correlations between cell abundances across the Atlantic Ocean and a combination of PCA scores and sea surface temperatures. The models retrieve high Prochlorococcus abundances in the Equatorial Convergence Zone and show their numerical dominance in oceanic gyres, with decreases in Prochlorococcus abundances towards temperate waters where Synechococcus flourishes, and an emergence of picoeukaryotes in temperate waters. Fine-scale in-situ sampling across ocean fronts provided a large dynamic range of measurements for the training dataset, which resulted in the successful detection of fine-scale Synechococcus patches. Satellite implementation of the models showed good performance (R(exp 2) > 0.50) when validated against in-situ data from six Atlantic Meridional Transect cruises. The improved relative performance of the hyperspectral models highlights the importance of future high spectral resolution satellite instruments, such as the NASA PACE mission’s Ocean Color Instrument, to extend our spatiotemporal knowledge about ecologically relevant phytoplankton assemblages.

Priscila Kienteca Lange↗

NASA NTRSDate not supplied

Implicit Large-Eddy Simulation of Single-Injector Cooling Flow

The turbulent heat flux vector plays a critical role in aero-propulsion flow. Currently, traditional RANS based methods do not currently have reliable closures which can accurately predict the turbulent transport of heat. Scale Resolving Simulations can provide critical insight into this fundamental fluid mechanism. Large-eddy Simulations (LES) were performed on the single-hole film-cooling experimental configuration from the recent experiments conducted at NASA Glenn Research Center (GRC)[1]. The experiment of Wernet et al. obtained mean and fluctuating temperatures which can be used to validate LES results predicting the turbulent heat flux vector. The FDL3DI flow solver was used to complete simulations of two blowing ratios of the THX - III dataset. A grid sensitivity study was also performed. Initial LES results show promising agreement between the simulation and experimental measurements.

High-Order methods↗

DOE OSTI2025

Validation of the DESI-DR1 3x2-pt analysis: scale cut and shear ratio tests

Combined survey analyses of galaxy clustering and weak gravitational lensing (3x2-pt studies) will allow new and accurate tests of the standard cosmological model. However, careful validation is necessary to ensure that these cosmological constraints are not biased by uncertainties associated with the modelling of astrophysical or systematic effects. In this study we validate the combined 3x2-pt analysis of the Dark Energy Spectroscopic Instrument Data Release 1 (DESI-DR1) spectroscopic galaxy clustering and overlapping weak lensing datasets from the Kilo-Degree Survey (KiDS), the Dark Energy Survey (DES), and the Hyper-Suprime-Cam Survey (HSC). By propagating the modelling uncertainties associated with the non-linear matter power spectrum, non-linear galaxy bias and baryon feedback, we design scale cuts to ensure that measurements of the matter density and the amplitude of the matter power spectrum are biased by less than 30% of the statistical error. We also test the internal consistency of the data and weak lensing systematics by performing new measurements of the lensing shear ratio. We demonstrate that the DESI-DR1 shear ratios can be successfully fit by the same model used to describe cosmic shear correlations, and analyse the additional information that can be extracted about the source redshift distributions and intrinsic alignment parameters. This study serves as crucial preparation for the upcoming cosmological parameter analysis of these datasets.

Emas, N. [Swinburne U., Ctr. Astrophys. Supercompu↗

DOE OSTI2021

Validation of Fault Displacements from Dynamic Rupture Simulations against the Observations from the 1992 Landers Earthquake

