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DOE OSTI2022

Ab Initio Structure Factors for Spin-Dependent Dark Matter Direct Detection

We present converged ab initio calculations of structure factors for elastic spin-dependent WIMP scattering off all nuclei used in dark matter direct-detection searches: 19 F, 23 Na, 27 Al, 29 Si, 73 Ge, 12 7I, and 129,131 Xe. From a set of established two- and three-nucleon interactions derived within chiral effective field theory, we construct consistent WIMP-nucleon currents at the one-body level, including effects from axial-vector two-body currents. We then apply the in-medium similarity renormalization group to construct effective valence-space Hamiltonians and consistently transformed operators of nuclear responses. Combining the recent advances of natural orbitals with three-nucleon forces expressed in large spaces, we obtain basis-space converged structure factors even in heavy nuclei. Generally results are consistent with previous calculations but large uncertainties in 127 I highlight the need for further study.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Precision Determination of the Neutral Weak Form Factor of Ca 48

In this work, we report a precise measurement of the parity-violating asymmetry $A_{\rm PV}$ in the elastic scattering of longitudinally polarized electrons from $^{48}{\rm Ca}$. We measure $A_{\rm PV} =2668\pm 106\ {\rm (stat)}\pm 40\ {\rm (syst)}$ parts per billion, leading to an extraction of the neutral weak form factor $F_{\rm W} (q=0.8733$ fm$^{-1}) = 0.1304 \pm 0.0052 \ {\rm (stat)}\pm 0.0020\ {\rm (syst)}$ and the charge minus the weak form factor $F_{\rm ch} - F_{\rm W} = 0.0277\pm 0.0055$. The resulting neutron skin thickness $R_n-R_p=0.121 \pm 0.026\ {\rm (exp)} \pm 0.024\ {\rm (model)}$~fm is relatively thin yet consistent with many model calculations. The combined CREX and PREX results will have implications for future energy density functional calculations and on the density dependence of the symmetry energy of nuclear matter.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Even-Denominator Fractional Quantum Hall State at Filling Factor ν = 3 / 4

Fractional quantum Hall states (FQHSs) exemplify exotic phases of low-disorder two-dimensional (2D) electron systems when electron-electron interaction dominates over the thermal and kinetic energies. Particularly intriguing among the FQHSs are those observed at even-denominator Landau level filling factors, as their quasiparticles are generally believed to obey non-Abelian statistics and be of potential use in topological quantum computing. Such states, however, are very rare and fragile, and are typically observed in the excited Landau level of 2D electron systems with the lowest amount of disorder. Here we report the observation of a new and unexpected even-denominator FQHS at filling factor ν = 3/4 in a GaAs 2D hole system with an exceptionally high quality (mobility). Furthermore, our magnetotransport measurements reveal a strong minimum in the longitudinal resistance at ν = 3/4, accompanied by a developing Hall plateau centered at (h/e 2 )/(3/4). This even-denominator FQHS is very unusual as it is observed in the lowest Landau level and in a 2D hole system. While its origin is unclear, it is likely a non-Abelian state, emerging from the residual interaction between composite fermions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Quantum Monte Carlo Calculations of Magnetic Form Factors in Light Nuclei

Here, we present Quantum Monte Carlo calculations of magnetic form factors in A = 6-10 nuclei, based on Norfolk two- and three-nucleon interactions, and associated one- and two-body electromagnetic currents. Agreement with the available experimental data for 6 Li, 7 Li, 9 Be and 10 B up to values of momentum transfer q ~ 3 fm -1 is achieved when two-nucleon currents are accounted for. We present a set of predictions for the magnetic form factors of 7 Be, 8 Li, 9 Li, and 9 C. In these systems, two body currents account for ~ 40-60% of the total magnetic strength. Measurements in any of these radioactive systems would provide valuable insights on the nuclear magnetic structure emerging from the underlying many-nucleon dynamics. A particularly interesting case is that of 7 Be, as it would enable investigations of the magnetic structure of mirror nuclei

