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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

The Efficacy and Safety of Mesalamine and Probiotics in Mild‐to‐Moderate Ulcerative Colitis: A Systematic Review and Meta‐Analysis

Objective . To evaluate the efficacy and safety of mesalamine in conjunction with probiotics for ulcerative colitis. Methods . Random controlled trials (RCTs) were searched in PubMed, EMBASE, Cochrane Library, China National Knowledge Infrastructure, Wanfang, and VIP (VIP Database for Chinese Technical Periodicals) from inception to October 2019. Methodological quality was assessed by the Cochrane Collaboration tool. The quality of evidence was rated by the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE). Data analysis was carried out in Review Manager 5.3. Results . A total of fifteen studies met the criteria for inclusion. Thirteen studies reported the clinical efficacy, three studies provided data on the clinical symptom scores, two trials reported disease activity index, four studies evaluated endoscopic score, and twelve studies reported adverse events. For ulcerative colitis (UC), mesalamine and probiotics had better clinical efficacy than mesalamine alone (≤8 weeks: RR = 1.12, 95% CI: 1.07–1.18, P < 0.0001; >8 weeks: RR = 1.25, 95% CI: 1.11–1.41, P = 0.0003). On the clinical symptom scores, disease activity index, and endoscopic score, UC patients receiving mesalamine and probiotics had significant difference than patients receiving mesalazine alone (MD = −2.02, 95% CI: −3.28 to −0.76, P = 0.002; MD = −1.20, 95% CI: −1.76 to −0.65, P < 0.001; and MD = −0.42, 95% CI: −0.61 to −0.23, P < 0.0001, respectively). There was no statistically significant difference in adverse events between the two groups (RR = 0.88, 95% CI: 0.54 to 1.43, P = 0.60). Conclusion . Our meta‐analysis results supported that mesalamine and probiotics were effective and safe in treating ulcerative colitis.

Tian, Chunying↗
DOE OSTI2020

Direct Numerical Simulation of the Flow through a Randomly Packed Pebble Bed

The proposition for molten salt and high-temperature gas-cooled reactors has increased the focus on the dynamics and physics in randomly packed pebble beds. Research is being conducted on the validity of these designs as a possible contestant for the fourth-generation nuclear power systems. A detailed understanding of the coolant flow behavior is required in order to ensure proper cooling of the reactor core during normal and accident conditions. In order to increase the understanding of the flow through these complex geometries and enhance the accuracy of lower-fidelity modeling, high-fidelity approaches such as direct numerical simulation (DNS) can be utilized. Nek5000, a spectral-element computational fluid dynamics (CFD) code, was used to develop DNS fluid flow data. The flow domain consisted of 147 pebbles enclosed by a bounding wall. In the work presented, the Reynolds numbers ranged from 430 to 1050 based on the pebble diameter and inlet velocity. Characteristics of the flow domain such as volume averaged porosity, axial porosity, and radial porosity were studied and compared with correlations available in the literature. Friction factors from the DNS results for all Reynolds numbers were compared with correlations in the literature. The first- and second-order statistics show good agreement with the available experimental data. Turbulence length scales were analyzed in the flow. Reynolds stress anisotropy was characterized by utilizing invariant analysis. Overall, the results of the analysis in this study provide deeper understanding of the flow behavior and the effect of the wall in packed beds.

Yildiz, Mustafa Alper↗
DOE OSTI2022

Determining protein polarization proteome-wide using physical dissection of individual Stentor coeruleus cells

Cellular components are non-randomly arranged with respect to the shape and polarity of the whole cell. Patterning within cells can extend down to the level of individual proteins and mRNA. But how much of the proteome is actually localized with respect to cell polarity axes? Proteomics combined with cellular fractionation has shown that most proteins localize to one or more organelles but does not tell us how many proteins have a polarized localization with respect to the large-scale polarity axes of the intact cell. Genome-wide localization studies in yeast found that only a few percent of proteins have a localized position relative to the cell polarity axis defined by sites of polarized cell growth. Here, we describe an approach for analyzing protein distribution within a cell with a visibly obvious global patterning - the giant ciliate Stentor coeruleus. Ciliates, including Stentor, have highly polarized cell shapes with visible surface patterning. A Stentor cell is roughly 2mmlong, allowing a ‘‘proteomic dissection’’ in which microsurgery is used to separate cellular fragments along the anterior-posterior axis, followed by comparative proteomic analysis. In our analysis, 25% of the proteome, including signaling proteins, centrin/SFI proteins, and GAS2 orthologs, shows a polarized location along the cell’s anterior-posterior axis. We conclude that a large proportion of all proteins are polarized with respect to global cell polarity axes and that proteomic dissection provides a simple and effective approach for spatial proteomics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Detection of surface water temperature variations of Mongolian lakes benefiting from the spatially and temporally gap-filled MODIS data

