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DOE OSTI2026

Compilation and utilization of a sorghum transcriptome compendium for gene regulatory network analysis and crop trait engineering

Sorghum bicolor (Sorghum) is a drought and heat tolerant C4 grass crop used to produce grain, forage, biofuels, and other bioproducts. Genetic improvement of sorghum hybrid crops is aided by a large and diverse germplasm, sorghum's diploid inbreeding genetics, and a relatively small genome that has facilitated genomic research. Over the past 20 years, the sorghum research community characterized the cytogenetic and recombinant landscapes of sorghum's 10 chromosomes, sequenced and annotated the sorghum genome, and used that information to identify genes/alleles that modulate flowering time, plant height, seed shattering, and other important traits. More recently, >1000 RNA-seq transcriptome profiles were collected from 15 sorghum genotypes to help understand the genetic basis of variation in growth and development of sorghum stems, tillers, roots, and leaves, and the regulation of biosynthetic pathways that produce epicuticular wax, dhurrin, and RFOs, compounds that contribute to sorghum's resilience. Transcriptome studies were designed to identify differentially expressed genes that are co-expressed during development or in response to a treatment to enable construction of gene regulatory networks. Co-expression and network analysis identified transcription factors and their cognate binding sites in target gene promoters and signaling pathways that modulate gene regulatory networks providing gene editing targets for further trait optimization. RNA-seq data from >20 experiments targeting sorghum organs, tissues, cell types, developmental stages, and responses to environmental conditions (i.e., diel, day-length, shading, water-deficit, temperature) has been compiled in a sorghum transcriptome compendium. The goal of this resource paper is to describe compendium content, accessibility, and a compendium data analysis pipeline and to illustrate the types of information that can be derived from the compendium with a focus on the elucidation of gene regulatory networks useful for guiding the improvement of sorghum traits through gene editing.

RNA-seq↗

NASA NTRSDate not supplied

Surface Radiation Budget

The Surface Radiation Budget (SRB) data sets contain global 3-hourly, daily and monthly averages of surface longwave and shortwave radiative properties, cloud amount, and meteorological properties computed using models. The main input data for these models include cloud information, top-of-atmosphere radiances and profiles of atmospheric water vapor and temperature. Some of the input data include Earth Radiation Budget Energy (ERBE) top-of-atmosphere clear-sky albedo and International Satellite Cloud Climatology Project (ISCCP) radiances and cloud amount. SRB parameters derived for the renewable energy community are also available from the Surface meteorology and Solar Energy (SSE) data set. Other SRB data are available from Clouds and the Earth's Radiant Energy System (CERES) and Multi-angle Imaging SpectroRadiometer (MISR). [Mission Objectives] The objective of the SRB Project is to produce and archive a global data set of shortwave (SW) and longwave (LW) surface and top of the atmosphere parameters. The data generated in the SRB project may be used in conjunction with other data sets to facilitate the development of renewable energy resources and increase understanding of radiative properties within the meteorological community. [Temporal_Coverage: Start_Date=1983-07-01; Stop_Date=2005-06-30] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180].

Stackhouse, Paul W.↗

NASA NTRS2006

Foundations of Supply Chain Management for Space Application

Supply Chain Management (SCM) is a key piece of the framework for America's space technology investment as the National Aeronautics and Space Administration (NASA), the aerospace industry, and international partners embark on a bold new vision of human and robotic space exploration beyond Low-Earth-Orbit (LEO). This type of investment is driven by the Agency's need for cost efficient operational support associated with, processing and operating space vehicles and address many of the biggest operational challenge including extremely tight funding profiles, seamless program-to-program transition activities and the reduction of the time gap with human spaceflight capabilities in the post-Shuttle era. An investment of this magnitude is a multiyear task and must include new patterns of thought within the engineering community to respect the importance of SCM and the integration of the material and information flow. Experience within the Department of Defense and commercial sectors which has shown that support cost reductions and or avoidances of upwards to 35% over business as usual are achievable. It is SCM that will ultimately bring the solar system within the economic sphere of our society.

