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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A Graphical Model for Fusing Diverse Microbiome Data

This paper develops a Bayesian graphical model for fusing disparate types of count data. The motivating application is the study of bacterial communities from diverse high-dimensional features, in this case, transcripts, collected from different treatments. In such datasets, there are no explicit correspondences between the communities and each corresponds to different factors, making data fusion challenging. We introduce a flexible multinomial-Gaussian generative model for jointly modeling such count data. This latent variable model jointly characterizes the observed data through a common multivariate Gaussian latent space that parameterizes the set of multinomial probabilities of the transcriptome counts. The covariance matrix of the latent variables induces a covariance matrix of co-dependencies between all the transcripts, effectively fusing multiple data sources. We present a computationally scalable variational Expectation-Maximization (EM) algorithm for inferring the latent variables and the parameters of the model. Here, the inferred latent variables provide a common dimensionality reduction for visualizing the data and the inferred parameters provide a predictive posterior distribution. In addition to simulation studies that demonstrate the variational EM procedure, we apply our model to a bacterial microbiome dataset.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

4D Multimodal Co-attention Fusion Network with Latent Contrastive Alignment for Alzheimer’s Diagnosis

Multimodal neuroimaging provides complementary structural and functional insights into both human brain organization and disease-related dynamics. Recent studies demonstrate enhanced diagnostic sensitivity for Alzheimer’s disease (AD) through synergistic integration of neuroimaging data (e.g., sMRI, fMRI) with tabular data (e.g., behavioral and cognitive tests). However, the intrinsic heterogeneity across modalities (e.g., 4D spatiotemporal fMRI dynamics vs. 3D anatomical sMRI structure) presents critical challenges for discriminative feature fusion, often leading to information loss or biased fusion. To bridge this gap, we propose M2M-AlignNet: a multimodal co-attention network with latent alignment for early AD diagnosis using sMRI and fMRI. At the core of our approach is a multi-patch-to-multi-patch (M2M) contrastive loss function that quantifies and reduces representational discrepancies via weighted patch correspondence, explicitly aligning fMRI components across brain regions with their sMRI structural substrates without one-to-one constraints. Additionally, we propose a latent-as-query co-attention module to autonomously discover fusion patterns, circumventing modality prioritization biases while minimizing feature redundancy. We conduct extensive experiments to confirm the effectiveness of our method and highlight the correspondence between fMRI and sMRI as AD biomarkers.

Wei, Yuxiang [Georgia Institute of Technology]↗
DOE OSTI2022

The incorporation of environmentally derived 87 Sr / 86 Sr and Sr/Ca in early otolith formation of Chinook salmon

Abstract Effective species management often requires understanding patterns of movement and habitat use. A common approach in identifying where individuals reside relies upon chemical tracers from the environment that are incorporated into an individual's tissues. For fish, isotopes in their otoliths, specifically the portion of their otolith formed during their larval stage, have been used to identify the natal origin. Complicating this work, however, is the fact that during this life stage, there is a shift in the source of isotopes deposited onto the growing otolith from maternally to environmentally derived. The objective of this study was to identify the portion of the otolith representing this transition to environmentally derived isotopes so as to accurately investigate questions of natal origin for a threatened population of fall Chinook salmon ( Oncorhynchus tshawytscha ). We exposed developing larvae to four treatments that differed in terms of their water strontium isotope ratio ( 87 Sr/ 86 Sr) and used change‐point analysis of otolith 87 Sr/ 86 Sr and strontium to calcium ratio (Sr/Ca) to identify the otolith radius corresponding to the transition to environmentally derived isotopes. Our results indicated this transition occurred, on average, at 132 μm ( 87 Sr/ 86 Sr; ±50 μm standard deviation) and 127 μm (Sr/Ca; ±29 μm) from the otolith core, which corresponded to the developmental time between hatching and exogenous feeding. A substantial proportion of our otoliths (i.e., 61%) did not show convergence between otolith and water 87 Sr/ 86 Sr by the end of the 113‐day experiment, which was likely due to the dietary contribution of marine‐based feed. Therefore, we were unable to recommend an otolith radius to target for the purposes of reconstructing natal origin apart from being beyond approximately 130 μm.