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2026

pyDiSCaMB : enabling the use of multipolar scattering factors in Phenix

Multipolar scattering models, such as the transferable aspherical atom model, account for atomic chemical interactions and provide a more accurate representation of experimental data. However, the simpler independent atom model (IAM), which assumes non-interacting atoms, is the only model available in the most widely used macromolecular refinement programs. This is primarily because IAM offers a hard-to-beat combination of computational efficiency and modelling power at typical macromolecular resolutions. By contrast, more accurate multipolar modelling has historically been limited due to its computational cost and the absence of an interface between software capable of calculating structure factors and gradients based on multipolar models and software designed for macromolecular refinement. This work introduces pyDiSCaMB , a Python software package designed to integrate between the computational crystallography toolbox ( cctbx ) and the quantum crystallography library DiSCaMB ( Densities in Structural Chemistry and Molecular Biology ), thus enabling multipolar scattering models in Phenix 's toolkit. The implementation, features and capabilities of pyDiSCaMB are presented, the runtimes for the calculation of structure factor and target gradients with respect to atomic parameters are explored, and Fourier images of electrostatic potential, electron density and deformation maps are computed as illustrative examples. The pyDiSCaMB library will make multipolar modelling widely available to the structural biology community, potentially transforming refinement and model-building for both crystallography and cryogenic electron microscopy (cryoEM).

MATTS data bank↗

DOE OSTI2024

Crystal structure of N-terminally hexahistidine-tagged Onchocerca volvulus macrophage migration inhibitory factor-1

Onchocerca volvulus causes blindness, onchocerciasis, skin infections and devastating neurological diseases such as nodding syndrome. New treatments are needed because the currently used drug, ivermectin, is contraindicated in pregnant women and those co-infected with Loa loa . The Seattle Structural Genomics Center for Infectious Disease (SSGCID) produced, crystallized and determined the apo structure of N-terminally hexahistidine-tagged O. volvulus macrophage migration inhibitory factor-1 (His- Ov MIF-1). Ov MIF-1 is a possible drug target. His- Ov MIF-1 has a unique jellyfish-like structure with a prototypical macrophage migration inhibitory factor (MIF) trimer as the `head' and a unique C-terminal `tail'. Deleting the N-terminal tag reveals an Ov MIF-1 structure with a larger cavity than that observed in human MIF that can be targeted for drug repurposing and discovery. Removal of the tag will be necessary to determine the actual biological oligomer of Ov MIF-1 because size-exclusion chomatographic analysis of His- Ov MIF-1 suggests a monomer, while PISA analysis suggests a hexamer stabilized by the unique C-terminal tails.

Kimble, Amber D. (ORCID:0000000167851596)↗

DOE OSTI2024

On Rank Selection for Nonnegative Matrix Factorization

Rank selection, i.e. the choice of factorization rank, is the first step in constructing Nonnegative Matrix Factorization (NMF) models. It is a long-standing problem which is not unique to NMF, but arises in most models which attempt to decompose data into its underlying components. Since these models are often used in the unsupervised setting, the rank selection problem is further complicated by the lack of ground truth labels. In this paper, we review and empirically evaluate the most commonly used schemes for NMF rank selection.

Eswar, Srinivas [Argonne National Laboratory]↗

DOE OSTI2024

Towards maintaining canine training aid integrity: Effects of environmental factors and operational use on the triacetone triperoxide polymer odor capture‐and‐release system