Lakes provide critical water resources for human activities and ecosystems, particularly in the Mongolian Plateau (MP), which is characterized by a dry climate and a harsh environment. As a region that is sensitive to anthropogenic warming, tracking lake surface water temperature (LSWT) changes in Mongolian lakes is crucial for understanding the consequences of a warming climate on lake ecosystems. However, the long-term monitoring of LSWT is restricted by the spatiotemporal gaps in the raw imagery of remote sensing-based land surface temperature (LST), e.g., the commonly used Moderate Resolution Imaging Spectroradiometer (MODIS) LST products. This study applied an improved gap-filling method by utilizing the discrete cosine transform-based penalized least squares (DCT-PLS) strategy in the spatial domain combined with the linear interpolation (LI) algorithm in the temporal domain. The method was applied to fill gaps in the LSWT imagery of 12 representative lakes across MP. The randomly sampled high-quality MODIS LSWT values in the spatial and temporal domains were excavated as false data gaps and considered “virtual true” validation datasets. The spatial validation results showed that the estimated LSWT for all the lake cases were comparable with the “virtual true” LSWT values, with the average values of the coefficient of determination, mean absolute error, mean square error, and root mean square error being 0.98, 0.38 °C, 0.45 °C, and 0.59 °C, respectively. Meanwhile, the error of nighttime LSWT results was relatively lower than that of daytime LSWT. For temporal interpolation validation, the LI algorithm exhibited relatively better performance and could more objectively indicate the variation in LSWT. Benefiting from the spatially and temporally well-constrained data, we analyzed the interannual and intra-annual change characteristics of the LSWTs of the 12 lakes. The long-term variations of annual and seasonal mean LSWTs in the 12 selected lakes exhibited no evident trends in 2000–2020, while presented apparent interannual fluctuations. The slight changes in the average LSWTs of the 12 selected lakes were in excellent synchronization with the surrounding LST derived from the reanalysis datasets, confirming the widely reported phenomenon of “global warming hiatus” that occurred in the early 21st century. This study improves the understanding of the LSWT variations in Mongolian lakes in response to global climate change. It has the potential to provide an effective approach for monitoring LSWT changes in other large-scale studies.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Simulation of Physics-Based 0-10Hz Strong Motion Using High Performance Computing Supporting Refinements to Regional Ground Motion Models for the Central Eastern US

In collaboration with the U.S. Nuclear Regulatory Commission (NRC) the LLNL has developed a computationally efficient simulation platform designed to perform physics-based ground motion simulations for crustal earthquakes in the Stable Continental Regions of Central and Eastern US (CEUS), using high-performance computing. The main objective of the earthquake simulations was to use synthetic ground motion to provide constrains to refinements of existing ergodic Ground Motion Models (GMMs), for large magnitude earthquakes and near-fault distances, for which these models are less reliable. Physics-based broadband (0-10Hz) ground motion simulations were used to estimate the near-fault ground motion amplitudes and within event and between-event variabilities associated with fault rupture characteristics. In our simulations we used a 3D regional velocity model that was based on Saikia’s 1D velocity model (1994). In simulations performed during the first stage of this project the Saikia’s velocity model demonstrated better performance in modelling high frequency regional wave propagation for the CEUS region recorded during the Mw5.0 November 7, 2016, Cushing Oklahoma (Taylor et al., 2017), and Mw5.8 September 3, 2016, Pawnee Oklahoma earthquakes. The proposed regional 3D model includes random perturbations to the 1D background model using the stochastic scheme of Pitarka and Mellors (2021). In addition, validation analysis of the rupture generator and regional wave propagation models, using comparisons with different GMMs for Mw6.5 and Mw7.0 scenario earthquakes in the CEUS region resulted in a very good match between the simulated and empirical ground motion models. For the purposes of seismic hazard assessment at the existing and planned nuclear power plants, NRC is interested in studies aimed at improving the current ground motion models (GMM) for both Stable Continental Regions (SCR) in the Central and Eastern US and Active Crustal Regions (ACR) in the Western US. Due to lack of recorded data, these improvements require synthetic data for short fault distances and large magnitude earthquakes for which the existing recorded data is not enough to uniquely constrain the GMMs. The need for simulations and strong motion data is especially critical for the CEUS region where we do not have recorded data from potentially large damaging earthquakes with moment magnitudes 6.0 and higher. In this the project, we focused on 10Hz simulations of Mw7.0 scenario earthquakes with strike slip and thrust faulting mechanisms. We used more than 50 Mw7.0 earthquake rupture scenarios to investigate the ground motion uncertainty due to unknown earthquake rupture parameters, in particular, the slip distribution, rupture velocity, and faulting mechanism, and their implication on ground motion amplification due to forward rupture directivity effects.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2021

