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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Modifying Network Guided Vehicle for Repeatable EcoCAR ACC Energy Testing

The newest iteration of the Department of Energy (DOE) Advanced Vehicle Technology Competitions is the EcoCAR Mobility Challenge. In this paper, ANL and HORIBA MIRA collaborate to propose and pilot a test method that enables controlled, repeatable track-based energy consumption testing of semi-autonomous features. The testing was performed at MIRA’s proving ground facility in Nuneaton, UK, using their Network Guided Vehicle (NGV) connectivity and automation test platform. The NGV served as a repeatable lead vehicle following prescribed drive traces around two different track circuits while the host vehicle under test, a Honda Civic with full speed range Adaptive Cruise Control, followed behind. Over the course of a two day test, multiple iterations of certification and custom EPA drive traces were performed on track, demonstrating the viability of a two vehicle energy test. Results were analyzed to assess NGV lead vehicle performance in following the prescribed cycle using SAE J2951 standard calculations in an effort to quantify how repeatably and accurately the lead vehicle followed the trace. Host vehicle energy consumption was assessed using both vehicle CAN bus monitoring and an on-board fuel flow meter.

ACC↗
DOE OSTI2023

Linking repeat lidar with Landsat products for large scale quantification of fire-induced permafrost thaw settlement in interior Alaska

The permafrost–fire–climate system has been a hotspot in research for decades under a warming climate scenario. Surface vegetation plays a dominant role in protecting permafrost from summer warmth, thus, any alteration of vegetation structure, particularly following severe wildfires, can cause dramatic top–down thaw. A challenge in understanding this is to quantify fire-induced thaw settlement at large scales (>1000 km 2 ). In this study, we explored the potential of using Landsat products for a large-scale estimation of fire-induced thaw settlement across a well-studied area representative of ice-rich lowland permafrost in interior Alaska. Six large fires have affected ~1250 km 2 of the area since 2000. We first identified the linkage of fires, burn severity, and land cover response, and then developed an object-based machine learning ensemble approach to estimate fire-induced thaw settlement by relating airborne repeat lidar data to Landsat products. The model delineated thaw settlement patterns across the six fire scars and explained ~65% of the variance in lidar-detected elevation change. Our results indicate a combined application of airborne repeat lidar and Landsat products is a valuable tool for large scale quantification of fire-induced thaw settlement.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Structure-based discovery of potent WD repeat domain 5 inhibitors that demonstrate efficacy and safety in preclinical animal models

WD repeat domain 5 (WDR5) is a core scaffolding component of many multiprotein complexes that perform a variety of critical chromatin-centric processes in the nucleus. WDR5 is a component of the mixed lineage leukemia MLL/SET complex and localizes MYC to chromatin at tumor-critical target genes. As a part of these complexes, WDR5 plays a role in sustaining oncogenesis in a variety of human cancers that are often associated with poor prognoses. Thus, WDR5 has been recognized as an attractive therapeutic target for treating both solid and hematological tumors. Previously, small-molecule inhibitors of the WDR5-interaction (WIN) site and WDR5 degraders have demonstrated robust in vitro cellular efficacy in cancer cell lines and established the therapeutic potential of WDR5. However, these agents have not demonstrated significant in vivo efficacy at pharmacologically relevant doses by oral administration in animal disease models. We have discovered WDR5 WIN-site inhibitors that feature bicyclic heteroaryl P 7 units through structure-based design and address the limitations of our previous series of small-molecule inhibitors. Importantly, our lead compounds exhibit enhanced on-target potency, excellent oral pharmacokinetic (PK) profiles, and potent dose-dependent in vivo efficacy in a mouse MV4:11 subcutaneous xenograft model by oral dosing. Furthermore, these in vivo probes show excellent tolerability under a repeated high-dose regimen in rodents to demonstrate the safety of the WDR5 WIN-site inhibition mechanism. Collectively, our results provide strong support for WDR5 WIN-site inhibitors to be utilized as potential anticancer therapeutics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Tetratricopeptide repeat protein SlREC2 positively regulates cold tolerance in tomato