Chittaro, Paul↗
DOE OSTI2022

Alterations in soil pH emerge as a key driver of the impact of global change on soil microbial nitrogen cycling: Evidence from a global meta-analysis

Soil nitrogen (N) cycling is critical to the productivity of terrestrial ecosystems. However, the impact of global change factors (GCFs) on the microbial mediators of N cycling pathways has yet to be synthesized, and it also remains unclear whether the response of the abundance of N-cycling genes can predict changes in their corresponding processes. We synthesized 8322 paired observations of soil microorganisms related to N cycling from field experiments in which GCFs (climate change and nutrient addition) were manipulated. We found that the abundance of soil microbes and most N-cycling genes were resistant to elevated CO 2 , experimental warming and water addition/reduction; however, N addition and the combination of N addition with other GCFs significantly increased the abundance of ammonia oxidizer bacteria (amoA-AOB). The results indicated that in steady-state (natural) conditions, the main factors driving the global abundance of soil bacteria, archaea and N-cycling genes varied in terms of the contributions of climatic and edaphic factors. However, upon manipulation of GCFs, the induced change in soil pH was the most essential factor associated with changes in the abundance of soil microbes and N-cycling genes. Notably, the changes in ammonia-oxidizing archaea (amoA-AOA) and amoA-AOB genes, in addition to genes involved in denitrification (nirS and nirK), were significantly correlated with the rates of their corresponding processes, but GCF-induced shifts in the potential nitrification rate (PNR) were explained well by changes in the abundance of the amoA-AOB gene under GCFs. In conclusion, our study highlights how ongoing GCFs impact the abundance of soil microbes and N-cycling genes, which might have a profound impact on terrestrial N cycling. Our field-based results provide new insights into the drivers of the abundance of soil microbes and N-cycling genes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

In situ characterization of residual stress evolution during heat treatment of SiC/SiC ceramic matrix composites using high-energy X-ray diffraction

Volumetric strains were measured in silicon carbide/silicon carbide melt-infiltrated ceramic matrix composites (CMCs) at ambient and high temperatures using high-energy synchrotron X-ray diffraction (XRD). Both silicon and silicon carbide constituents were interrogated utilizing a broad spectrum of diffracting planes that would be largely inaccessible to common laboratory XRD equipment. Residual room-temperature principal strains in the melt-infiltrated silicon phase were found to be approximately 1100 mu epsilon in compression, corresponding to stresses of approximately 300 MPa using simplifying constitutive assumptions. Residual room-temperature principal strains in silicon carbide particles found throughout the matrix were approximately 500 mu epsilon in tension, corresponding to approximately 300 MPa. Residual strains were found to decrease considerably as temperatures increased from ambient temperature to 1250 degrees C. Additionally, residual strains returned to approximately preheat treatment values after cool-down to ambient temperature. Strain measurements in the silicon phase were found to be significantly affected by dissolved boron dopant levels causing contraction of the silicon lattice. This contraction must be accounted for in high-temperature experiments for accurate calculation of stresses in the silicon phase.

36 MATERIALS SCIENCE↗
DOE OSTI2022

When One Cannot Bypass the Byproducts: Plastic Packaging Waste Embedded in Production and Export

While packaging is praised for reducing waste of perishable food products, packaging waste is a growing concern. Its least recyclable type, plastics waste, is increasingly polluting the marine environment and many developing countries are now refusing to take the waste from developed countries. Before responsibility can be established, one has to identify the key producers and consumers. This paper adjusts the packaging waste satellite account in EXIOBASE 3 by combining the official waste data published by the World Bank. Based on input-output methods, we find that the world's top suppliers of plastic packaging waste are the United States, China, and Brazil. Food and beverage products constitute the bulk of the problem. Yet, 21% of these countries' plastic packaging waste is induced export. At the global level, it is 25.8%. About 76.0% of export-induced plastic packaging waste corresponds to packaging of the exported goods that will ultimately be disposed of in the destination country; while the others correspond to the packaging used in their supply-chain and wasted domestically. We conclude that international efforts need to assign shared responsibility and promote improvement in plastic packaging recyclability.

