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DOE OSTI2020

General Bayesian Inference over the Stiefel Manifold via the Givens Transform

We introduce here an approach based on the Givens representation for posterior inference in statistical models with orthogonal matrix parameters, such as factor models and probabilistic principal component analysis (PPCA). We show how the Givens representation can be used to develop practical methods for transforming densities over the Stiefel manifold into densities over subsets of Euclidean space. We demonstrate how to deal with issues arising from the topology of the Stiefel manifold and how to inexpensively compute the change-of-measure terms. We introduce an auxiliary parameter approach that limits the impact of topological issues. We provide both analysis of our methods and numerical examples demonstrating the effectiveness of the approach. We also discuss how our Givens representation can be used to define general classes of distributions over the space of orthogonal matrices. We then give demonstrations on several examples showing how the Givens approach performs in practice in comparison with other methods.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Reducing the matrix effect in mass spectral imaging of biofilms using flow-cell culture

The interactions between soil microorganisms and soil minerals play a crucial role in the formation and evolution of minerals and the stability of soil aggregates. Due to the heterogeneity and diversity of the soil environment, the under-standing of the functions of bacterial biofilms in soil minerals at the microscale is limited. A soil mineral-bacterial biofilm system was used as a model in this study, and it was analyzed by time-of-flight secondary ion mass spectrometry (ToF-SIMS) to acquire molecular level information. Static culture in multi-wells and dynamic flow-cell culture in microfluidics of biofilms were investigated. Our results show that more characteristic molecules of biofilms can be observed in SIMS spectra of the flow-cell culture. In contrast, biofilm signature peaks are buried under the mineral components in SIMS spectra in the static culture case. Spectral overlay was used in peak selection prior to performing Principal component analysis (PCA). Comparisons of the PCA results between the static and flow-cell culture show more pronounced molecular features and higher loadings of organic peaks of the dynamic cultured specimens. For example, fatty acids secreted from bacterial biofilm extracellular polymeric substance are likely to be responsible for biofilm dispersal due to mineral treatment up to 48 h. Such findings suggest that the use of microfluidic cells to dynamically culture biofilms be a more suitable method for reducing the matrix effect arisen from the growth medium and minerals as a perturbation fac-tor for improved spectral and multivariate analysis of complex mass spectral data in ToF-SIMS. These results show that the interaction mechanism between biofilms and soil minerals at the molecular level can be better studied using the flow-cell culture and advanced mass spectral imaging techniques like ToF-SIMS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Hierarchical Modeling to Enhance Spectrophotometry Measurements—Overcoming Dynamic Range Limitations for Remote Monitoring of Neptunium

A robust hierarchical model has been demonstrated for monitoring a wide range of neptunium concentrations (0.75–890 mM) and varying temperatures (10–80 °C) using chemometrics and feature selection. The visible–near infrared electronic absorption spectrum (400–1700 nm) of monocharged neptunyl dioxocation (Np(V) = NpO2+) includes many bands, which have molar absorption coefficients that differ by nearly 2 orders of magnitude. The shape, position, and intensity of these bands differ with chemical interactions and changing temperature. These challenges make traditional quantification by univariate methods unfeasible. Measuring Np(V) concentration over several orders of magnitude would typically necessitate cells with varying path length, optical switches, and/or multiple spectrophotometers. Alternatively, the differences in the molar extinction coefficients for multiple absorption bands can be used to quantify Np(V) concentration over 3 orders of magnitude with a single optical path length (1 mm) and a hierarchical multivariate model. In this work, principal component analysis was used to distinguish the concentration regime of the sample, directing it to the relevant partial least squares regression submodels. Each submodel was optimized with unique feature selection filters that were selected by a genetic algorithm to enhance predictions. Through this approach, the percent root mean square error of prediction values were ≤1.05% for Np(V) concentrations and ≤4% for temperatures. This approach may be applied to other nuclear fuel cycle and environmental applications requiring real-time spectroscopic measurements over a wide range of conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Accurate Thermochemistry of Complex Lignin Structures via Density Functional Theory, Group Additivity, and Machine Learning