Abstract There are many factors that may affect the longevity of or guide the use of canine training aids. Literature to date has mainly focused on identifying the headspace volatiles associated with training aids or odors and only minimal research exists into how different variables may alter those volatiles. The current study examines several factors affecting canine training aids: humidity, air flow, transportation, and operational deployment, using the triacetone triperoxide polymer odor capture‐and‐release canine training aid (TATP POCR) as the target. The TATP POCR is an absorption‐based canine training aid developed to be used to safely train canines to detect the odor of the explosive TATP in operational settings. Comparisons of the TATP POCR to neat TATP are made throughout the manuscript. First, humidity increased the background components of the POCR matrix, as well as the amount of TATP recovered was above the POCR. Humidity thus affected the amount of TATP detected but did not prevent detection. Second, air flow lessened the lifetime of the TATP POCR. Third, the practice of using primary and secondary containment successfully prevented contamination, cross‐contamination, and significant target loss, thereby maintaining kit integrity. Finally, the absorption of background odors from training environments was not observed. TATP headspace concentrations between a Deployed and Control POCR kit were not significantly different at time 0 (i.e., upon opening), which suggests that the operational use does not affect the function of the TATP POCR system. This information provides pivotal evidence for explosives detection canine handlers or trainers who utilize the TATP POCR.

Legal Medicine↗

DOE OSTI2024

Uncertainties in greenhouse gas emission factors: A comprehensive analysis of switchgrass‐based biofuel production

Abstract This study investigates uncertainties in greenhouse gas (GHG) emission factors related to switchgrass‐based biofuel production in Michigan. Using three life cycle assessment (LCA) databases—US lifecycle inventory (USLCI) database, GREET, and Ecoinvent—each with multiple versions, we recalculated the global warming intensity (GWI) and GHG mitigation potential in a static calculation. Employing Monte Carlo simulations along with local and global sensitivity analyses, we assess uncertainties and pinpoint key parameters influencing GWI. The convergence of results across our previous study, static calculations, and Monte Carlo simulations enhances the credibility of estimated GWI values. Static calculations, validated by Monte Carlo simulations, offer reasonable central tendencies, providing a robust foundation for policy considerations. However, the wider range observed in Monte Carlo simulations underscores the importance of potential variations and uncertainties in real‐world applications. Sensitivity analyses identify biofuel yield, GHG emissions of electricity, and soil organic carbon (SOC) change as pivotal parameters influencing GWI. Decreasing uncertainties in GWI may be achieved by making greater efforts to acquire more precise data on these parameters. Our study emphasizes the significance of considering diverse GHG factors and databases in GWI assessments and stresses the need for accurate electricity fuel mixes, crucial information for refining GWI assessments and informing strategies for sustainable biofuel production.

Kim, Seungdo↗

DOE OSTI2020

Biology of extracellular vesicles secreted from senescent cells as senescence‐associated secretory phenotype factors

The increase of the morbidity rate in age‐related diseases, such as cancer, Alzheimer’s disease, arteriosclerosis and pulmonary fibrosis, has become a profound social problem. Recent reports have pointed out that senescent cells accumulated in the body with aging might cause these aged‐related pathologies. Cellular senescence is known as an irreversible cell cycle arrest induced by various stresses, and can function as an important tumor suppression mechanism to exclude the premalignant cells. In contrast, senescent cells provoke the phenomenon, termed the senescence‐associated secretory phenotype, which causes the secretion of various inflammatory proteins, and it is at risk of facilitating chronic inflammation and oncogenic transformation to surrounding cells. We have previously reported that senescent cells secrete not only inflammatory proteins, but also extracellular vesicles (EV). EV include various cellular components, such as proteins, lipids and nucleic acids, which are proven to be important factors for cell‐to‐cell communication. Recent evidence suggests that EV secreted from senescent cells might contribute to tumorigenesis and age‐associated pathologies as new senescence‐associated secretory phenotype factors. In addition, we also showed that the EV secretion pathway is one of the essential defense mechanisms to maintain cellular homeostasis by excretion of intercellular toxic substances into extracellular space. Herein, this review shows the biological functions of EV secreted from senescent cells. Geriatr Gerontol Int 2020; ••: ••–•• .