Abstract Cold stress is a key environmental constraint that dramatically affects the growth, productivity, and quality of tomato (Solanum lycopersicum); however, the underlying molecular mechanisms of cold tolerance remain poorly understood. In this study, we identified REDUCED CHLOROPLAST COVERAGE 2 (SlREC2) encoding a tetratricopeptide repeat protein that positively regulates tomato cold tolerance. Disruption of SlREC2 largely reduced abscisic acid (ABA) levels, photoprotection, and the expression of C-REPEAT BINDING FACTOR (CBF)-pathway genes in tomato plants under cold stress. ABA deficiency in the notabilis (not) mutant, which carries a mutation in 9-CIS-EPOXYCAROTENOID DIOXYGENASE 1 (SlNCED1), strongly inhibited the cold tolerance of SlREC2-silenced plants and empty vector control plants and resulted in a similar phenotype. In addition, foliar application of ABA rescued the cold tolerance of SlREC2-silenced plants, which confirms that SlNCED1-mediated ABA accumulation is required for SlREC2-regulated cold tolerance. Strikingly, SlREC2 physically interacted with β-RING CAROTENE HYDROXYLASE 1b (SlBCH1b), a key regulatory enzyme in the xanthophyll cycle. Disruption of SlBCH1b severely impaired photoprotection, ABA accumulation, and CBF-pathway gene expression in tomato plants under cold stress. Taken together, this study reveals that SlREC2 interacts with SlBCH1b to enhance cold tolerance in tomato via integration of SlNCED1-mediated ABA accumulation, photoprotection, and the CBF-pathway, thus providing further genetic knowledge for breeding cold-resistant tomato varieties.

Zhang, Ying (ORCID:0000000169841164)↗
DOE OSTI2021

Repeatability and sensitivity characterization of the far-field high-energy diffraction microscopy instrument at the Advanced Photon Source

In the last two decades, far-field high-energy diffraction microscopy (FF-HEDM) and similar non-destructive techniques have been actively developed at synchrotron light sources around the world. As these techniques (and associated analysis tools) are becoming more available for the general users of these light sources, it is important and timely to characterize their performance and capabilities. In this work, the FF-HEDM instrument implemented at the 1-ID-E endstation of the Advanced Photon Source (APS) is summarized. The set of measurements conducted to characterize the instrument's repeatability and sensitivity to changes in grain orientation and position are also described. When an appropriate grain matching method is used, the FF-HEDM instrument's repeatability is approximately 5 µm in translation, 0.02° in rotation, and 2 × 10 −4 in strain; the instrument sensitivity is approximately 5 µm in translation and 0.05° in rotation.

3DXRD↗
DOE OSTI2024

A Science Gateway for the Repeatable Analysis of Machine Learning Predicted Gravity Anomalies

In recent years, deep learning has become an increasingly popular alternative for modeling in geoscience applications due to its scalability and efficiency. However, the interpretability, compute, data volume, and hyperparameter tuning requirements of deep learning models make development and monitoring difficult. Furthermore, model explainability and communicating results obtained by these models to users or domain experts is a challenge, as domain experts in geoscience also need to have a deep understanding of how those models function in order to support their scientific works. Here, we describe a science gateway and machine learning pipeline for predicting gravity anomalies from geophysical data. The gateway, built on open-source technologies, provides a holistic view of the pipeline through interactive visualizations aimed at enabling efficient exploratory data analysis. The repeatability, reproducibility, and monitoring capabilities of this overall system allow us to iterate and analyze at scale. Using this pipeline and gateway, we can repeatedly produce accurate high-resolution gravity anomaly datasets. By describing the underlying technologies, implementation, and results, here we provide a foundation for the broader adoption of science gateways into cross-cutting geoscience and machine learning research projects as a means to improve the scientific discovery and collaboration in the geophysics and computational sciences community.