A molecular-level understanding of lignin structures and bond dissociation energies could facilitate depolymerization technologies. Still, this information is currently limited due to the lack of databases and the simplification of surrogate models. Here, substitution effects on seven common linkages in lignin polymers are systematically investigated. An automated reaction network generator is employed to create a database of structures. A new group additivity (GA) model based on principal component analysis (PCA) descriptors is introduced and trained on gas-phase density functional theory data of 4100 species at the M06-2X/6-311++G(d,p) level. Hydrogen bonds, local steric, and nonaromatic ring contributions are also incorporated. Lastly, we improve the accuracy of the group additivity model to reach the G4 theory by computing a data set of 770 species at this level and using a data fusion approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2023

Portland Urban Development: Quantifying and Visualizing Urban Heat with Compounding Vulnerabilities to Support Community Depaving Initiatives

Urban heat is a pressing concern in Portland, Oregon as climate change induced heat waves increase. Cities experience higher temperatures due to the urban heat island effect (UHI), and environmental injustice and disenfranchisement in minority communities expose low-income and Black, Indigenous, and People of Color (BIPOC) residents to more extreme and debilitating heat events. Our team identified Portland’s communities on the frontlines of urban heat impacts by overlapping environmental and social vulnerabilities using NASA Earth observations. We partnered with Depave, a Portland-based nonprofit that works alongside communities to replace pavement with greenspace in historically disenfranchised areas. Using Landsat 8 Thermal Infrared Sensor (TIRS) imagery, we mapped Land Surface Temperature (LST) and developed a heat-specific Social Vulnerability Index (SVI) through a Principal Component Analysis (PCA) to identify Portland’s communities with the highest potential heat vulnerability. Then, we calculated the temperature change of depaving in six case studies to quantify Depave's efforts in heat mitigation and environmental justice. Our analysis demonstrated that, throughout Portland, there are frontline communities experiencing high potential social vulnerability to extreme temperatures due to environmental injustices and over-pavement. Finally, Depave’s impact on urban heat is observable and quantifiable using remote-sensing data and tools, with an average of 1ºF LST decrease across the six case studies. We illustrated the significance of local urban heat mitigation efforts and propose next steps for conducting inclusive and intentional research that highlights the lived experiences and resilience of frontline communities.

Environmental justice↗

DOE OSTI2022

The Effect of APS-HVOF Bond Coating Thickness Ratio on TBC Furnace Cycle Lifetime

In this work, combinations of NiCoCrAlY APS and high-velocity oxygen fuel (HVOF) bond coatings were deposited on alloy 247 disk substrates with APS yttria-stabilized zirconia (YSZ) top coatings to assess the benefit of air plasma sprayed (APS) ‘flash’ bond coatings. Using 1-h cycles at 1100 °C in air with 10% H 2 O and HVOF-only and APS-only bond coatings as a baseline, it was found that APS flash coatings extended the average coating lifetime by 16% to 35% with the thicker flash coating performing best. Principal component analysis and energy dispersive spectroscopy (EDS) compositional mapping on coatings characterized after 0, 100, 300 and 500 cycles and after failure showed that the Al in the bond coatings was depleted due to both oxidation and back diffusion into the substrate. The APS-only bond coating had significant oxidation throughout the bond coating and was so depleted in Al, that Al diffused from the substrate to the coating. Residual stress maps of the thermally-grown alumina scale were obtained every 100 cycles using photo-stimulated luminescence piezospectroscopy (PLPS) revealing that the Thick Flash coating had the slowest rate of damage accumulation in the oxide scale.

alumina scale↗

NASA NTRSDate not supplied

Derivation of Integrated Load Distributions from Resampled Computational Data

Principal component analysis (PCA) has been the center of many surrogate models used to characterize fluid flows in recent years. However, little work has been done to character- ize the uncertainty in the PCA transform itself and its effect on derived surrogate models. To explore the uncertainty, a typical interpolated surrogate model is constructed for a represen- tative aerodynamic body from computational data. The computational data is then resampled to explore the robustness of the PCA transformation. The variations of the model predictions during this resampling are analyzed to get a measure of confidence in the PCA transformation, which is then applied to the interpolated surrogate model to get uncertainty on integrated force predictions. An initial test case has been explored with promising results.