A data-driven global soil heterotrophic respiration dataset and the drivers of its inter-annual variability

Soil heterotrophic respiration (SHR), one of the primary carbon fluxes from terrestrial ecosystems to the atmosphere, is important for carbon-climate feedbacks because of its sensitivity to available litter and soil carbon, climatic conditions, and nutrient availability. However, until recently limited SHR data were available, and most published global SHR estimates have either a short time span, coarse spatial resolution, or reply on overly-simple model formulations. To better understand and quantify the global distribution of SHR and its sensitivity to climate variability, we produced a new global SHR dataset using Random Forest algorithms, up-scaling 455 point data from the Global Soil Respiration Database (SRDB 4.0) with gridded fields of climatic, edaphic and productivity as explanatory variables. We estimated a global total SHR of 46.8 Pg C yr-1 over 1985-2013 (95% confidence interval: 38.6-56.3 Pg C yr-1), with a significant increasing trend of 0.03 Pg C yr-2 during this period. We found that the choice of soil moisture datasets contributes more to the difference among these data-driven SHR members rather than that of productivity, temperature and precipitation data sources. We also analyzed the influence of climatic variables on the inter-annual variability (IAV) of our SHR product. Water availability was the dominant driver of IAV at global scales, although the inferred sensitivity depends on the choice of the soil moisture gridded dataset. At the ecosystem scale, temperature strongly controls the IAV of SHR in tropical forests, while water availability dominates in extra-tropical forest and semi-arid regions. Our machine-learning gridded SHR dataset and outputs from process-based land surface models (TRENDYv6) show agreement for a strong association between water variability and SHR IAV at the global scale, but the two approaches lead to different temporal trend globally and different controlling variables for IAV at the ecosystem scale. Our study provides evidence for the pervasive and important role of water availability in driving SHR, indicating both a direct effect limiting decomposition rates and an indirect effect through the amount of fresh organic matter made available to SHR from productivity. In consideration of potential limitations and uncertainties remaining in our data-driven SHR datasets, we call for a more scientifically designed observation network for SHR, more observation data compilation, and increased use of deep learning methods making maximum use of observation data in hand. This will benefit process-based models, and improve our understanding of SHR response to future anomalous environmental conditions.

Yao, Yitong↗
DOE OSTI2023

Application of a Distributed Element Roughness Model to Additively Manufactured Internal Cooling Channels

Abstract Design for cooling effectiveness in turbine blades relies on accurate models for dynamic losses and heat transfer of internal cooling passages. Metal additive manufacturing (AM) has expanded the design space for these configurations, but can give rise to large-scale roughness features. The range of roughness length scales in these systems makes morphology resolved computational fluid dynamics (CFD) impractical. However, volumetric roughness models can be leveraged, as they have computational costs orders of magnitude lower. In this work, a discrete element roughness model (DERM), based on the double-averaged Navier–Stokes equations, is presented and applied to additively manufactured rough channels, representative of gas turbine blade cooling passages. Unique to this formulation of DERM is a generalized sheltering-based treatment of drag, a two-layer model for spatially averaged Reynolds stresses, and explicit treatment of dispersion. Six different AM rough surface channel configurations are studied, with roughness trough to peak sizes ranging from 15% to 60% nominal channel passage half-width, and the roughness Reynolds number ranges from Rek = 60 to 300. DERM predictions for spatially and temporally averaged mean flow quantities are compared to previously reported direct numerical simulation results. Good agreement in the mean velocity profiles, stress balances, and drag partitions are observed. While DERM models are typically calibrated to specific deterministic roughness morphologies at comparatively small roughness Reynolds numbers, the present more generalized DERM formulation has wider applicability. Here, it is demonstrated that the model can accommodate random roughness of large scale, typical of AM.