58 GEOSCIENCES↗
DOE OSTI2023

Multiple mechanisms explain loss of anthocyanins from betalain‐pigmented Caryophyllales, including repeated wholesale loss of a key anthocyanidin synthesis enzyme

Summary In this study, we investigate the genetic mechanisms responsible for the loss of anthocyanins in betalain‐pigmented Caryophyllales, considering our hypothesis of multiple transitions to betalain pigmentation. Utilizing transcriptomic and genomic datasets across 357 species and 31 families, we scrutinize 18 flavonoid pathway genes and six regulatory genes spanning four transitions to betalain pigmentation. We examined evidence for hypotheses of wholesale gene loss, modified gene function, altered gene expression, and degeneration of the MBW (MYB‐bHLH‐WD40) trasnscription factor complex, within betalain‐pigmented lineages. Our analyses reveal that most flavonoid synthesis genes remain conserved in betalain‐pigmented lineages, with the notable exception of TT19 orthologs, essential for the final step in anthocyanidin synthesis, which appear to have been repeatedly and entirely lost. Additional late‐stage flavonoid pathway genes upstream of TT19 also manifest strikingly reduced expression in betalain‐pigmented species. Additionally, we find repeated loss and alteration in the MBW transcription complex essential for canonical anthocyanin synthesis. Consequently, the loss and exclusion of anthocyanins in betalain‐pigmented species appear to be orchestrated through several mechanisms: loss of a key enzyme, downregulation of synthesis genes, and degeneration of regulatory complexes. These changes have occurred iteratively in Caryophyllales, often coinciding with evolutionary transitions to betalain pigmentation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Quantum Network Repeater Simulation Package (QNPack) v1.0.0

Existing quantum network testbeds and prototypes are typically implemented in laboratory experiments with limited functionality and operate in a tightly coupled manner. These characteristics make it difficult to evaluate the behavior of emerging quantum platforms and protocols beyond local resource limitations. The QNPack software enables full-stack modeling of quantum repeater networks that allows researchers to simulate new approaches, and understand emergent behaviors, from local to national scales. Novel capabilities include: (1) performant and accurate quantum models that can be executed as independent simulations, which will allow users to characterize specific analog quantum processes, quantum devices, and protocols, (2) a modular and extensible approach to the simulation architecture to accommodate new quantum technologies, protocols, and topologies as they are developed across the quantum repeater generations under evaluation, and (3) a focus on managing the interactions between the simulation framework sub-components so that they may be re-used and composed in flexible ways.

Kissel, Ezra [Lawrence Berkeley National Laborator↗
DOE OSTI2020

A willow sex chromosome reveals convergent evolution of complex palindromic repeats

Background: Sex chromosomes have arisen independently in a wide variety of species, yet they share common characteristics, including the presence of suppressed recombination surrounding sex determination loci. Mammalian sex chromosomes contain multiple palindromic repeats across the non-recombining region that show sequence conservation through gene conversion and contain genes that are crucial for sexual reproduction. In plants, it is not clear if palindromic repeats play a role in maintaining sequence conservation in the absence of homologous recombination. Results: Here we present the first evidence of large palindromic structures in a plant sex chromosome, based on a highly contiguous assembly of the W chromosome of the dioecious shrub Salix purpurea . The W chromosome has an expanded number of genes due to transpositions from autosomes. It also contains two consecutive palindromes that span a region of 200 kb, with conspicuous 20-kb stretches of highly conserved sequences among the four arms that show evidence of gene conversion. Four genes in the palindrome are homologous to genes in the sex determination regions of the closely related genus Populus , which is located on a different chromosome. These genes show distinct, floral-biased expression patterns compared to paralogous copies on autosomes. Conclusion: The presence of palindromes in sex chromosomes of mammals and plants highlights the intrinsic importance of these features in adaptive evolution in the absence of recombination. Convergent evolution is driving both the independent establishment of sex chromosomes as well as their fine-scale sequence structure.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Low-velocity repeated impact behaviors of Polymer Fiber Reinforced Plastics (PFRPs)