Principal Component Analysis↗

DOE OSTI2021

Correlated conformational dynamics of the human GluN1-GluN2A type N-methyl-D-aspartate (NMDA) receptor

N-Methyl-D-aspartate receptors (NMDARs) are glutamate-gated ion channels found in the nerve cell membranes. As a result of overexcitation of NMDARs, neuronal death occurs and may lead to diseases such as epilepsy, stroke, Alzheimer’s disease, and Parkinson’s disease. In this study, human GluN1- GluN2A type NMDAR structure is modeled based on the X-ray structure of the Xenopus laevis template and missing loops are added by ab-initio loop modeling. The final structure is chosen according to two different model assessment scores. To be able to observe the structural changes upon ligand binding, glycine and glutamate molecules are docked into the corresponding binding sites of the receptor. Subsequently, molecular dynamics simulations of 1.3 μs are performed for both apo and ligand-bound structures. Structural parameters, which have been considered to show functionally important changes in previous NMDAR studies, are monitored as conformational rulers to understand the dynamics of the conformational changes. Moreover, principal component analysis (PCA) is performed for the equilibrated part of the simulations. Additionally, from these analyses, the differences in between apo and ligand-bound simulations can be summarized as the following: The girdle right at the beginning of the pore loop, which connects M2 and M3 helices of the ion channel, partially opens. Ligands act like an adhesive for the ligand-binding domain (LBD) by keeping the bi-lobed structure together and consequently this is reflected to the overall dynamics of the protein as an increased correlation of the LBD with especially the amino-terminal domain (ATD) of the protein.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRSDate not supplied

Derivation of Integrated Load Distributions from Resampled Computational Data

Computational Fluid Dynamics↗

DOE OSTI2021

Short-term nodal load forecasting based on machine learning techniques

This paper introduces an advanced Short-term Nodal Load Forecasting (STNLF) method that forecasts nodal load profiles for the next day in power systems, based on the combined use of three machine learning techniques. Least Absolute Shrinkage and Selection Operator (LASSO) is employed to reduce the number of features for a single nodal load forecasting. Principal Component Analysis (PCA) is used to capture the features of historical loads in low-dimensional space compared to the original high-dimensional load space where features are barely possible to depict. Additionally, Bayesian Ridge Regression (BRR) is utilized to decide the parameters of the prediction model from a statistics perspective. Tests based on modified PJM load data demonstrate the effectiveness of the proposed STNLF method compared to the state-of-the-art General Regression Neural Network (GRNN) method. Moreover, the reliability of the day-ahead Unit Commitment (UC) solution is shown to have been improved, based on the forecasted load data using the proposed STNLF method.

24 POWER TRANSMISSION AND DISTRIBUTION↗

NASA NTRS2023

Coronado Ecological Conservation: Assessing Vegetation Change Due to Border Wall Construction and Shifting Social Trails

Species monitoring is essential for mitigating the impacts of plant invasion, such as radical changes in an area’s ecosystem, degraded soil health, increased wildfire severity, landslides, and increased flooding. For this project, NASA DEVELOP partnered with the National Park Service (NPS) to investigate invasive species in disturbed lands: specifically, areas affected by off-trail travel and U.S.-Mexico border construction activities. The team assessed how construction has impacted the distribution of Lehmann’s lovegrass and Russian thistle invasives throughout Coronado National Memorial, AZ from 1986-2022. Using data from Landsat 5 and 8, Sentinel-2, NAIP, and PlanetScope, the team computed NDVI, NDMI, MSAVI2, EVI, and Tasseled Cap Wetness, Brightness, and Greenness transformations as vegetation health indicators to input into various machine learning algorithms. To minimize noise, the team conducted Principal Component Analysis on vegetation indices and spectral bands before running k-means clustering and random forest classification algorithms. Between all datasets, the team found that the median area fully overtaken by invasive plants was 5.37% of the park’s total area in 2022. The NPS will use end products to help increase restoration efforts in disturbed areas with high concentrations of invasive plants, and this project can serve as a jumping off point for future invasive species monitoring. The NPS’s collection of ground data for 2022-2023, in conjunction with future data collection, will notably improve the accuracy of classification models, leading to more precise monitoring of invasive species spread over time.