environment responsibility↗
DOE OSTI2025

Amino acid substrate specificities and tissue expression profiles of the nine CYP79A encoding genes in Sorghum bicolor

Cytochrome P450s of the CYP79 family catalyze two N-hydroxylation reactions, converting a selected number of amino acids into the corresponding oximes. The sorghum genome (Sorghum bicolor) harbours nine CYP79A encoding genes, and here sequence comparisons of the CYP79As along with their substrate recognition sites (SRSs) are provided. The substrate specificity of previously uncharacterized CYP79As was investigated by transient expression in Nicotiana benthamiana and subsequent transformation of the oximes formed into the corresponding stable oxime glucosides catalyzed by endogenous UDPG-glucosyltransferases (UGTs). CYP79A61 uses phenylalanine as a substrate, whereas CYP79A91, CYP79A93, and CYP79A95 use valine and isoleucine as substrates, with CYP79A93 showing the ability also to use phenylalanine. CYP79A94 uses isoleucine as a substrate. Analysis of 249 sorghum transcriptomes from two different sorghum cultivars showed the expression levels and tissue-specific expression of the CYP79As. CYP79A1 is the committed gene in dhurrin formation and was the highest expressed gene in most tissues/organs. CYP79A61 was primarily expressed in fully developed leaf blades and leaf sheaths. CYP79A91 and CYP79A92 were expressed mainly in roots >200 cm below ground, while CYP79A93 and CYP79A94 were most highly expressed in the leaf collar and leaf sheath, respectively. Here, the possible signalling effects of the oximes and their metabolites produced in different sorghum tissues are discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Experimental Measurements of the Wake of a Sphere at Subcritical Reynolds Numbers

This work experimentally investigated the flow phenomena and vortex structures in the wake of a sphere located in a water loop at Reynolds numbers of Re = 850, 1,250, and 1,700. Velocity fields in the wake region were obtained by applying the time-resolved stereoscopic particle image velocimetry (TR-SPIV) technique. From the acquired TR-SPIV velocity vector fields, the statistical values of mean and fluctuating velocities were computed. Spectral analysis, two-point velocity–velocity cross-correlation, proper orthogonal decomposition (POD) and vortex identification analyses were also performed. The velocity fields show a recirculation region that decreases in length with an increase of Reynolds numbers. The power spectra from the spectral analysis had peaks corresponding to a Strouhal number of St = 0.2, which is a value commonly found in the literature studies of flow over a sphere. The two-point cross-correlation analysis revealed elliptical structures in the wake, with estimated integral length scales ranging between 12% and 63% of the sphere diameter. The POD analysis revealed the statistically dominant flow structures that captured the most flow kinetic energy. It is seen that the flow kinetic energy captured in the smaller scale flow structures increased as Reynolds number increased. The POD modes contained smaller structure as the Reynolds number increased and as mode order increased. In addition, spectral analysis performed on the POD temporal coefficients revealed peaks corresponding to St = 0.2, similar to the spectral analysis on the fluctuating velocity. The ability of POD to produce low-order reconstructions of the flow was also utilized to facilitate vortex identification analysis, which identified average vortex sizes of 0.41D for Re1, 0.33D for Re2, and 0.32D for Re3.

Engineering↗
DOE OSTI2021

On the Bandwidth and Beam Profile Characteristics of a Simple Low-Frequency Collimated Ultrasound Beam Source