Modern fiber-reinforced composites have become ubiquitous across multiple industries due to their excellent weight-to-strength ratio. Typically glass or carbon fibers are widely used. While Glass or Carbon Fiber-Reinforced Plastics (GFPRs or CFPRs) have good stiffness, strength, and fatigue life, they are expensive and difficult to recycle. Researchers are exploring Polymer Fiber-Reinforced Plastics (PFRPs) as an alternative solution. PFRPs utilize polymer fibers and a polymer matrix. A wide range of materials options is available, including low-cost thermoplastics such as polyethylene or polypropylene. These thermoplastics are easy to handle and recyclable without special methods. Manufacturing parts using thermoplastics are well-established as well. However, their mechanical performances have not been extensively studied compared to GFRPs or CFRPs. This study examines the low-velocity impact resistance of PFRPs made of different thermoplastics. The low-velocity impacts are applied through a drop-weight tower. The experiment is divided into two cases: a single perforation impact and low-energy repeated impacts. Energy absorption and the number of impacts to failure are measured. The results are compared to traditional CFRPs which have a thermoset matrix. The PFRPs demonstrate energy absorption capabilities comparable to or greater than those of CFRPs with respect to specimen thickness and density. Additionally, the PFRPs show significantly higher impacts-to-failure than the CFRPs in low-energy repeated impact tests. This is particularly noteworthy considering that the PFRPs are much simpler and more economical to manufacture than CFRPs. To further

Ko, Seunghyun↗
DOE OSTI2023

Tandem repeats in giant archaeal Borg elements undergo rapid evolution and create new intrinsically disordered regions in proteins

Borgs are huge, linear extrachromosomal elements associated with anaerobic methane-oxidizing archaea. Striking features of Borg genomes are pervasive tandem direct repeat (TR) regions. Here, we present six new Borg genomes and investigate the characteristics of TRs in all ten complete Borg genomes. We find that TR regions are rapidly evolving, recently formed, arise independently, and are virtually absent in host Methanoperedens genomes. Flanking partial repeats and A-enriched character constrain the TR formation mechanism. TRs can be in intergenic regions, where they might serve as regulatory RNAs, or in open reading frames (ORFs). TRs in ORFs are under very strong selective pressure, leading to perfect amino acid TRs (aaTRs) that are commonly intrinsically disordered regions. Proteins with aaTRs are often extracellular or membrane proteins, and functionally similar or homologous proteins often have aaTRs composed of the same amino acids. We propose that Borg aaTR-proteins functionally diversify Methanoperedens and all TRs are crucial for specific Borg–host associations and possibly cospeciation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structure-aware annotation of leucine-rich repeat domains

Protein domain annotation is typically done by predictive models such as HMMs trained on sequence motifs. However, sequence-based annotation methods are prone to error, particularly in calling domain boundaries and motifs within them. These methods are limited by a lack of structural information accessible to the model. With the advent of deep learning-based protein structure prediction, existing sequenced-based domain annotation methods can be improved by taking into account the geometry of protein structures. We develop dimensionality reduction methods to annotate repeat units of the Leucine Rich Repeat solenoid domain. The methods are able to correct mistakes made by existing machine learning-based annotation tools and enable the automated detection of hairpin loops and structural anomalies in the solenoid. The methods are applied to 127 predicted structures of LRR-containing intracellular innate immune proteins in the model plant Arabidopsis thaliana and validated against a benchmark dataset of 172 manually-annotated LRR domains.

Xu, Boyan↗
DOE OSTI2021

The leucine-rich repeats in allelic barley MLA immune receptors define specificity towards sequence-unrelated powdery mildew avirulence effectors with a predicted common RNase-like fold