Coronado National Memorial↗

DOE OSTI2018

Occurrence and ecological risk of pharmaceuticals in river surface water of Bangladesh

Highlights: • Twelve pharmaceuticals were investigated in river surface water. • Nine pharmaceuticals were detected at ng L{sup −1} level. • MNZ was dominant followed by TMP, ERY-H{sub 2}O and SMX. • Contamination of SMX, TMP and TYL was associated with fed aquaculture. • Preliminary ecological risk assessment showed the medium to low risks. Pharmaceutical contamination in the aquatic environment is a global issue that affects aquatic animals, micro-organisms and human health. The occurrence and preliminary ecological risk of 12 (11 antibiotics and 1 antiepileptic drug) pharmaceuticals were investigated for the first time in the surface water of the old Brahmaputra River, where open-water-fed aquaculture activities are being practiced in Bangladesh. The pharmaceuticals were quantified by high-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS), operated with positive electrospray ionization (ESI{sup +}) and a multiple reaction monitoring (MRM) mode. Nine pharmaceuticals were detected in the river surface water, whereas three were below the limit of detection (LOD). Metronidazole was detected in all the samples with concentrations ranging from 0.05 to 13.51 ng L{sup −1}. Trimethoprim had the second highest frequency of detection (95%) with the highest concentration (17.20 ng L{sup −1}). The ranges of concentration and detection frequency of sulfonamides and macrolides were < LOD-11.35 and < LOD-16.68 ng L{sup −1}; 35–70 and 60–85%, respectively, whereas carbamazepine was in the range of < LOD-8.80 ng L{sup −1} and had a detection frequency of 65%. The concentrations of sulfamethoxazole, trimethoprim, erythromycin-H{sub 2}O and tylosin were distinctly higher in the fed aquaculture areas. The principal component analysis confirmed that fed aquaculture activities contributed most of the pharmaceutical contamination in the river surface water. Hospitals, nursing homes, sewage wastewater or surface runoff from the surrounding areas might all contribute to the presence of metronidazole and carbamazepine. The preliminary ecological risk assessment revealed that sulfamethoxazole, erythromycin-H{sub 2}O and tylosin showed medium risk, and carbamazepine displayed low risk to sensitive aquatic organisms for maximum measured concentrations. Thus, this study suggests that pharmaceutical contamination in different rivers and seasons needs to be quantified, and ecological as well as human health risks need to be assessed in Bangladesh.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Impacts on product quality attributes of monoclonal antibodies produced in CHO cell bioreactor cultures during intentional mycoplasma contamination events