ABSTRACT Coseismic fault displacements in large earthquakes have caused significant damage to structures and lifelines on and near fault lines. Coseismic displacements represent a real threat, especially to distributed infrastructure systems. For infrastructure systems that can not avoid active faults, engineering displacement demands are defined using probabilistic fault-displacement hazard analyses (PFDHA). However, PFDHA models are sparse and poorly constrained partly due to the scarcity of detailed fault-displacement observations. Advancements in dynamic rupture simulation methods make them an attractive approach to address this important issue. Because fault displacements can be simulated for various geologic conditions as constrained by current knowledge about earthquake processes, they can be used to supplement the observation datasets. In addition to providing on-fault displacements, when used with appropriate constitutive models for the bulk medium, they can capture off-fault distributed inelastic deformations as well. For viable extrapolation, simulations must first be validated against data. In this article, we summarize the calibration and validation of the dynamic rupture model against the observations of the well-documented 1992 Landers earthquake. We defined a preferred model that reproduces several first-order fault-displacement metrics such as the on-fault partition of the total displacement, the mean fault-zone width, and the location of the peak displacement. Simulated ground motions consistent with the observations ensure that all physics important to modeling have been properly parameterized. For the extrapolation, we generated a suite of dynamic rupture models to quantify expected fault-displacement metrics, their intercorrelations, and magnitude dependencies, which are in part supported by the Landers and other recent earthquakes. Our validation and extrapolation exercise paves the way for using dynamic rupture modeling to quantitatively address fault-displacement hazard on a broader scale. The results are promising and are expected to be useful to inform PFDHA model development.

Geochemistry & Geophysics↗

NASA NTRSDate not supplied

The Multiplatform Precipitation Feature (MPF) Database: Synthesizing Satellite and Ground-Based Precipitation and Lightning Datasets for Convective Studies

NASA’s Lightning Imaging Sensor (LIS) and the Global Precipitation Measurement (GPM) mission have contributed a wealth of data toward global lightning and precipitation studies, respectively. Combining lightning and precipitation datasets leverages their unique insights into deep convective processes that inform about characteristics of convection and its intensity. Recent efforts to synthesize the LIS and GPM datasets prepare the opportunity for unprecedented large-scale, value-added multiplatform analyses of convection. This data synthesis proof-of-concept study elaborates on the creation of a database of reflectivity-based multiplatform precipitation features (MPFs) that capture a combination of information extracted from spatiotemporally coincident lightning and precipitation data within individual storm features. The space-based GPM Dual-frequency Precipitation Radar (DPR) provides a record of precipitation data, while the GPM Validation Network (VN) additionally incorporates ground-based polarimetric Doppler radar data to provide microphysical and kinematic context to DPR data. The LIS instrument onboard the International Space Station has contributed lightning observations since 2017. MPFs encapsulating information from these datasets are created from isolated regions of filtered, smoothed DPR reflectivity data to which ellipses are fit. Each MPF includes feature location, size, and eccentricity information as well as summary reflectivity characteristics. They also include summaries of precipitation microphysics and derived three-dimensional wind available from ground-based radar data. LIS data provides standard lightning characteristics such as flash count and density to each MPF as well as other informative metrics such as flash area and radiance. Each MPF file includes information about the original data from which the MPF and its characteristics were determined, allowing end-user reconstruction of the ellipse and deeper “level I” analysis of captured data. This database of VN-LIS MPFs enables broad statistical analysis of the relationships between the microphysical, kinematic, and electrical properties of convection. Preliminary results from a demonstration of the database will be described as well as ongoing efforts and avenues for future work.

Lightning↗

DOE OSTI2024

EGS Collab Experiment 2: Microseismic Monitoring

This dataset contains continuous seismic waveform data recorded during stimulation and thermal circulation tests for the Enhanced Geothermal Systems (EGS) Collab Experiment #2, conducted from February to September 2022 at the Sanford Underground Research Facility in Lead, South Dakota. This experiment aimed to study and validate models of geothermal systems by injecting high-pressure fluids into rock formations 1200-1500 meters below the surface, inducing microseismic events. The seismic monitoring system included 16 three-component accelerometers and a 24-channel hydrophone array, installed in boreholes surrounding the test area. Data were recorded at high sampling rates using a continuous waveform recording system to monitor seismic activity in real time. The dataset contains the raw data stored in binary format, with files named based on timestamps, and includes calibration certificates for some sensors to facilitate corrections to real units. Users are strongly advised to consult the accompanying detailed report, which outlines the experimental setup, sensor specifications, installation procedures, and data processing methods. The report also describes important nuances, such as the hardware filters on hydrophones, sensor calibration details, and the naming conventions for the recorded data. Proper use of this dataset may require familiarity with seismic data analysis tools, such as the Obspy Python package, and an understanding of the SEED naming conventions used for channel identification.