supply chain managemen↗

NASA NTRS2012

Effect of Inflow Boundary Conditions on Hovering Tilt-Rotor Flows

A study on the effect of inflow turbulence boundary conditions on the local flow on and around a body in flight has been carried out. The study has been carried out using OVERFLOW2 flow solver using the default Spalart-Allmaras turbulence model in OVERFLOW. Many OVERFLOW turbulent flow simulations have been reported using the SA-fv3 model1 over the years. The present study demonstrates that the turbulence levels imposed as a boundary condition (b.c.) in the far-field as implemented in OVERFLOW are not correct. In fact, very low level of turbulence at the far-field boundary as implemented in OVERFLOW results in the SA-fv3 model predicting transition-like profiles on a given body. By choosing sufficiently high levels of the Reynolds number of turbulence, Rt, as a boundary condition, this anomalous behavior of SA-fv3 model is eliminated. Since numerous papers using OVERFLOW have been presented in the literature including that by the author2 using low level of inflow turbulence, it will be beneficial to the CFD community at large and in particular to the OVERFLOW community to understand this effect of the inflow b.c. in the SA-fv3 model. Various results reported over the years in domains such as high-lift applications, drag prediction applications and rotorcraft flow applications can be revisited using the new turbulence inflow boundary condition prescription as suggested in this study. It has been demonstrated in the literature that the effect of inflow turbulence level on the downstream development of flow is too important to be ignored. Demonstrative results are shown and compared with experiment for the case of hovering XV-15 rotor flow at a tip Reynolds number of 4.9 x 10(exp 6) and Mach number of 0.69 in Figs. 1 and 2 below. Fig. 1(a,b) shows skin friction predictions at radial station of r/R = 0.28 corresponding to 5 different inflow boundary conditions obtained with the SA-fv3 model. As the inflow turbulence is increased monotonically, from a value of Rt = 0.1 to 100.0 as shown in Fig. 1, a fully developed turbulent skin friction profile is realized progressively as shown in Fig. 1(b). Similarly skin friction results shown in Fig. 2(a,b) corresponding to radial stations of r/R = 0.72 reinforce the postulate made here that as the inflow turbulence level is increased gradually, fully turbulent on-the-blade simulation is realized uniformly. In the full paper extensive results on skin friction, pressure and velocity profiles as well as the Figure of Merit will be presented and compared with experiment that will illustrate the substantial effect of the inflow boundary conditions on the development of hovering rotor flow downstream.

Kaul, Upender K.↗

DOE OSTI2021

Biogeography of microbial bile acid transformations along the murine gut

Bile acids, which are synthesized from cholesterol by the liver, are chemically transformed along the intestinal tract by the gut microbiota, and the products of these transformations signal through host receptors, affecting overall host health. These transformations include bile acid deconjugation, oxidation, and 7α-dehydroxylation. An understanding of the biogeography of bile acid transformations in the gut is critical because deconjugation is a prerequisite for 7α-dehydroxylation and because most gut microorganisms harbor bile acid transformation capacity. Here, we used a coupled metabolomic and metaproteomic approach to probe in vivo activity of the gut microbial community in a gnotobiotic mouse model. Results revealed the involvement of Clostridium scindens in 7α-dehydroxylation, of the genera Muribaculum and Bacteroides in deconjugation, and of six additional organisms in oxidation (the genera Clostridium, Muribaculum, Bacteroides, Bifidobacterium, Acutalibacter, and Akkermansia). Furthermore, the bile acid profile in mice with a more complex microbiota, a dysbiosed microbiota, or no microbiota was considered. For instance, conventional mice harbor a large diversity of bile acids, but treatment with an antibiotic such as clindamycin results in the complete inhibition of 7α-dehydroxylation, underscoring the strong inhibition of organisms that are capable of carrying out this process by this compound. Finally, a comparison of the hepatic bile acid pool size as a function of microbiota revealed that a reduced microbiota affects host signaling but not necessarily bile acid synthesis. In this study, bile acid transformations were mapped to the associated active microorganisms, offering a systematic characterization of the relationship between microbiota and bile acid composition.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2011