Abstract A mycoplasma contamination event in a biomanufacturing facility can result in costly cleanups and potential drug shortages. Mycoplasma may survive in mammalian cell cultures with only subtle changes to the culture and penetrate the standard 0.2‐µm filters used in the clarification of harvested cell culture fluid. Previously, we reported a study regarding the ability of Mycoplasma arginini to persist in a single‐use, perfusion rocking bioreactor system containing a Chinese hamster ovary (CHO) DG44 cell line expressing a model monoclonal immunoglobulin G 1 (IgG1) antibody. Our previous work showed that M. arginini affects CHO cell growth profile, viability, nutrient consumption, oxygen use, and waste production at varying timepoints after M. arginini introduction to the culture. Careful evaluation of certain identified process parameters over time may be used to indicate mycoplasma contamination in CHO cell cultures in a bioreactor before detection from a traditional method. In this report, we studied the changes in the IgG1 product quality produced by CHO cells considered to be induced by the M. arginini contamination events. We observed changes in critical quality attributes correlated with the duration of contamination, including increased acidic charge variants and high mannose species, which were further modeled using principal component analysis to explore the relationships among M. arginini contamination, CHO cell growth and metabolites, and IgG1 product quality attributes. Finally, partial least square models using NIR spectral data were used to establish predictions of high levels (≥10 4 colony‐forming unit [CFU/ml]) of M. arginini contamination, but prediction of levels below 10 4 CFU/ml were not reliable. Contamination of CHO cells with M. arginini resulted in significant reduction of antibody product quality, highlighting the importance of rapid microbiological testing and mycoplasma testing during particularly long upstream bioprocesses to ensure product safety and quality.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Elemental and isotopic signatures of Asteroid Ryugu support three early Solar System reservoirs

Understanding the number and locations of different reservoirs present in the early Solar System is crucial to understanding the Solar System’s origin and evolution. Previous work has suggested that three unique isotopic reservoirs existed in the early Solar System but subsequent works have challenged that idea. Here we present elemental abundances along with Ca, Ti, Cr, Fe, Ni, and Zn isotopic data from primitive material returned by the Japan Aerospace Exploration Agency’s (JAXA) Hayabusa2 mission to asteroid (162173) Ryugu to make inferences on the Solar System’s early architecture. Data from Ryugu particle A0208 are consistent with a close genetic heritage between Ryugu and CI chondrites. Here, we employ principal component analysis (PCA) on these Ryugu and published meteorite data to demonstrate that Ryugu and CI chondrites are distinct from other known astromaterials, strongly supporting the existence of a third major isotopic reservoir in the early Solar System.

Isotopes↗

DOE OSTI2025

Accelerating the Structure Exploration of Diverse Bi–Pt Nanoclusters via Physics‐Informed Machine Learning Potential and Particle Swarm Optimization

Bimetallic Bi–Pt nanoclusters exhibit diverse structural motifs, including core-shell, Janus, and mixed alloy configurations, due to the unique bonding characteristics between Bi and Pt atoms. Using density functional theory refinements from ChIMES physically machine-learned potential and CALYPSO particle swarm optimization global searches, 34 Bi20-Pt20 nanoclusters are systematically classified. The results reveal that Bi atoms predominantly occupy surface sites, driven by charge transfer effects. Cohesive energy trends alone prove insufficient for structure differentiation, necessitating a data-driven approach employing principal component analysis and K-means clustering. Furthermore, vibrational, electronic, and infrared spectral analyses provide additional insights into structure-property relationships. The findings offer an original framework for the automated classification and analysis of bimetallic nanoclusters, enhancing the understanding of their stability and functional properties.

bimetallic nanoparticles↗

NASA NTRS2021

Moisture and Temperature Influences on Nonlinear Vegetation Trends in Serengeti National Park

While long-term vegetation greening trends have appeared across large land areas over the late 20th century, uncertainty remains in identifying and attributing finer-scale vegetation changes and trends, particularly across protected areas. Serengeti National Park (SNP) is a critical East African protected area, where seasonal vegetation cycles support vast populations of grazing herbivores and a host of ecosystem dynamics. Previous work has shown how non-climate drivers (e.g. land use) shape the SNP ecosystem, but it is still unclear to what extent changing climate conditions influence SNP vegetation, particularly at finer spatial and temporal scales. We fill this research gap by evaluating long-term (1982–2016) changes in SNP leaf area index (LAI) in relation to both temperature and moisture availability using Ensemble Empirical Mode Decomposition and Principal Component Analysis with regression techniques. We find that SNP LAI trends are nonlinear, display high sub-seasonal variation, and are influenced by lagged changes in both moisture and temperature variables and their interactions. LAI during the long rains (e.g. March) exhibits a greening-to-browning trend reversal starting in the early 2000s, partly due to antecedent precipitation declines. In contrast, LAI during the short rains (e.g. November, December) displays browning-to-greening alongside increasing moisture availability. Rising temperature trends also have important, secondary interactions with moisture variables to shape these SNP vegetation trends. Our findings show complex vegetation-climate interactions occurring at important temporal and spatial scales of the SNP, and our rigorous statistical approaches detect these complex climate-vegetation trends and interactions, while guarding against spurious vegetation signals.