Nucleotide-binding domain leucine-rich repeat-containing receptors (NLRs) in plants can detect avirulence (AVR) effectors of pathogenic microbes. The Mildew locus a (Mla) NLR gene has been shown to confer resistance against diverse fungal pathogens in cereal crops. In barley, Mla has undergone allelic diversification in the host population and confers isolate-specific immunity against the powdery mildew-causing fungal pathogen Blumeria graminis forma specialis hordei (Bgh). We previously isolated the Bgh effectors AVR A1 , AVR A7 , AVR A9 , AVR A13 , and allelic AVR A10 /AVR A22 , which are recognized by matching MLA1, MLA7, MLA9, MLA13, MLA10 and MLA22, respectively. Here, we extend our knowledge of the Bgh effector repertoire by isolating the AVR A6 effector, which belongs to the family of catalytically inactive RNase-Like Proteins expressed in Haustoria (RALPHs). Using structural prediction, we also identified RNase-like folds in AVR A1 , AVR A7 , AVR A10 /AVR A22 , and AVR A13 , suggesting that allelic MLA recognition specificities could detect structurally related avirulence effectors. To better understand the mechanism underlying the recognition of effectors by MLAs, we deployed chimeric MLA1 and MLA6, as well as chimeric MLA10 and MLA22 receptors in plant co-expression assays, which showed that the recognition specificity for AVR A1 and AVR A6 as well as allelic AVR A10 and AVR A22 is largely determined by the receptors’ C-terminal leucine-rich repeats (LRRs). The design of avirulence effector hybrids allowed us to identify four specific AVR A10 and five specific AVR A22 aa residues that are necessary to confer MLA10- and MLA22-specific recognition, respectively. This suggests that the MLA LRR mediates isolate-specific recognition of structurally related AVR A effectors. Thus, functional diversification of multi-allelic MLA receptors may be driven by a common structural effector scaffold, which could be facilitated by proliferation of the RALPH effector family in the pathogen genome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Improving Self-Driving Labs: Quantifying System-Level Experiment Repeatability and Broadening Instrument-Level Compatibility

Modular Autonomous Research System (MARS) is a self-driving laboratory (SDL) which performs wet-lab science with peptide-lanthanide combinations in an automated and, ultimately, an autonomous manner to aid in soil analysis for domestic lithium mining. Autonomous experimentation involves automated experimentation, experiment planning, and active learning. MARS consists of a 6-axis robotic arm (UR5e) on a linear rail, pipette robots (Opentrons 2), and microplate readers. These components transport, operate on, and collect data with chemical solutions in standard labware. For effective autonomy, MARS must perform system-level labware operations repeatably, plan experiments autonomously, and be portable between research-domains. Repeatability is evaluated by labware placement precision, such that future operations can properly locate labware, as well as the elapsed time, so that low variance mean estimates of experiment duration can inform high-level researcher decision making. Autonomous experiment planning is the next step to decouple experimentation from human management; however, there is a conflict between the ideal system-level experiment goals and the constraints imposed by instruments’ limitations. Sub-domain portability is a long-term goal to extend MARS’ research beyond the chemistry of peptide-lanthanide binding to other sub-domains without having to invest significant overhead to system retrofitting. To address these goals, we manually trained the robotic arm labware placement and modelled statistical failurerate and uncertainty Additionally, we benchmarked the duration and variance of each experiment sub-operation as a heuristic for research decision making. Next, we use a parameterized geometric program (PGP) approach to design experiments that optimize system-level objectives and satisfy instrument-level constraints. Lastly, we proposed a Python framework to maximize MARS’ extensibility to other scientific sub-domains through a JSON-based experiment specification.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Row selection in remote sensing from four-row plots of maize and sorghum based on repeatability and predictive modeling

Remote sensing enables the rapid assessment of many traits that provide valuable information to plant breeders throughout the growing season to improve genetic gain. These traits are often extracted from remote sensing data on a row segment (rows within a plot) basis enabling the quantitative assessment of any row-wise subset of plants in a plot, rather than a few individual representative plants, as is commonly done in field-based phenotyping. Nevertheless, which rows to include in analysis is still a matter of debate. The objective of this experiment was to evaluate row selection and plot trimming in field trials conducted using four-row plots with remote sensing traits extracted from RGB (red-green-blue), LiDAR (light detection and ranging), and VNIR (visible near infrared) hyperspectral data. Uncrewed aerial vehicle flights were conducted throughout the growing seasons of 2018 to 2021 with data collected on three years of a sorghum experiment and two years of a maize experiment. Traits were extracted from each plot based on all four row segments (RS) (RS1234), inner rows (RS23), outer rows (RS14), and individual rows (RS1, RS2, RS3, and RS4). Plot end trimming of 40 cm was an additional factor tested. Repeatability and predictive modeling of end-season yield were used to evaluate performance of these methodologies. Plot trimming was never shown to result in significantly different outcomes from non-trimmed plots. Significant differences were often observed based on differences in row selection. Plots with more row segments were often favorable for increasing repeatability, and excluding outer rows improved predictive modeling. These results support long-standing principles of experimental design in agronomy and should be considered in breeding programs that incorporate remote sensing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A guayule C-repeat binding factor is highly activated in guayule under freezing temperature and enhances freezing tolerance when expressed in Arabidopsis thaliana