MAVEN - Mars Atmosphere and Volatile EvolutioN Mission

NASA's MAVEN mission (to be launched in late 2013) is the first mission to Mars devoted to sampling all of the upper atmosphere neutral and plasma environments, including the well-mixed atmosphere, the exosphere, ionosphere, outer magnetosphere and near-Mars solar wind. It will fill in some measurement gaps remaining from the successful Mars Global Surveyor and the on-going Mars Express missions. The primary science objectives of MAVEN are: 1. Provide a comprehensive picture of the present state of the upper atmosphere and ionosphere of Mars; 2. Understand the processes controlling the present state; and 3. Determine how loss of volatiles to outer space in the present epoch varies with changing solar condition - EUY, solar wind and interplanetary magnetic field measurements will provide the varying solar energy inputs into the system. Knowing how these processes respond to the Sun's energy inputs in the current epoch will provide a framework for projecting atmospheric processes back in time to profile MARS' atmospheric evolution and to explore "where the water went", A description will be given of the science objectives, the instruments, and the current status of the project, emphasizing the value of having collaborations between the MAVEN project and the Mars upper atmosphere science community.

Grebowsky, Joseph M.↗

NASA NTRS2012

Transition of AIRS Products to the National Weather Service

Short-term Prediction Research and Transition Center (SPoRT) is a proven community leader for transitioning satellite products to operational end users and is working hard to bring data from Atmospheric Infrared Sounder (AIRS) to forecasters. SPoRT products using AIRS data are currently or will soon be evaluated at WFOs and National Centers (1) T and q profiles: HWT, Alaska WFOs, HRD/OPC, HMT (2) Ozone profiles: HPC/OPC (3) Carbon Monoxide: Southern and Western Region WFOs SPoRT is actively evaluating differences between V5 and V6 profiles for selected cases and will continue to provide feedback to the AIRS team as V6 development efforts conclude.

Zavodsky, Bradley↗

DOE OSTI2025

Unlocking America's Abundant Marine Energy Resources

NREL Marine Energy One-Pager: A resource designed for use during NREL campus visits - especially with high-profile guests - as well as at events in Washington, D.C., when engaging with the new administration, and for displays at WPTO or lab booths. The U.S. holds vast untapped marine energy resources - wave, tidal, river, and ocean currents - that can strengthen grid resilience, support coastal communities, and advance energy independence. NREL leads innovation in this space through advanced modeling tools, patented technologies, and world-class testing facilities. NREL's simulation platforms, like OpenFAST and SAM, help reduce development time and risk. Patented devices such as PKelp and FlexWEC demonstrate flexible, resilient approaches to energy capture. At Flatirons Campus, NREL offers motion simulation, structural testing, wave tanks, and megawatt-scale microgrid emulation via the ARIES platform. These capabilities help developers refine and validate devices before in-water trials. With upcoming open-water testing at PacWave and strong partnerships, NREL is accelerating the path to commercialization - positioning the U.S. as a global leader in marine energy innovation.

17 WIND ENERGY↗

DOE OSTI2020

Elucidating algal-bacterial community interactions by tracking volatile biomarkers (Final Report)

This feasibility study project aimed to lay further groundwork for studying and understanding how microorganisms interact with each other at the molecular level using model algal-bacterial co-cultures. A better understanding of such interactions is critical to optimizing and operating biotic platforms for a number of applications, including bioenergy, algal bioproducts and agriculture, and carbon capture. Here we explored the feasibility of characterizing and following these interactions by identifying and tracking volatile metabolites and biomarkers in the complex gaseous headspace of such cultures. We set up an experimental platform using a co-culture of Phaeodactylum tricornutum and Marinobacter subspecies 3-2 as a model system, used solid-phase microextraction fibers for volatile collection at various time points throughout culture growth, and employed gas chromatography mass spectrometry-based instrumentation available at LLNL for compound identification and quantification. We found that it is feasible to determine volatile profiles from the growth of Phaeodactylum tricornutum and Marinobacter subspecies 3-2 using our methodology and monitor profile changes over time. We also observed that volatiles distinguishing between cultures of the individual species and the co-cultures could be detected. We expect that results of this project will feed into the ongoing LLNL’s DOE BER funded Biofuels Scientific Focus Area (SFA) on algal-bacterial interactions and pave the way for future expanded volatile studies supported by DOE. The approach and technologies developed here would also be applicable and transferable to other microbial communities under study, such as cyanobacteria, rhizosphere communities and biofilms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Late Holocene Cliff Retreat in Del Mar, CA, Revealed From Shore Platform 10 Be Concentrations and Numerical Modeling