Moisture↗

DOE OSTI2014

Assimilation of Time-Averaged Pseudoproxies for Climate Reconstruction

The efficacy of a novel ensemble data assimilation (DA) technique is examined in the climate field reconstruction (CFR) of surface temperature. A minimalistic, computationally inexpensive DA technique is employed that requires only a static ensemble of climatologically plausible states. Pseudoproxy experiments are performed with both general circulation model (GCM) and Twentieth Century Reanalysis (20CR) data by reconstructing surface temperature fields from a sparse network of noisy pseudoproxies. The DA approach is compared to a conventional CFR approach based on principal component analysis (PCA) for experiments on global domains. DA outperforms PCA in reconstructing global-mean temperature in all experiments and is more consistent across experiments, with a range of time series correlations of 0.69–0.94 compared to 0.19–0.87 for the PCA method. DA improvements are even more evident in spatial reconstruction skill, especially in sparsely sampled pseudoproxy regions and for 20CR experiments. It is hypothesized that DA improves spatial reconstructions because it relies on coherent, spatially local temperature patterns, which remain robust even when glacial states are used to reconstruct nonglacial states and vice versa. These local relationships, as utilized by DA, appear to be more robust than the orthogonal patterns of variability utilized by PCA. Comparing results for GCM and 20CR data indicates that pseudoproxy experiments that rely solely on GCM data may give a false impression of reconstruction skill.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

Decline in malaria incidence in a typical county of China: Role of climate variance and anti-malaria intervention measures

Highlights: • Malaria incidence shows a steeply interannual decline and an obvious seasonality. • Malaria incidence highly correlates to temperature, precipitation and humidity. • Two favorable climate conditions are determined for high incidence of malaria. • There is good agreement between a decreasing malaria incidence and slightly declined climate variance in epidemic months. • Malaria incidence is declined rapidly because of the persistent progress of anti-malaria interventions. Malaria is an important vector-borne disease which is widespread in tropical and subtropical areas worldwide as well as in south China. Previous research has separately focused on the association between malaria incidence and meteorological variables or between malaria incidence and anti-malaria intervention measures in China, especially in Yunnan Province. Therefore, a typical county, Tengchong County, in Yunnan Province with high malaria incidence was selected as the study area to investigate the integrated influence of climate variance and anti-malaria intervention measures. Malaria incidence and meteorological variables were analyzed with a 2-month lag. The variables include average monthly temperature, minimum temperature, maximum temperature, cumulative precipitation, wind speed, maximum wind speed, relative humidity and minimum relative humidity. First, the principal component analysis was introduced to investigate the relationship between malaria incidence and meteorological variables; classification and regression trees were used to clarify contributions of key meteorological variables to malaria incidence afterwards. Second, based on existing anti-malaria intervention measures and above results, the integrated impact of climate variance and anti-malaria interventions on interannual trends of malaria incidence was analyzed. High malaria incidence occurred under one of the two meteorological conditions: 1) high minimum temperature combined with high minimum relative humidity or both precipitation and minimum relative humidity above middle level; 2) middle minimum temperature combined with both precipitation and minimum relative humidity below middle levels. Moreover, the steep interannual decline of malaria incidence in Tengchong was determined by slight climate variance and persistent anti-malaria intervention measures during malaria epidemics, predominantly by the latter. These findings will provide evidence data for developing malaria surveillance strategies in China.

54 ENVIRONMENTAL SCIENCES↗