Engineering↗
DOE OSTI2025

Si content in methacrylamide-containing A- b -(B- r -C) block copolymers and its impact on reactive ion etching properties

Block copolymers (BCPs) of an A-block-(B-random-C) architecture have been explored as materials for nanolithography because the composition and chemistry of the random block enables modification of thermodynamic and wetting properties to meet manufacturing criteria. Here, in this study, A-b-(B-r-C) BCPs created by an amidation reaction of polystyrene-block-poly(pentafluorophenyl methacrylate) (PS-b-PPFMA) with controlled amounts of Si add insight to previous conclusions about the dual contributions of BCP chemistry and reactive ion etch (RIE) gas chemistry on etch properties. We focus on two RIE etch characteristics: organosilicon etch resistance in H 2 /N 2 plasma etching and enhanced removal of non-styrenic structures in an Ar/O 2 etch. Consistent with previous studies, higher amounts of Si result in greater etch resistance under H 2 /N 2 RIE, where at least ∼10 wt. % Si is necessary to exhibit sufficient etch resistance. By contrast, Ar/O 2 etching resulted in etch rates independent of Si content. We observe previously unreported surface roughening aligned with morphological domains during the H 2 /N 2 etch of modified PS-b-PPFMA BCPs. Limited in the amount of allowable Si to attain equal surface energy between blocks, these BCPs are further disqualified in forming a Si-containing mask. However, in an Ar/O 2 etch, the same BCPs exhibit suitable etch contrast and smooth domain structures, forming a uniform PS mask. Ultimately, this study uses the chemical flexibility of these materials to demonstrate the mechanisms of interactions between BCP and etch chemistry that must be considered to design effective materials for pattern transfer applications.

Eom, Christopher J. [University of Chicago, IL (Un↗
DOE OSTI2024

Electronic structure, magnetic correlations, and superconducting pairing in the reduced Ruddlesden-Popper bilayer La 3 Ni 2 O 6 under pressure: Different role of d 3 z 2 - r 2 orbital compared with La 3 Ni 2 O 7

The recent discovery of superconductivity in bilayer La 3 Ni 2 O 7 (327-LNO) under pressure stimulated much interest in layered nickelates. However, superconductivity was not found in another bilayer nickelate system, La 3 Ni 2 O 6 (326-LNO), even under pressure. To understand the similarities and differences between 326-LNO and 327-LNO, using density functional theory and the random phase approximation (RPA), we systematically investigate 326-LNO under pressure. The large crystal-field splitting between the e g orbitals caused by the missing apical oxygen moves the d 3z 2 -r 2 orbital farther away from the Fermi level, implying that the d 3z 2 -r 2 orbital plays a less important role in 326-LNO than in 327-LNO. This also results in a smaller bandwidth for the d x 2 -y 2 orbital and a reduced energy gap for the bonding-antibonding splitting of the d 3z 2 -r 2 orbital in 326-LNO, as compared to 327-LNO. Moreover, the in-plane hybridization between the d x 2 -y 2 and d 3z 2 -r 2 orbitals is found to be small in 326-LNO, while it is much stronger in 327-LNO. Furthermore, the low-spin ferromagnetic state is found to be the likely ground state in 326-LNO under high pressure. The weak interlayer coupling suggests that s ± -wave pairing is unlikely in 326-LNO. The robust in-plane ferromagnetic coupling also suggests that d-wave superconductivity, which is usually caused by antiferromagnetic fluctuations of the d x 2 -y 2 orbital, is also unlikely in 326-LNO. These conclusions are supported by our many-body RPA calculations of the pairing behavior. Additionally, contrasting with the cuprates, for the bilayer cuprate HgBa 2 CaCu 2 O 6 , we find a strong self-doping effect of the d x 2 -y 2 orbital under pressure, with the charge of Cu being reduced by approximately 0.13 electrons from 0 GPa to 25 GPa. In contrast, we do not observe such a change in the electronic density in 326-LNO under pressure, establishing another important difference between the nickelates and the cuprates.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Dosimetric and biological impact of activity extravasation of radiopharmaceuticals in PET imaging