Rocky coast cliff retreat presents a hazard to coastal communities and infrastructure that is potentially amplified under rising sea level conditions, among other factors. Unfortunately, constraints on retreat rates are typically limited to those derived from imagery and maps spanning the last ~100 years. Here, we use a newly developed coupled model of shore platform profile evolution and cosmogenic radionuclide production that considers the influence of relative sea level (RSL) rise, weathering, material resistance, and wave height decay to model cliff retreat over millennial timescales and its potential drivers in Del Mar, California. We demonstrate the ability to use topographic and bathymetric measurements from a narrow shore platform along with a limited data set of nine cosmogenic 10Be concentrations extending ~125 m from the cliff base to obtain modeled cliff retreat rates that steadily range from 5.0 to 12.5 cm yr -1 over the last two millennia until 100 years before present. These rates are consistent with modern retreat rates of about 2–19 cm yr -1 here. RSL rise in Southern California remained relatively constant during the late Holocene, potentially explaining the relatively stable modeled cliff retreat rate over this time. We also explore the relative influence of weathering, material resistance, and wave erosion efficacy and find that both weathering and wave-driven erosion are necessary to replicate the measured data at this location, with the latter exerting a stronger control on model acceptance, suggesting that waves may provide a possible mechanism by which RSL rise may influence coastal cliff erosion in southern California.

58 GEOSCIENCES↗

DOE OSTI2023

Scaling from Flux Towers to Ecosystem Models: Regional Constraints on Carbon Cycle Processes from Atmospheric Carbonyl Sulfide (Final Report)

DOE supported research suggests that gross primary productivity (GPP) is largely underestimated by global earth system models [Welp et al., 2011], reflecting the persistent challenge in extrapolating from local-scale GPP observations to global-scale earth system models. This poor understanding of GPP at large spatial scales is of particular concern in tropical forests. In tropical forests, some earth systems models forecast a powerful feedback between a warming climate and a decline in GPP resulting in forest dieback. While this simulated feedback is intensely debated, we lack robust large-scale constraints on GPP that are needed to resolve this debate. In particular, carbon dioxide measurements provide valuable information on net carbon flux, but not on the gross flux associated with GPP. Here we conducted a study of regional-to-global scale GPP using atmospheric carbonyl sulfide to provide a new constraint on GPP mechanisms in earth system models. Our project activities integrated modeling, in situ measurement, and remote sensing techniques to resolve GPP for the Amazon as well as global scale trends. The results of this work included initiating airborne carbonyl sulfide monitoring in the Amazon, training for postdocs and graduate students at a Hispanic Serving Institution, fundamental advances in carbonyl sulfide budgets [e.g. Hilton et al., Nature Climate Change, 2017], and high-profile publications that focused on GPP trends for the Amazon [Stinecipher et al., GRL, 2022] and global historical GPP trends [Campbell, et al., Nature, 2017]. Based on the suggestion of our DOE program manager, we published a state-of-the-science commentary to the scientific community on GPP monitoring with COS [Campbell et al., EOS, 2017] which was selected as the cover story. DOE support was acknowledged in all reports. The importance of this research to understanding climate change was communicated to the general public through community seminars (Rotary, Public Libraries, State Parks), an op-ed (SF Chronicle), and interviews in the mass media including two stories in the New York Times (4/5/17; 7/30/18), one of which was especially widely read after it was featured in the New York Time’s Quote of the Day.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Who Is Metabolizing What? Discovering Novel Biomolecules in the Microbiome and the Organisms Who Make Them

Even as the field of microbiome research has made huge strides in mapping microbial community composition in a variety of environments and organisms, explaining the phenotypic influences on the host by microbial taxa – both known and unknown – and their specific functions still remain major challenges. A pressing need is the ability to assign specific functions in terms of enzymes and small molecules to specific taxa or groups of taxa in the community. This knowledge will be crucial for advancing personalized therapies based on the targeted modulation of microbes or metabolites that have predictable outcomes to benefit the human host. This perspective article advocates for the combined use of standards-free metabolomics and activity-based protein profiling strategies to address this gap in functional knowledge in microbiome research via the identification of novel biomolecules and the attribution of their production to specific microbial taxa.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2000