Natural Rubber (NR)-producing guayule (Parthenium argentatum Gray) has been developed as a new crop to diversify NR production. Guayule NR is mainly synthesized in its stem and is upregulated by cold temperatures. A guayule C-repeat binding factor 4 (PaCBF4) was highly expressed in cold-treated stem tissue, coinciding with active rubber biosynthesis and accumulation. Sequence alignments of PaCBF4 with other CBFs indicated that PaCBF4 contains DNA-binding domains responsible for regulating cold-regulated (COR) gene expression. Spatial gene expression profiling of PaCBF4 revealed that stems had the highest expression level among different organs examined. We further confirmed the function of PaCBF4 as regulator of cold-signaling processes by expressing it in the model plant Arabidopsis under a constitutive ubiquitin promoter from potato. Further, the resulting transgenic Arabidopsis lines expressing PaCBF4 turned on expression of a set of Arabidopsis COR genes under both room (24ºC) and cold (4ºC) temperatures, in contrast to the wild-type Arabidopsis that expressed these COR genes solely upon cold treatment. Furthermore, the transgenic plants displayed enhanced freezing tolerance at -5ºC, exhibiting a survival rate of 88–98% compared with 0% survival rate of wild-type plants. Our results suggest that PaCBF4 is a functional member of the guayule CBF gene family and plays a significant role in cold and freeze tolerance. Interestingly, overexpressing PaCBF4 in Arabidopsis did not affect the normal phenotype of the plant during vegetative and inflorescence growth, but the gene led to more undeveloped siliques after flowering.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Robust, versatile DNA FISH probes for chromosome-specific repeats in Caenorhabditis elegans and Pristionchus pacificus

Repetitive DNA sequences are useful targets for chromosomal fluorescence in situ hybridization. We analyzed recent genome assemblies of Caenorhabditis elegans and Pristionchus pacificus to identify tandem repeats with a unique genomic localization. Based on these findings, we designed and validated sets of oligonucleotide probes for each species targeting at least 1 locus per chromosome. These probes yielded reliable fluorescent signals in different tissues and can easily be combined with the immunolocalization of cellular proteins. Synthesis and labeling of these probes are highly cost-effective and require no hands-on labor. The methods presented here can be easily applied in other model and nonmodel organisms with a sequenced genome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Micro-Transfer Printing of Repeaters on Passive Interposer

Silicon-based sensors are central to particle physics experiments and particle tracking detectors. New-generation Large Focal Plane Arrays (LFPAs) cover areas that extend beyond several square meters. Distributing power and transporting data across such areas while maintaining good signal integrity is a complicated challenge. Tiling the detector on an organic interposer would be far too expensive and take too much space while offering little to no advantage regarding signal integrity. Passive silicon interposers are much less expensive and more integrable but would worsen signal integrity because of their inherent higher dielectric constant. Active interposers are a good compromise from the economic and signal integrity standpoint; unfortunately, their yield trends to zero for areas greater than a reticle size, making this technology incompatible with our application. NHanced proposes to duplicate the behavior of a high-yield, low-cost active interposer by printing active microcomponents on a passive interposer with our die-to-wafer micro-transfer printing (MTP) technology. This resolves the signal integrity and power distribution limitations. In Phase I, we designed and simulated analog and digital repeaters to be MTPed onto a passive silicon interposer test wafer.

2.5D↗