Misawa, Tomoka↗

DOE OSTI2022

MYC transcription factors coordinate tryptophan–dependent defence responses and compromise seed yield in Arabidopsis

Robust plant immunity negatively affects other fitness traits, including growth and seed production. Jasmonate (JA) confers broad-spectrum protection against plant consumers by stimulating the degradation of JASMONATE ZIM-DOMAIN (JAZ) proteins, which in turn relieves repression on transcription factors (TFs) coincident with reduced growth and fecundity. The molecular mechanisms underlying JA-mediated decreases in fitness remain largely unknown. To assess the contribution of MYC TFs to growth and reproductive fitness at high levels of defence, we mutated three MYC genes in a JAZ-deficient mutant (jazD) of Arabidopsis thaliana that exhibits strong defence and low seed yield. Genetic epistasis analysis showed that de-repression of MYC TFs in jazD not only conferred strong resistance to insect herbivory but also reduced shoot and root growth, fruit size and seed yield. We also provided evidence that the JAZ–MYC module coordinates the supply of tryptophan with the production of indole glucosinolates and the proliferation of endoplasmic reticulum bodies that metabolise glucosinolates through the action of b-glucosidases. Our results establish MYCs as major regulators of growth- and reproductive–defence tradeoffs and further indicate that these factors coordinate tryptophan availability with the production of amino acid-derived defence compounds.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Genotype-dependent contribution of CBF transcription factors to long-term acclimation to high light and cool temperature

When grown under cool temperature, winter annuals upregulate photosynthetic capacity as well as freezing tolerance. Here, the role of three cold-induced C-repeat-binding factor (CBF1–3) transcription factors in photosynthetic upregulation and freezing tolerance was examined in two Arabidopsis thaliana ecotypes originating from Italy (IT) or Sweden (SW), and their corresponding CBF1–3-deficient mutant lines it: cbf123 and sw: cbf123 . Photosynthetic, morphological and freezing-tolerance phenotypes, as well as gene expression profiles, were characterized in plants grown from the seedling stage under different combinations of light level and temperature. Under high light and cool (HLC) growth temperature, a greater role of CBF1–3 in IT versus SW was evident from both phenotypic and transcriptomic data, especially with respect to photosynthetic upregulation and freezing tolerance of whole plants. Overall, features of SW were consistent with a different approach to HLC acclimation than seen in IT, and an ability of SW to reach the new homeostasis through the involvement of transcriptional controls other than CBF1–3. These results provide tools and direction for further mechanistic analysis of the transcriptional control of approaches to cold acclimation suitable for either persistence through brief cold spells or for maximisation of productivity in environments with continuous low temperatures.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Data-Driven Forgetting and Discount Factors for Vehicle Speed Forecasting in Ecological Adaptive Cruise Control

Abstract This paper investigates temporal correlations in human driving behavior using real-world driving to improve speed forecasting accuracy. These correlations can point to a measurement weighting function with two parameters: a forgetting factor for past speed measurements that the vehicle itself drove with, and a discount factor for the speeds of vehicles ahead based on information from vehicle-to-vehicle communication. The developed weighting approach is applied to a vehicle speed predictor using polynomial regression, a prediction method well-known in the literature. The performance of the developed approach is then assessed in both real-world and simulated traffic scenarios for accuracy and robustness. The new weighting method is applied to an ecological adaptive cruise control system, and its influence is analyzed on the prediction accuracy and the performance of the ecological adaptive cruise control in an electric vehicle powertrain model. The results show that the new prediction method improves energy saving from the eco-driving by up to 4.7% compared to a baseline least-square-based polynomial regression. This is a 10% improvement over the constant speed/acceleration model, a conventional speed predictor.

Automation & Control Systems↗

DOE OSTI2024

Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts

Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Two general paradigms have been proposed to explain this variation: (i) trade-offs between performance efficiency and breadth and (ii) the joint influence of extrinsic (environmental) and intrinsic (genomic) factors. We assembled genomic, metabolic, and ecological data from nearly all known species of the ancient fungal subphylum Saccharomycotina (1154 yeast strains from 1051 species), grown in 24 different environmental conditions, to examine niche breadth evolution. We found that large differences in the breadth of carbon utilization traits between yeasts stem from intrinsic differences in genes encoding specific metabolic pathways, but we found limited evidence for trade-offs. Furthermore, these comprehensive data argue that intrinsic factors shape niche breadth variation in microbes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