15 GEOTHERMAL ENERGY↗

NASA NTRSDate not supplied

A Comparative Study of Contrail Frequency Indices and GOES-16 Contrail Data Set

Contrail formations have been shown to contribute to the greenhouse effect: they are practically transparent to incoming solar radiation and do little to reflect heat away from Earth but are highly effective at trapping heat within Earth’s atmosphere. To understand the impact contrails have on climate change, contrail frequency indices (CFIs) can be used as a method to quantify aircraft-induced persistent contrails. These indices are capable of tracking long-term contrail formation and identify regions of airspace with the highest contrail formation rates. In this aper, an algorithm is proposed which is capable of using NASA Sherlock and Global Forecast System (GFS) datasets and computing CFIs over large geographic regions and long temporal intervals using NASA Ames’ High-End Computing Capability (HECC) supercomputing system. CFIs are computed using nowcast weather data and previously flown flight tracks. This paper calculated the CFIs of all twenty Air Route Traffic Control Centers in the National Airspace System on October 28th, 2019 and compared the distribution of non-zero CFIs with observed contrail data collected from GOES-16 Satellite data in order to assess the accuracy of the CFI system as a contrail prediction model. It was ultimately determined that the computed CFIs were broadly distributed in the same way as the GOES-16 contrail data and that the individual CFIs computed at the latitude/longitude points at which GOES-16 contrail masks were available had high precision and recall (at 0.75 and 0.86 respectively). While these validation results bode well for the accuracy of the CFI method, the number of provided GOES-16 masks was quite small. Future work should aim to increase the size of the GOES-16 dataset in order to perform a more comprehensive comparison between these two datasets.

Contrails↗

NASA NTRSDate not supplied

A Comparative Study of Contrail Frequency Indices and GOES-16 Contrail Data Set

Contrails↗

DOE OSTI2025

Performance of wind assessment datasets in United States coastal areas

The atmospheric dynamics that occur near the intersection of land and water offer exciting and challenging opportunities for wind energy deployment in coastal locations. New models and tools are continually being developed in support of wind resource assessment, and three recent products are explored in this work for their performance in representing characteristics of the wind resource at coastal locations: the Global Wind Atlas 3 (GWA3), the 2023 National Offshore Wind dataset (NOW-23), and the wind climate simulations that are a component of the Wind Integration National Dataset (WIND) Toolkit Long-Term Ensemble Dataset (WTK-LED Climate). These relatively new products are freely available and user-friendly so that anyone – from a utility-scale developer to a resident or business owner – can evaluate the potential for wind energy generation at their location of interest. The validations in this work provide guidance on the accuracy of wind resource assessments for coastal customers interested in installing small or midsize wind turbines (≤ 1 MW in capacity) to support energy needs at the residential, business, or community scale, such as the island and remotely located participants of the U.S. Department of Energy's Energy Transitions Initiative Partnership Project. At 23 coastal locations across the United States, dataset performance varies according to different evaluation metrics. All three recent datasets tend to overestimate the observed coastal wind resource. GWA3 produces the smallest annual average wind speed relative errors, whereas WTK-LED Climate is in best agreement in terms of representing diurnal wind speed cycles. NOW-23 is the highest performing of the datasets for representing seasonal and interannual trends in the coastal wind resource. While GWA3 and WTK-LED Climate are relatively insensitive to the dataset output heights selected for wind resource assessment at small and midsize wind turbine hub heights (20–60 m), significant variation in the NOW-23 representation of wind shear across the wind profile in the lowest 100 m of the atmosphere leads to notable differences in wind speed estimates according to the dataset output heights selected for evaluation. GWA3 exhibits challenges in the representation of observed wind speed diurnal cycles at small and midsize turbine hub heights, likely due to the dataset's consistent treatment of hourly wind speed trends regardless of altitude.

17 WIND ENERGY↗