We numerically investigate the bandwidth and collimation characteristics of ultrasound beams generated by a simple collimated ultrasound beam source that consists of a piezoelectric disk operated near its radial mode resonances. We simulate the ultrasound beam generated in a fluid medium as a function of the excitation frequency for two cases: (1) free piezoelectric disk that corresponds to zero-traction along the lateral edge and (2) fixed piezoelectric disk that corresponds to zero-displacement along the lateral edge. We present and discuss the physical mechanism underpinning the frequency-dependent collimation and bandwidth properties of the ultrasound beams. We observe that the collimated beam generated by the free disk repeatedly lengthens/shortens and also extends/retracts sidelobes with increasing frequency. Alternatively, fixing the piezoelectric disk results in a consistent beam profile shape across a broad range of frequencies. This facilitates generating broadband signals such as a Gaussian pulse or chirp, which are common in ultrasound imaging. Thus, the fixed piezoelectric disk finds application as a collimated ultrasound beam source in a wide range of applications including medical ultrasound imaging, scanning acoustic microscopy, sonar detection, and other nondestructive ultrasound inspection techniques.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Drying of a Fully Saturated Porous Medium With Excess Water Layers: A Numerical Study

Abstract Drying of moist porous media can be very energy inefficient. For example, in the pulp and paper industry, paper drying consumes more than two-thirds of the total energy used in paper machines. Novel drying technologies can decrease the energy used for drying and lessen the manufacturing processes' carbon footprint. Developing next-generation drying technologies to dry moist porous media may require an understanding of removing moisture from a fully saturated porous material with excess water. This paper provides a fundamental understanding of heat and mass transfer in a fully saturated porous medium with excess water. This is relevant, for example, in drying tissue as well as pulp or paper for the purpose of thermal insulation where pressing is preferred to be avoided to overcome the reduction in the sheet thickness. For this purpose, a theoretical drying model is developed where the porous medium corresponds to paper and is assumed to be sandwiched between two excess-water layers (bottom and top). The conjugate model consists of energy and mass conservation equations for each layer. The model is validated with corresponding experimental data. In the model, the thickness of each water layer is calculated as a function of drying time based on local temperature and total moisture content. The numerical model is transient and one-dimensional in space (i.e., in the thickness direction). This paper demonstrates the governing equations, boundary conditions, and results when the saturated porous medium with water layers is heated from one side. Moisture and temperature profiles are estimated in the thickness direction of the porous medium as it dries.

Engineering↗
DOE OSTI2024

Reliability of Copper Inverse Opal Surfaces for Extreme-Heat-Flux Micro-Coolers in Low-Global-Warming-Potential Refrigerant R-1233zd Pool Boiling Experiments

This presentation provides a brief snapshot of the InterPACK paper InterPACK2023-113781. The paper explores copper inverse opal (CIO) surface reliability in pool boiling experiments in water and a new, low-global-warming-potential (GWP = 1) hydrofluoroolefin (HFO) refrigerant R-1233zd. The CIO-based structure is intended to develop enhanced two-phase heat transfer surfaces for extreme-heat-flux (approximately 1 kW/cm2) micro-coolers. In this study, a limited number of pool boiling experiments were performed using water and HFO-1233zd fluid, and the reliability of the CIO-based surfaces was evaluated. Critical heat flux (CHF) values in HFO-1233zd at 40 Degrees Celsius to 45 Degrees Celsius saturation temperatures and the corresponding saturation pressures were also measured. The CHF values with the refrigerant are significantly lower compared to those with water, but the refrigerant allows for a wider usable temperature range in the end application of the micro-coolers and is not limited to data centers with controlled ambient conditions. Reliability experiments with CIO surface samples - involving pool boiling with water on the CIO surfaces for approximately 48 hours and with HFO-1233zd for 144 hours - showed no structural degradation of the enhanced surface or any significant performance drop in heat transfer coefficients. The CIO surface samples in water were oxidized, most likely due to the presence of air in water and in the experimental vessel.

critical heat flux↗
DOE OSTI2022

Absolute measurement of vacuum ultraviolet photon flux in an inductively coupled plasma using a Au thin film

A new method for absolute measurement of the vacuum ultraviolet (VUV) photon flux at the edge of a plasma is described. The light produced by the plasma was allowed to strike a negatively biased, gold-coated copper substrate remote from the plasma. The resulting photoelectron emission current was measured, and the absolute photon flux was then found from the known photoelectron yield of Au. The method was used to quantify the amount of VUV light produced by an Ar/He inductively coupled plasma (ICP). Strong emissions at 104.82 and 106.67 nm, corresponding to the 1s 2 and 1s 4 resonant states of Ar, were observed. The maximum, integrated VUV photon flux measured at the remote location was 3.2 × 10 13 photons/cm 2 s. This was estimated to correspond to a flux of 5 × 10 15 photons/cm 2 s at the edge of the ICP, in the range of reported values under similar conditions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Recycling of multilayer plastic packaging materials by solvent-targeted recovery and precipitation