The increasing use of nuclear medicine and PET imaging has intensified scrutiny of radiotracer extravasation. To our knowledge, this topic is understudied but holds great potential for enhancing our understanding of extravasation in clinical PET imaging. This work aims to (1) quantify the absorbed doses from radiotracer extravasation in PET imaging, both locally at the site of extravasation and with the extravasation location as a source of exposure to bodily organs and (2) assess the biological ramifications within the injection site at the cellular level. A radiation dosimetry simulation was performed using a whole-body 4D Extended Cardiac-Torso (XCAT) phantom embedded in the GATE Monte Carlo platform. A 10-mCi dose of 18 F-FDG was chosen to simulate a typical clinical PET scan scenario, with 10% of the activity extravasated in the antecubital fossa of the right arm of the phantom. The extravasation volume was modeled as a 5.5 mL rectangle in the hypodermal layer of skin. Absorbed dose contributions were calculated for the first two half-lives, assuming biological clearance thereafter. Dose calculations were performed as absorbed doses at the organ and skin levels. Energy deposition was simulated both at the local extravasation site and in multiple organs of interest and converted to absorbed doses based on their respective masses. Each simulation was repeated ten times to estimate Monte Carlo uncertainties. Biological impacts on cells within the extravasated volume were evaluated by randomizing cells and exposing them to a uniform radiation source of 18 F and 68 Ga. Particle types, their energies, and direction cosines were recorded in phase space files using a separate Geant4 simulation to characterize their entry into the nucleus of the cellular volume. Subsequently, the phase space files were imported into the TOPAS-nBio simulation to assess the extent of DNA damage, including double-strand breaks (DSBs) and single-strand breaks (SSBs). Organ-level dosimetric estimations are presented for 18 F and 68 Ga radionuclides in various organs of interest. With 10% extravasation, the hypodermal layer of the skin received the highest absorbed dose of 1.32 ± 0.01 Gy for 18 F and 0.99 ± 0.01 Gy for 68 Ga. The epidermal and dermal layers received absorbed doses of 0.07 ± 0.01 Gy and 0.13 ± 0.01 Gy for 18 F, and 0.14 ± 0.01 Gy and 0.29 ± 0.01 Gy for 68 Ga, respectively. In the extravasated volume, 18 F caused an average absorbed dose per nucleus of 0.17 ± 0.01 Gy, estimated to result in 10.58 ± 0.50 DSBs and 268.11 ± 12.43 SSBs per nucleus. For 68 Ga, the absorbed dose per nucleus was 0.11 ± 0.01 Gy, leading to an estimated 6.49 ± 0.34 DSBs and 161.24 ± 8.12 SSBs per nucleus. Absorbed doses in other organs were on the order of micro-gray (µGy). The likelihood of epidermal erythema resulting from extravasation during PET imaging is low, as the simulated absorbed doses to the epidermis remain below the thresholds that trigger such effects. Moreover, the organ-level absorbed doses were found to be clinically insignificant across various simulated organs. The minimal DNA damage at the extravasation site suggests that long-term harm, such as radiation-induced carcinogenesis, is highly unlikely.

DNA strand breaks↗
DOE OSTI2021

Predicting Intensive Care Unit Length of Stay and Mortality Using Patient Vital Signs: Machine Learning Model Development and Validation

Background: Patient monitoring is vital in all stages of care. In particular, intensive care unit (ICU) patient monitoring has the potential to reduce complications and morbidity, and to increase the quality of care by enabling hospitals to deliver higher-quality, cost-effective patient care, and improve the quality of medical services in the ICU. Objective: We here report the development and validation of ICU length of stay and mortality prediction models. The models will be used in an intelligent ICU patient monitoring module of an Intelligent Remote Patient Monitoring (IRPM) framework that monitors the health status of patients, and generates timely alerts, maneuver guidance, or reports when adverse medical conditions are predicted. Methods: We utilized the publicly available Medical Information Mart for Intensive Care (MIMIC) database to extract ICU stay data for adult patients to build two prediction models: one for mortality prediction and another for ICU length of stay. For the mortality model, we applied six commonly used machine learning (ML) binary classification algorithms for predicting the discharge status (survived or not). For the length of stay model, we applied the same six ML algorithms for binary classification using the median patient population ICU stay of 2.64 days. For the regression-based classification, we used two ML algorithms for predicting the number of days. We built two variations of each prediction model: one using 12 baseline demographic and vital sign features, and the other based on our proposed quantiles approach, in which we use 21 extra features engineered from the baseline vital sign features, including their modified means, standard deviations, and quantile percentages. Results: We could perform predictive modeling with minimal features while maintaining reasonable performance using the quantiles approach. The best accuracy achieved in the mortality model was approximately 89% using the random forest algorithm. The highest accuracy achieved in the length of stay model, based on the population median ICU stay (2.64 days), was approximately 65% using the random forest algorithm. Conclusions: The novelty in our approach is that we built models to predict ICU length of stay and mortality with reasonable accuracy based on a combination of ML and the quantiles approach that utilizes only vital signs available from the patient’s profile without the need to use any external features. This approach is based on feature engineering of the vital signs by including their modified means, standard deviations, and quantile percentages of the original features, which provided a richer dataset to achieve better predictive power in our models.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Computational discovery of two-dimensional rare-earth iodides: promising ferrovalley materials for valleytronics