The military gear microbiome: risk factors surrounding the warfighter

ABSTRACT Combat extremity wounds are highly susceptible to contamination from surrounding environmental material. This bioburden could be partially transferred from materials in immediate proximity to the wound, including fragments of the uniform and gear. However, the assessment of the microbial bioburden present on military gear during operational conditions of deployment or training is relatively unexplored. Opportunistic pathogens that can survive on gear represent risk factors for infection following injury, especially following combat blasts, where fibers and other materials are embedded in wounded tissue. We utilized 16S rRNA sequencing to assess the microbiome composition of different military gear types (boot, trouser, coat, and canteen) from two operational environments (training in Hawai’i and deployed in Indonesia) across time (days 0 and 14). We found that microbiome diversity, stability, and composition were dependent on gear type, training location, and sampling timepoint. At day 14, species diversity was significantly higher in Hawai’i samples compared to Indonesia samples for boot, coat, and trouser swabs. In addition, we observed the presence of potential microbial risk factors, as opportunistic pathogenic species, such as Acinetobacter , Pseudomonas, and Staphylococcus , were found to be present in all sample types and in both study sites. These study outcomes will be used to guide the design of antimicrobial materials and uniforms and for infection control efforts following combat blasts and other injuries, thereby improving treatment guidance during military training and deployment. IMPORTANCE Combat extremity wounds are vulnerable to contamination from environments of proximity to the warfighter, leading to potential detrimental outcomes such as infection and delayed wound healing. Therefore, microbial surveillance of such environments is necessary to aid the advancement of military safety and preparedness through clinical diagnostics, treatment protocols, and uniform material design.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Hybridization capture sequencing for Vibrio spp. and associated virulence factors

ABSTRACT Proliferation ofVibriospp. in aquatic ecosystems is associated with climate change and, concomitantly, increased incidence of vibriosis. They are autochthonous to aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenicVibriospp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing (HCS) was employed to profile low-abundanceVibriospp. in environmental samples. The HCS panel targeted a family of molecular chaperones (CPN60) specific to 69Vibriospp. and 162Vibrio-specific virulence factors. This approach was evaluated in parallel with traditional whole-community shotgun sequencing in a metagenomic analysis of water and oyster samples collected from the Chesapeake Bay. In addition,Vibrio parahaemolyticusandVibrio vulnificusstrains isolated from the samples were subjected to whole-genome sequencing to determine the genetic characteristics of pathogenicVibriospp. circulating in an aquatic environment. HCS, employed to determine the incidence and characterization of specificVibriospp., yielded significantly greater metagenomic insight, notably a variety of otherVibriospp., including detection ofVibrio cholerae,Vibrio fluvialis, andVibrio aestuarianus, in addition toVibrio parahaemolyticusandVibrio vulnificus, and also important virulence factors not detectable using traditional molecular methods. Thus, pathogenicVibriospp. in aquatic ecosystems may be far more common than currently understood. It is concluded that environmental surveillance should include HCS, a valuable tool for the detection and characterization of pathogenic agents in aquatic ecosystems, notably vibrios. IMPORTANCE The increasing prevalence of pathogenicVibriospp. in aquatic ecosystems, driven by climate change, is closely linked to a rise in cholera and vibriosis cases, emphasizing the need for improved environmental surveillance. Vibrios are naturally occurring in aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenicVibriospp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing was employed to profile low-abundanceVibriospp. in metagenomic samples, namely water and oysters collected from the Chesapeake Bay. This approach was evaluated in parallel with traditional whole-community shotgun sequencing and whole-genome sequencing ofVibrio parahaemolyticusandVibrio vulnificusstrains isolated from the samples. Results suggest pathogenicVibriospp. in aquatic ecosystems may be far more common than currently understood, when multiple methods are considered for environmental surveillance.

