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At least 1,351 records · Page 75

Introducing Molecular Hypernetworks for Discovery in Multidimensional Metabolomics Data

Orthogonal separations of data from high-resolution mass spectrometry can provide insight into sample composition and address challenges of complete annotation of molecules in untargeted metabolomics. “Molecular networks” (MNs), as used in the Global Natural Products Social Molecular Networking platform, are a prominent strategy for exploring and visualizing molecular relationships and improving annotation. MNs are mathematical graphs showing the relationships between measured multidimensional data features. MNs also show promise for using network science algorithms to automatically identify targets for annotation candidates and to dereplicate features associated with a single molecular identity. Here, this paper introduces “molecular hypernetworks” (MHNs) as more complex MN models able to natively represent multiway relationships among observations. Compared to MNs, MHNs can more parsimoniously represent the inherent complexity present among groups of observations, initially supporting improved exploratory data analysis and visualization. MHNs also promise to increase confidence in annotation propagation, for both human and analytical processing. We first illustrate MHNs with simple examples, and build them from liquid chromatography- and ion mobility spectrometry-separated MS data. We then describe a method to construct MHNs directly from existing MNs as their “clique reconstructions”, demonstrating their utility by comparing examples of previously published graph-based MNs to their respective MHNs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

FleetREDI Insight: Intrastate Coach Bus Dataset

Capturing real-world data is critical to improving efficiency and supporting technology advancements in commercial vehicles. FleetREDI’s insights provide detailed duty cycle information and highlight unique aspects of the given dataset. Each insight delivers a quick look at the collected data by summarizing the operation and identifying key findings of the initial analysis. This FleetREDI insight explores coach buses operating in Colorado. Coach buses are a primary mover for intrastate transit and are primarily used for longer trips with more comfortable seats and a restroom. All Aboard America! Holdings Inc. offers various fixed-service and charter routes across Colorado on its Bustang fleet out of its depot in Golden, Colorado. NLR installed logging devices and collected operational data on nine 40-foot Bustang motorcoaches operating on fixed routes from May through August 2022. Using NLR’s FleetREDI data platform, this dataset provides a summary of daily operation to help understand duty cycle characteristics. This includes daily distance, fuel use, and estimated engine-produced energy consumption for nine motorcoaches that operated more than 33,000 miles. These vehicles primarily operated on Interstate 25 and Interstate 70. ![FleetREDI interstate bus](FleetREDI-interstate-bus.jpg)

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Assessing pore network heterogeneity across multiple scales to inform CO2 injection models

Geologic heterogeneity is a key feature that must be considered when translations of scaled data are performed. This paper presents the assessment of geologic heterogeneity using a multiscale workflow that includes image analysis-based methods coupled with well log analysis to provide data in which fractals and machine learning methods estimate the carbon dioxide (CO 2 ) storage resource potential of a reservoir. The heterogeneity of rock properties of the complex Bell Creek reservoir in Montana, USA, was explored at the pore scale (~nm to mm), core scale (~mm to m), and well scale (~cm to m). The data used in this study included advanced image analysis of micro-CT (computed tomography) images (pore scale), thin sections (pore scale), plugs and core images (core scale) and well logs (well scale). The micro-CT images were segmented using a U-net segmentation approach into objects of pores and grains. Further, the segmented images were reconstructed into subvolumes of different sizes. Physical properties (porosity and permeability) and fractal dimensions were calculated for the various subvolumes, and Lorenz coefficient (Lc) values, a single parameter to describe the degree of heterogeneity within a pay zone section, were calculated from thin-section images and well logs. Porosity and fractal dimension values were used to estimate the 188-µm threshold of representative elementary volume (REV) in this study. Both the Lc and fractal dimension values were found to be negatively correlated. When these two parameters are combined, it is possible to discern differences in the complex porous networks of the samples analyzed in this study.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Advancing Geophysical Techniques to Image a Stratigraphic Hydrothermal Resource