Two-dimensional Ferrovalley materials with intrinsic valley polarization are rare but highly promising for valley-based nonvolatile random access memory and valley filter devices. These ferromagnetic materials exhibit valleys at or near the Fermi level with intrinsic magnetism. The strong coupling between magnetism and spin–orbit coupling induces intrinsic valley polarization. Using Kinetically Limited Minimization, an unconstrained crystal structure prediction algorithm, and prototype sampling based on first-principles calculations, we have discovered new Ferrovalley materials, rare-earth iodides RI 2 , where R is a rare-earth element belonging to Sc, Y, or La-Lu, and I is Iodine. The rare-earth iodides are layered and demonstrate either 2H, 1T, or 1T d phase as the ground state in bulk, analogous to transition metal dichalcogenides (TMDCs). The calculated exfoliation energy of monolayers (MLs) is comparable to that of graphene and TMDCs, suggesting possible experimental synthesis. The MLs in the 2H phase exhibit ferromagnetism due to unpaired electrons in d and f orbitals. Throughout the rare-earth series, d bands have valley polarization at K and $\overline{K}$ points in the Brillouin zone in the vicinity of the Fermi level. Large intrinsic valley polarization in the range of 15–143 meV without external stimuli is observed in these Ferrovalley materials, which can be enhanced further by applying an in-plane bi-axial strain. These valleys can selectively be probed and manipulated for information storage and processing, potentially offering superior performance beyond conventional electronics and spintronics. Here we further show that the 2H ferromagnetic phase of RI 2 MLs possesses non-zero Berry curvature and exhibits anomalous valley Hall effect with considerable anomalous Hall conductivity. Our work will incite exploratory synthesis of the predicted Ferrovalley materials and their application in valleytronics and beyond.

2D materials↗
DOE OSTI2022

Temporal regulation of cold transcriptional response in switchgrass

Switchgrass low-land ecotypes have significantly higher biomass but lower cold tolerance compared to up-land ecotypes. Understanding the molecular mechanisms underlying cold response, including the ones at transcriptional level, can contribute to improving tolerance of high-yield switchgrass under chilling and freezing environmental conditions. Here, by analyzing an existing switchgrass transcriptome dataset, the temporal cis- regulatory basis of switchgrass transcriptional response to cold is dissected computationally. We found that the number of cold-responsive genes and enriched Gene Ontology terms increased as duration of cold treatment increased from 30 min to 24 hours, suggesting an amplified response/cascading effect in cold-responsive gene expression. To identify genomic sequences likely important for regulating cold response, machine learning models predictive of cold response were established using k -mer sequences enriched in the genic and flanking regions of cold-responsive genes but not non-responsive genes. These k -mers, referred to as putative cis -regulatory elements (pCREs) are likely regulatory sequences of cold response in switchgrass. There are in total 655 pCREs where 54 are important in all cold treatment time points. Consistent with this, eight of 35 known cold-responsive CREs were similar to top-ranked pCREs in the models and only these eight were important for predicting temporal cold response. More importantly, most of the top-ranked pCREs were novel sequences in cold regulation. Our findings suggest additional sequence elements important for cold-responsive regulation previously not known that warrant further studies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