Many plastic packaging materials manufactured today are composites made of distinct polymer layers (i.e., multilayer films). Billions of pounds of these multilayer films are produced annually, but manufacturing inefficiencies result in large, corresponding postindustrial waste streams. Although relatively clean (as opposed to municipal wastes) and of near-constant composition, no commercially practiced technologies exist to fully deconstruct postindustrial multilayer film wastes into pure, recyclable polymers. Here, we demonstrate a unique strategy we call solvent-targeted recovery and precipitation (STRAP) to deconstruct multilayer films into their constituent resins using a series of solvent washes that are guided by thermodynamic calculations of polymer solubility. We show that the STRAP process is able to separate three representative polymers (polyethylene, ethylene vinyl alcohol, and polyethylene terephthalate) from a commercially available multilayer film with nearly 100% material efficiency, affording recyclable resins that are cost-competitive with the corresponding virgin materials.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Bacterial response to the 2021 Orange County, California, oil spill was episodic but subtle relative to natural fluctuations

ABSTRACT An oil spill began in October 2021 off the coast of Orange County, California, releasing 24,696 gallons of crude oil into coastal environments. Although oil spills, such as this one, are recurrent accidents along the California coast, no prior studies have been performed to examine the severity of the local bacterial response. A coastal 10-year time series of short-read metagenomes located within the impacted area allowed us to quantify the magnitude and duration of the disturbance relative to natural fluctuations. We found that the largest change in bacterial beta-diversity occurred at the end of October. The change in taxonomic beta-diversity corresponded with an increase in the sulfur-oxidizing clade Candidatus Thioglobus, an increase in the total relative abundance of potential hydrocarbon-degrading bacteria, and an anomalous decline in the picocyanobacteria Synechococcus . Similarly, changes in function were related to anomalous declines in photosynthetic pathways and anomalous increases in sulfur metabolism pathways as well as aromatic degradation pathways. There was a lagged response in taxonomy and function to peaks in total PAHs. One week after peaks in total PAH concentrations, the largest shifts in taxonomy were observed, and 1 week after the taxonomy shifts were observed, unique functional changes were seen. This response pattern was observed twice during our sampling period, corresponding with the combined effect of resuspended PAHs and increased nutrient concentrations due to physical transport events. Thus, the impact of the spill on bacterial communities was temporally extended and demonstrates the need for continued monitoring for longer than 3 months after initial oil exposure. IMPORTANCE Oil spills are common occurrences in waterways, releasing contaminants into the aquatic environment that persist for long periods of time. Bacterial communities are rapid responders to environmental disturbances, such as oil spills. Within bacterial communities, some members will be susceptible to the disturbance caused by crude oil components and will decline in abundance, whereas others will be opportunistic and will be able to use crude oil components for their metabolism. In many cases, when an oil spill occurs, it is difficult to assess the oil spill’s impact because no samples were collected prior to the accident. Here, we examined the bacterial response to the 2021 Orange County oil spill using a 10-year time series that lies within the impacted area. The results presented here are significant because (i) susceptible and opportunistic taxa to oil spills within the coastal California environment are identified and (ii) the magnitude and duration of the in situ bacterial response is quantified for the first time.