Sedimentary-hosted geothermal energy systems are permeable structural, structural-stratigraphic, and/or stratigraphic horizons with sufficient temperature for direct use and/or electricity generation. Sedimentary-hosted (i.e., stratigraphic) geothermal reservoirs may be present in multiple locations across the central and eastern Great Basin of the USA, thereby constituting a potentially large base of untapped, economically accessible energy resources. Sandia National Laboratories has partnered with a multi disciplinary group of collaborators to evaluate a stratigraphic system in Steptoe Valley, Nevada using both established and novel geophysical imaging techniques. The goal of this study is to inform an optimized strategy for subsequent exploration and development of this resource and analogous ones. Building from prior Nevada Play Fairway Analysis (PFA), this team is primarily 1) collecting additional geophysical data, 2) employing novel joint geophysical inversion/modeling techniques to update existing 3D geologic models, and 3) integrating the geophysical results to produce a working, geologically constrained thermo-hydrological reservoir model. Prior PFA work highlights Steptoe Valley as a favorable resource basin that likely has both sedimentary and hydrothermal characteristics. However, there remains significant uncertainty on the nature and architecture of the resource(s) at depth, which increases the risk in exploratory drilling. Newly acquired gravity, magnetic, magnetotelluric, and controlled-source electromagnetic data products, in conjunction with new and preexisting geoscientific measurements and observations, are being integrated and evaluated for efficacy in understanding stratigraphic geothermal resources and mitigating exploration risk. Furthermore, the influence of hydrothermal activity on sedimentary-hosted reservoirs in favorable structural settings, and whether fault-controlled systems may locally enhance temperature and permeability in some deep stratigraphic reservoirs, will also be evaluated.

Geothermal, Sedimentary Heat, Geophysics, Seismic,↗

Angular clustering properties of the DESI QSO target selection using DR9 Legacy Imaging Surveys

ABSTRACT The quasar target selection for the upcoming survey of the Dark Energy Spectroscopic Instrument (DESI) will be fixed for the next 5 yr. The aim of this work is to validate the quasar selection by studying the impact of imaging systematics as well as stellar and galactic contaminants, and to develop a procedure to mitigate them. Density fluctuations of quasar targets are found to be related to photometric properties such as seeing and depth of the Data Release 9 of the DESI Legacy Imaging Surveys. To model this complex relation, we explore machine learning algorithms (random forest and multilayer perceptron) as an alternative to the standard linear regression. Splitting the footprint of the Legacy Imaging Surveys into three regions according to photometric properties, we perform an independent analysis in each region, validating our method using extended Baryon Oscillation Spectroscopic Survey (eBOSS) EZ-mocks. The mitigation procedure is tested by comparing the angular correlation of the corrected target selection on each photometric region to the angular correlation function obtained using quasars from the Sloan Digital Sky Survey (SDSS) Data Release 16. With our procedure, we recover a similar level of correlation between DESI quasar targets and SDSS quasars in two-thirds of the total footprint and we show that the excess of correlation in the remaining area is due to a stellar contamination that should be removed with DESI spectroscopic data. We derive the Limber parameters in our three imaging regions and compare them to previous measurements from SDSS and the 2dF QSO Redshift Survey.

79 ASTRONOMY AND ASTROPHYSICS↗

Resource selection functions based on hierarchical generalized additive models provide new insights into individual animal variation and species distributions

Habitat selection studies are designed to generate predictions of species distributions or inference regarding general habitat associations and individual variation in habitat use. Such studies frequently involve either individually indexed locations gathered across limited spatial extents and analyzed using resource selection functions (RSFs) or spatially extensive locational data without individual resolution typically analyzed using species distribution models. Both analytical methodologies have certain desirable features, but analyses that combine individual- and population-level inference with flexible non-linear functions may provide improved predictions while accounting for individual variation. Here, we describe how RSFs can be fit using hierarchical generalized additive models (HGAMs) using widely available software, providing a means to explore individual variation in habitat associations and to generate species distribution maps. We used GPS tracking data from golden eagles Aquila chrysaetos from across eastern North America with four environmental predictors to generate monthly distribution models. We considered three model structures that assumed different amounts of individual variation in the functional relationship between predictors and habitat use and used k-fold cross-validation to compare model performance. Models accounting for individual variability in shape and smoothness of functional responses performed best. Eagles exhibited the least amount of individual variation in response to land cover variables during winter months, with most individuals more closely adhering to the population-level trend. During the summer months, eagles exhibited more substantial individual variation in shape and smoothness of the functional relationships, suggesting some need to account for individual variation in eagle habitat use for both inferential and predictive purposes, during this time of year. Because they allow users to blend flexible functions with random effects structures and are well-supported by a variety of software platforms, we believe that HGAMs provide a useful addition to the suite of analyses used for modeling habitat associations or predicting species distributions.