De Sitter diagrammar and the resummation of time

Light scalars in inflationary spacetimes suffer from logarithmic infrared divergences at every order in perturbation theory. This corresponds to the scalar field values in different Hubble patches undergoing a random walk of quantum fluctuations, leading to a simple toy “landscape” on superhorizon scales, in which we can explore questions relevant to eternal inflation. However, for a sufficiently long period of inflation, the infrared divergences appear to spoil computability. Some form of renormalization group approach is thus motivated to resum the log divergences of conformal time. Such a resummation may provide insight into De Sitter holography. We present here a novel diagrammatic analysis of these infrared divergences and their resummation. Basic graph theory observations and momen- tum power counting for the in-in propagators allow a simple and insightful determination of the leading-log contributions. One thus sees diagrammatically how the superhorizon sector consists of a semiclassical theory with quantum noise evolved by a first-order, interacting classical equation of motion. This rigorously leads to the “Stochastic Inflation” ansatz developed by Starobinsky to cure the scalar infrared pathology nonperturbatively. Our approach is a controlled approximation of the underlying quantum field theory and is systematically improvable.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Genome-wide fitness profiling reveals molecular mechanisms that bacteria use to interact with Trichoderma atroviride exometabolites

Trichoderma spp. are ubiquitous rhizosphere fungi capable of producing several classes of secondary metabolites that can modify the dynamics of the plant-associated microbiome. However, the bacterial-fungal mechanisms that mediate these interactions have not been fully characterized. Here, a random barcode transposon-site sequencing (RB-TnSeq) approach was employed to identify bacterial genes important for fitness in the presence of Trichoderma atroviride exudates. We selected three rhizosphere bacteria with RB-TnSeq mutant libraries that can promote plant growth: the nitrogen fixers Klebsiella michiganensis M5aI and Herbaspirillum seropedicae SmR1, and Pseudomonas simiae WCS417. As a non-rhizosphere species, Pseudomonas putida KT2440 was also included. From the RB-TnSeq data, nitrogen-fixing bacteria competed mainly for iron and required the siderophore transport system TonB/ExbB for optimal fitness in the presence of T . atroviride exudates. In contrast, P . simiae and P . putida were highly dependent on mechanisms associated with membrane lipid modification that are required for resistance to cationic antimicrobial peptides (CAMPs). A mutant in the Hog1-MAP kinase (Δ tmk 3) gene of T . atroviride showed altered expression patterns of many nonribosomal peptide synthetase (NRPS) biosynthetic gene clusters with potential antibiotic activity. In contrast to exudates from wild-type T . atroviride , bacterial mutants containing lesions in genes associated with resistance to antibiotics did not show fitness defects when RB-TnSeq libraries were exposed to exudates from the Δ tmk3 mutant. Unexpectedly, exudates from wild-type T . atroviride and the Δ tmk 3 mutant rescued purine auxotrophic mutants of H . seropedicae , K . michiganensis and P . simiae . Metabolomic analysis on exudates from wild-type T . atroviride and the Δ tmk 3 mutant showed that both strains excrete purines and complex metabolites; functional Tmk3 is required to produce some of these metabolites. This study highlights the complex interplay between Trichoderma -metabolites and soil bacteria, revealing both beneficial and antagonistic effects, and underscoring the intricate and multifaceted nature of this relationship.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Fine-scale landscape characteristics, vegetation composition, and snowmelt timing control phenological heterogeneity across low-Arctic tundra landscapes in Western Alaska

The Arctic is warming at over twice the rate of the rest of the Earth, resulting in significant changes in vegetation seasonality that regulates annual carbon, water, and energy fluxes. However, a crucial knowledge gap exists regarding the intricate interplay among climate, permafrost, and vegetation that generates high phenology variability across extensive tundra landscapes. This oversight has led to significant discrepancies in phenological patterns observed across warming experiments, long-term ecological observations, and satellite and modeling studies, undermining our ability to understand and forecast plant responses to climate change in the Arctic. To address this problem, we assessed plant phenology across three low-Arctic tundra landscapes on the Seward Peninsula, Alaska, using a combination of in-situ phenocam observations and high-resolution PlanetScope CubeSat data. We examined the patterns and drivers of phenological diversity across the landscape by (1) quantifying phenological diversity among dominant plant function types (PFTs) and (2) modeling the interrelations between plant phenology and fine-scale landscape features, such as topography, snowmelt, and vegetation. Our findings reveal that both spring and fall phenology varied significantly across Arctic PFTs, accounting for about 25%–44% and 34%–59% of the landscape-scale variation in the start of spring [SOS] and start of fall [SOF], respectively. Deciduous tall shrubs (e.g. alder and willow) had a later SOS (~7 d behind the mean of other PFTs), but completed leaf expansion (within 2 weeks) considerably faster compared to other PFTs. We modeled the landscape-scale variation in SOS and SOF using Random Forest, which showed that plant phenology can be accurately captured by a suite of variables related to vegetation composition, topographic characteristics, and snowmelt timing (variance explained: 53%–68% for SOS and 59%–82% for SOF). Notably, snowmelt timing was a crucial determinant of SOS, a factor often neglected in most spring phenology models. Our study highlights the impact of fine-scale vegetation composition, snow seasonality, and landscape features on tundra phenological heterogeneity. Improved understanding of such considerable intra-site phenological variability and associated proximate controls across extensive Arctic landscapes offers critical insights for representation of tundra phenology in process models and associated impact assessments with climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Model Inputs, Outputs, and Scripts associated with: “Combined effects of stream hydrology and land use on basin-scale hyporheic zone denitrification in the Columbia River Basin”