Brock, Melissa L. (ORCID:0000000340329241)↗
DOE OSTI2022

Effect of vaccination on the case fatality rate for COVID-19 infections 2020–2021: multivariate modelling of data from the US Department of Veterans Affairs

Objectives: To evaluate the benefits of vaccination on the case fatality rate (CFR) for COVID-19 infections. Design, setting and participants: The US Department of Veterans Affairs has 130 medical centres. We created multivariate models from these data—339 772 patients with COVID-19—as of 30 September 2021. Outcome measures: The primary outcome for all models was death within 60 days of the diagnosis. Logistic regression was used to derive adjusted ORs for vaccination and infection with Delta versus earlier variants. Models were adjusted for confounding factors, including demographics, comorbidity indices and novel parameters representing prior diagnoses, vital signs/baseline laboratory tests and outpatient treatments. Patients with a Delta infection were divided into eight cohorts based on the time from vaccination to diagnosis. A common model was used to estimate the odds of death associated with vaccination for each cohort relative to that of unvaccinated patients. Results: 9.1% of subjects were vaccinated. 21.5% had the Delta variant. 18 120 patients (5.33%) died within 60 days of their diagnoses. The adjusted OR for a Delta infection was 1.87±0.05, which corresponds to a relative risk (RR) of 1.78. The overall adjusted OR for prior vaccination was 0.280±0.011 corresponding to an RR of 0.291. Raw CFR rose steadily after 10–14 weeks. The OR for vaccination remained stable for 10–34 weeks. Conclusions: Our CFR model controls for the severity of confounding factors and priority of vaccination, rather than solely using the presence of comorbidities. Our results confirm that Delta was more lethal than earlier variants and that vaccination is an effective means of preventing death. After adjusting for major selection biases, we found no evidence that the benefits of vaccination on CFR declined over 34 weeks. We suggest that this model can be used to evaluate vaccines designed for emerging variants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Leveraging Multitime Hamilton–Jacobi PDEs for Certain Scientific Machine Learning Problems

Hamilton-Jacobi partial differential equations (HJ PDEs) have deep connections with a wide range of fields, including optimal control, differential games, and imaging sciences. By considering the time variable to be a higher dimensional quantity, HJ PDEs can be extended to the multi-time case. In this paper, we establish a novel theoretical connection between specific optimization problems arising in machine learning and the multi-time Hopf formula, which corresponds to a representation of the solution to certain multi-time HJ PDEs. Through this connection, we increase the interpretability of the training process of certain machine learning applications by showing that when we solve these learning problems, we also solve a multi-time HJ PDE and, by extension, its corresponding optimal control problem. As a first exploration of this connection, we develop the relation between the regularized linear regression problem and the Linear Quadratic Regulator (LQR). We then leverage our theoretical connection to adapt standard LQR solvers (namely, those based on the Riccati ordinary differential equations) to design new training approaches for machine learning. Lastly, we provide some numerical examples that demonstrate the versatility and possible computational advantages of our Riccati-based approach in the context of continual learning, post-training calibration, transfer learning, and sparse dynamics identification.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Search for top squark pair production using dilepton final states in ${\text {p}}{\text {p}}$ collision data collected at $\sqrt{s}=13\,\text {TeV} $

A search is presented for supersymmetric partners of the top quark (top squarks) in final states with two oppositely charged leptons (electrons or muons), jets identified as originating from ${\text {b}}$quarks, and missing transverse momentum. The search uses data from proton-proton collisions at $\sqrt{s}=13\,\text {TeV} $ collected with the CMS detector, corresponding to an integrated luminosity of 137$\,{\text {fb}}^{-1}$. Hypothetical signal events are efficiently separated from the dominant top quark pair production background with requirements on the significance of the missing transverse momentum and on transverse mass variables. No significant deviation is observed from the expected background. Exclusion limits are set in the context of simplified supersymmetric models with pair-produced lightest top squarks. For top squarks decaying exclusively to a top quark and a lightest neutralino, lower limits are placed at $95\%$ confidence level on the masses of the top squark and the neutralino up to 925 and 450$\,\text {GeV}$, respectively. If the decay proceeds via an intermediate chargino, the corresponding lower limits on the mass of the lightest top squark are set up to 850$\,\text {GeV}$ for neutralino masses below 420$\,\text {GeV}$. For top squarks undergoing a cascade decay through charginos and sleptons, the mass limits reach up to 1.4$\,\text {TeV}$ and 900$\,\text {GeV}$ respectively for the top squark and the lightest neutralino.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