Critical Evaluation of 0-30 km Profile Information in Ground-Based Zenith-Sky and Satellite-Measured Backscattered UV Radiation

We now have several decades of experience in deriving vertical ozone profiles from the measurements of diffuse ultraviolet radiation by both ground and satellite-based instruments using Umkehr and BUV techniques. Continuing technological advances are pushing the state-of-the-art of these measurements to high spectral resolution and broader wavelength coverage. These modern instruments include the ground-based Brewer and satellite-based Global Ozone Monitoring Experiment (GOME) instruments, as well as advanced instruments being developed by ESA(SCIAMACHY), Netherlands(OMI) and Japan(ODUS). However, one of the issues that remains unresolved is the 0-30 km ozone profile information retrievable from these measurements. Though it is commonly believed that both the Umkehr and the satellite-based BUV techniques have very limited profile information below 30 km, there are those who argue that the data from these instruments should continue to be reported in this altitude range for they compare well with ozonesondes and hence there is useful scientific information. Others claim that the limitations of the Umkehr and BUV techniques are largely due to their low spectral resolution, and that the profile information below 30 km can be greatly improved by going to high spectral resolution instruments, such as Brewer and GOME. The purpose of this paper is to provide a critical evaluation of the 0-30 km ozone profile information in the various UV remote sensing techniques. We use a database of individual ozone profiles created using ozonesondes and SAGE and 4D ozone fields generated by data assimilation techniques to simulate radiances measured by the various techniques. We then apply a common inversion approach to all the methods to systematically examine how much profile information is available simply from the knowledge of total ozone, how much additional profile information is added by the traditional Dobson Umkehr and satellite buv techniques, and how much better one can do by adding additional wavelengths and by going to higher spectral resolution. An open and honest discussion of these issues is critical to provide the ozone science community a realistic assessment of the quality of data in the lower stratosphere and troposphere expected from both past and future instruments.

Bhartia, Pawan↗

NASA NTRS1971

Applications of aerospace technology in industry, a technology transfer profile: Fire safety

The fire safety field is considered as being composed of three parts: an industry, a technology base, and a user base. An overview of the field is presented, including a perspective on the magnitude of the national fire safety problem. Selected NASA contributions to the technology of fire safety are considered. Communication mechanisms, particularly conferences and publications, used by NASA to alert the community to new developments in the fire safety field, are reviewed. Several examples of nonaerospace applications of NASA-generated fire safety technology are also presented. Issues associated with attempts to transfer this technology from the space program to other sectors of the American economy are outlined.

Kottenstette, J. P.↗

NASA NTRS2007

Review of Cranked-Arrow Wing Aerodynamics Project: Its International Aeronautical Community Role

This paper provides a brief history of the F-16XL-1 aircraft, its role in the High Speed Research (HSR) program and how it was morphed into the Cranked Arrow Wing Aerodynamics Project (CAWAP). Various flight, wind-tunnel and Computational Fluid Dynamics (CFD) data sets were generated during the CAWAP. These unique and open flight datasets for surface pressures, boundary-layer profiles and skinfriction distributions, along with surface flow data, are described and sample data comparisons given. This is followed by a description of how the project became internationalized to be known as Cranked Arrow Wing Aerodynamics Project International (CAWAPI) and is concluded by an introduction to the results of a 4 year CFD predictive study of data collected at flight conditions by participating researchers.