Microbiology↗

DOE OSTI2022

The Transcription Factor Roc1 Is a Key Regulator of Cellulose Degradation in the Wood-Decaying Mushroom Schizophyllum commune

Wood-decaying fungi of the class Agaricomycetes (phylum Basidiomycota) are saprotrophs that break down lignocellulose and play an important role in nutrient recycling. They secrete a wide range of extracellular plant cell wall degrading enzymes that break down cellulose, hemicellulose, and lignin, the main building blocks of plant biomass. Although the production of these enzymes is regulated mainly at the transcriptional level, no activating regulators have been identified in any wood-decaying fungus in the class Agaricomycetes. We studied the regulation of cellulase expression in the wood-decaying fungus Schizophyllum commune. Comparative genomics and transcriptomics on two wild isolates revealed a Zn 2 Cys 6 -type transcription factor gene (roc1) that was highly upregulated during growth on cellulose, compared to glucose. It is only conserved in the class Agaricomycetes. A roc1 knockout strain showed an inability to grow on medium with cellulose as sole carbon source, and growth on cellobiose and xylan (other components of wood) was inhibited. Growth on non-wood-related carbon sources was not inhibited. Cellulase gene expression and enzyme activity were reduced in the Δroc1 strain. ChIP-Seq identified 1474 binding sites of the Roc1 transcription factor. Promoters of genes involved in lignocellulose degradation were enriched with these binding sites, especially those of LPMO (lytic polysaccharide monooxygenase) CAZymes, indicating that Roc1 directly regulates these genes. A conserved motif was identified as the binding site of Roc1, which was confirmed by a functional promoter analysis. Together, Roc1 is a key regulator of cellulose degradation and the first identified in wood-decaying fungi in the phylum Basidiomycota.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Physiological roles of an Acinetobacter -specific σ factor

ABSTRACT The Gram-negative pathogen Acinetobacter baumannii is considered an “urgent threat” to human health due to its propensity to become antibiotic resistant. Understanding the distinct regulatory paradigms used by A. baumannii to mitigate cellular stresses may uncover new therapeutic targets. Many γ-proteobacteria use the extracytoplasmic function (ECF) σ factor, RpoE, to invoke envelope homeostasis networks in response to stress. Acinetobacter species contain the poorly characterized ECF “SigAb”; however, it is unclear if SigAb has the same physiological role as RpoE. Here, we show that SigAb is a metal stress-responsive ECF that appears unique to Acinetobacter species and distinct from RpoE-like ECFs. We combine promoter mutagenesis, motif scanning, and chromatin immunoprecipitation-sequencing (ChIP-seq) to define the direct SigAb regulon, which consists of genes encoding SigAb itself, the stringent response mediator, RelA, and the uncharacterized small RNA, “SabS.” However, RNA-seq of strains overexpressing SigAb revealed a large, indirect regulon containing hundreds of genes. Metal resistance genes are key elements of the indirect regulon, as CRISPRi knockdown of sigAb or sabS resulted in increased copper sensitivity and excess copper-induced SigAb-dependent transcription. Furthermore, we found that two uncharacterized genes in the sigAb operon, “ aabA ” and “ aabB ,” have anti-SigAb activity. Finally, employing a targeted Tn-seq approach that uses CRISPR-associated transposons, we show that sigAb , aabA , and aabB are important for fitness even during optimal growth conditions. Our work reveals new physiological roles for SigAb and SabS, provides a novel approach for assessing gene fitness, and highlights the distinct regulatory architecture of A. baumannii . IMPORTANCE Acinetobacter baumannii is a hospital-acquired pathogen, and many strains are resistant to multiple antibiotics. Understanding how A. baumannii senses and responds to stress may uncover novel routes to treat infections. Here, we examine how the Acinetobacter -specific transcription factor, SigAb, mitigates stress. We find that SigAb directly regulates only a small number of genes, but indirectly controls hundreds of genes that have substantial impacts on cell physiology. We show that SigAb is required for maximal growth, even during optimal conditions, and is acutely required during growth in the presence of elevated copper. Given that copper toxicity plays roles in pathogenesis and on copper-containing surfaces in hospitals, we speculate that SigAb function may be important in clinically relevant contexts.

Bacon, Emily E. (ORCID:0000000180907689)↗