This data package is associated with the publication “Combined effects of stream hydrology and land use on basin‐scale hyporheic zone denitrification in the Columbia River Basin”, published in Water Resource Research (Son et al.2022) available at https://doi.org/10.1029/2021WR031131. This data package includes the key model inputs/outputs of the river corridor model for the Columbia River Basin (CRB) and the model source codes used in the manuscript. The model is a carbon-nitrogen-coupled river corridor model (RCM), and the model is used to quantify hyporheic zone (HZ) denitrification at the NHDPLUS stream reach scales. The RCM used in this study combines empirical substrate models derived from observations and three microbially driven reactions, including two-step denitrification and aerobic respiration, are considered within the HZ. The key input data of the model are exchange flux, residence time, and stream solute (dissolved organic carbon (DOC), dissolved oxygen (DO), and nitrate concentrations). These inputs are constant over time and represent long-term averaged values. This study uses the RCM to explore the spatial patterns of HZ denitrification across reaches with different sizes and land use in the CRB. Our main objective is to use the RCM as a virtual reality model, and the machine-learning models as surrogates that encapsulate the complexities of the physics-based model while identifying the importance of different variables that are not evident in the model conceptualization. We do not include a direct comparison of the modeled HZ denitrification and measurements; however, the RCM can capture the overall spatial patterns of the HZ denitrification because the model inputs and its reaction networks are based on well-established theory and a physical-based model. The combination of the model-based predictions and a machine-learning approach (e.g., random forest) is used to improve our understanding of what variables of the model are associated with spatial patterns of the modeled denitrification across reaches with different sizes and land uses, and to develop a proxy model using measurable variables to reproduce the simulated patterns.This dataset contains five folders: (1) model_inputs, (2) model_outputs, (3) Rscripts, (4) figures, and (5) model_codes. It also contains a readme, file level metadata (FLMD), and data dictionary (dd). Please see the FLMD for a list of all the files contained in this data package and descriptions for each. The model_inputs folder contains the model inputs used to drive the model simulations. The model_outputs folder contains key model output files from the river corridor model. The Rscripts folder contains the Rscripts for pre- and post- processing model results. The figures folder contains the raw figures associated with the manuscript. The model_codes folder includes key model source codes/input files. All files are .jpg, .jpeg, .out, .e, .od, .dat, .sub, .F90, .0, .R, .sbx, .cpg, .sbn, .shx, .shp, .dbf, .prj, .tfw, .tif, .xml, .pdf, or .csv.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Integrated quantum optical phase sensor in thin film lithium niobate

Abstract The quantum noise of light, attributed to the random arrival time of photons from a coherent light source, fundamentally limits optical phase sensors. An engineered source of squeezed states suppresses this noise and allows phase detection sensitivity beyond the quantum noise limit (QNL). We need ways to use quantum light within deployable quantum sensors. Here we present a photonic integrated circuit in thin-film lithium niobate that meets these requirements. We use the second-order nonlinearity to produce a squeezed state at the same frequency as the pump light and realize circuit control and sensing with electro-optics. Using 26.2 milliwatts of optical power, we measure (2.7 ± 0.2)% squeezing and apply it to increase the signal-to-noise ratio of phase measurement. We anticipate that photonic systems like this, which operate with low power and integrate all of the needed functionality on a single die, will open new opportunities for quantum optical sensing.

47 OTHER INSTRUMENTATION↗