Lamar, John E.↗

NASA NTRS2018

Improvement of Stratospheric Aerosol Extinction Retrieval from OMPS/LP Using a New Aerosol Model

The Ozone Mapping and Profiler Suite Limb Profiler (OMPS/LP) has been flying on the Suomi National Polar-orbiting Partnership (S-NPP) satellite since October 2011. It is designed to produce ozone and aerosol vertical profiles at 2-kilometer vertical resolution over the entire sunlit globe. Aerosol extinction profiles are computed with Mie theory using radiances measured at 675 nanometers. The operational Version 1.0 (V1.0) aerosol extinction retrieval algorithm assumes a bimodal lognormal aerosol size distribution (ASD) whose parameters were derived by combining an in situ measurement of aerosol microphysics with the Stratospheric Aerosol and Gas Experiment (SAGE II) aerosol extinction climatology. Internal analysis indicates that this bimodal lognormal ASD does not sufficiently explain the spectral dependence of LP-measured radiances. In this paper we describe the derivation of an improved aerosol size distribution, designated Version 1.5 (V1.5), for the LP retrieval algorithm. The new ASD uses a gamma function distribution that is derived from Community Aerosol and Radiation Model for Atmospheres (CARMA)-calculated results. A cumulative distribution fit derived from the gamma function ASD gives better agreement with CARMA results at small particle radii than bimodal or unimodal functions. The new ASD also explains the spectral dependence of LP-measured radiances better than the V1.0 ASD. We find that the impact of our choice of ASD on the retrieved extinctions varies strongly with the underlying reflectivity of the scene. Initial comparisons with collocated extinction profiles retrieved at 676 nanometers from the SAGE III instrument on the International Space Station (ISS) show a significant improvement in agreement for the LP V1.5 retrievals. Zonal mean extinction profiles agree to within 10 percent between 19 and 29 kilometers, and regression fits of collocated samples show improved correlation and reduced scatter compared to the V1.0 product. This improved agreement will motivate development of more sophisticated ASDs from CARMA results that incorporate latitude, altitude and seasonal variations in aerosol properties.

Ozone Mapping Profiler Suite Limb Profiler (OMPS/L↗

DOE OSTI2020

Energy storage emerging: A perspective from the Joint Center for Energy Storage Research

Energy storage is an integral part of modern society. A contemporary example is the lithium (Li)-ion battery, which enabled the launch of the personal electronics revolution in 1991 and the first commercial electric vehicles in 2010. Most recently, Li-ion batteries have expanded into the electricity grid to firm variable renewable generation, increasing the efficiency and effectiveness of transmission and distribution. Important applications continue to emerge including decarbonization of heavy-duty vehicles, rail, maritime shipping, and aviation and the growth of renewable electricity and storage on the grid. This perspective compares energy storage needs and priorities in 2010 with those now and those emerging over the next few decades. The diversity of demands for energy storage requires a diversity of purpose-built batteries designed to meet disparate applications. Advances in the frontier of battery research to achieve transformative performance spanning energy and power density, capacity, charge/discharge times, cost, lifetime, and safety are highlighted, along with strategic research refinements made by the Joint Center for Energy Storage Research (JCESR) and the broader community to accommodate the changing storage needs and priorities. Innovative experimental tools with higher spatial and temporal resolution, in situ and operando characterization, first-principles simulation, high throughput computation, machine learning, and artificial intelligence work collectively to reveal the origins of the electrochemical phenomena that enable new means of energy storage. This knowledge allows a constructionist approach to materials, chemistries, and architectures, where each atom or molecule plays a prescribed role in realizing batteries with unique performance profiles suitable for emergent demands.

Trahey, Lynn↗

DOE OSTI2020

Profiles of upcoming HPC Applications and their Impact on Reservation Strategies

With the expected convergence between HPC, BigData and AI, new applications with different profiles are coming to HPC infrastructures. Here, we aim at better understanding the features and needs of these applications in order to be able to run them efficiently on HPC platforms. The approach followed is bottom-up: we study thoroughly an emerging application from the neuroscience community (SLANT) to understand its behavior. Based on these observations, we derive a generic, yet simple, application model (namely, a linear sequence of stochastic jobs). We expect this model to be representative for a large set of upcoming applications that require the computational power of HPC clusters without fitting the typical behavior of large-scale traditional applications. In a second step, we show how one can manipulate this generic model in a scheduling framework. Specifically we consider the problem of making reservations (both time and memory) for an execution on an HPC platform. We derive solutions using the model of the first step of this work. We experimentally show the robustness of the model, even with very few data or with another application, to generate the model, and provide performance gains with regards to standard and more recent approaches used in the neuroscience community.

97 MATHEMATICS AND COMPUTING↗