54 ENVIRONMENTAL SCIENCES↗

SPRUCE Methane Transport in Plants at S1 Bog, Marcell Experimental Forest, Minnesota, 2017-2019

This data set contains measurements of methane (CH4) transport by plants (both ground-layer and trees) and diffusion, as well as whole-plot emissions, taken in September 2018 and June 2019 in S1 Bog outside of the SPRUCE (Spruce and Peatland Responses Under Changing Environments) experimental enclosures. Additionally, CH4 and carbon dioxide (CO2) stable isotope data in porewater and atmospheric emissions were taken in July 2017 in the SPRUCE enclosures to explore the relative magnitude of CH4 oxidation. Episodic ebullition rates for S1 Bog are taken from Gill et al. (2017). Methane transport is an important component of many ecosystem models of peatlands. The results were compared to two methane models that have been developed for the SPRUCE project, ELM-SPRUCE (Earth Land Model) and TECO_SPRUCE (Terrestrial ECOsystem model). This dataset contains six data files in comma separate (.csv) format. Additional metadata are provided: six data dictionaries and a file-level metadata file in comma separate (.csv) format and a user guide in PDF (*.pdf) format.

54 ENVIRONMENTAL SCIENCES↗

Deep Neural Networks are Adaptive to Function Regularity and Data Distribution in Approximation and Estimation

Deep learning has exhibited remarkable results across diverse areas. To understand its success, substantial research has been directed towards its theoretical foundations. Nev- ertheless, the majority of these studies examine how well deep neural networks can model functions with uniform regularities. In this paper, we explore a different angle: how deep neural networks can adapt to varying degrees of smoothness in functions and nonuni- form data distributions across different locations and scales. More precisely, we focus on a broad class of functions defined by nonlinear tree-based approximation methods. This class encompasses a range of function types, such as functions with uniform regularities and discontinuous functions. We develop nonparametric approximation and estimation theories for this class using deep ReLU networks. Our results show that deep neural networks are adaptive to the nonuniform smoothness of functions and nonuniform data distributions at different locations and scales. We apply our results to several function classes, and derive the corresponding approximation and generalization errors. The validity of our results is demonstrated through numerical experiments.

97 MATHEMATICS AND COMPUTING↗

Reducing Data Center Peak Cooling Demand and Energy Costs with Underground Thermal Energy Storage (UTES)

By recent estimates, data center energy demands are projected to consume between 6.7% and 12% of U.S. annual electricity generation by the year 2028, driven primarily by expanded demands from cloud services, big data analytics, and Artificial Intelligence (AI) (Shehabi et al., 2024). As much as 40% of data center total energy consumption are loads associated with the site infrastructure cooling systems, and these are often highly water consumptive (Aljbour et al., 2024). For energy system planners, this presents significant challenges to meeting and managing the anticipated loads, and especially the peak loads of projected data center deployments. Geothermal technologies offer two unique solutions to these challenges: 1) by serving loads through the deployment of new conventional and/or next-generation geothermal power technologies such as EGS and 2) through an often-overlooked opportunity to reduce data center peak cooling loads. The latter is the focus of this paper which explores Cold Underground Thermal Energy Storage ("Cold UTES") as an emerging industrial-scale geothermal cooling solution. This cooling solution is energy efficient, non-water-consumptive, and utilizes long duration energy storage (LDES) on both diurnal and seasonal time scales. Cold UTES has the potential to also function as a virtual power plant (VPP). The US Department of Energy's Geothermal Technologies Office is supporting R&D to understand the grid and system-wide value, costs, and impacts of deploying this emergent cooling solution at scale.

AI↗

Beyond Optimization: Exploring Novelty Discovery in Autonomous Experiments

Autonomous experiments (AEs) are transforming how scientific research is conducted by integrating artificial intelligence with automated experimental platforms. Current AEs primarily focus on the optimization of a predefined target; while accelerating this goal, such an approach limits the discovery of unexpected or unknown physical phenomena. Here, we introduce a novel framework, INS 2 ANE (Integrated Novelty Score−Strategic Autonomous Non-Smooth Exploration), to enhance the discovery of novel phenomena in autonomous microscopy experimentation. Our method integrates two key components: (1) a novelty scoring system that evaluates the uniqueness of experimental results and (2) a strategic sampling mechanism that promotes exploration of under-sampled regions even if they appear less promising by conventional criteria. We validate this approach on a preacquired data set with a known ground truth comprising of image−spectral pairs. We further implement the process on autonomous scanning probe microscopy experiments. INS 2 ANE significantly increases the diversity of explored phenomena in comparison to conventional optimization routines, enhancing the likelihood of discovering previously unobserved phenomena. These results demonstrate the potential for autonomous microscopy experiments to enhance the scientific discovery by navigating complex experimental spaces to uncover novel phenomena.

Materials↗

Evaluation of Oak Ridge National Laboratory Health Physics Research Reactor Operation Data for Critical Benchmark Creation

The Oak Ridge National Laboratory (ORNL) Health Physics Research Reactor (HPRR) was a research reactor designed and built at ORNL in 1961. The critical assembly used a highly enriched uranium and molybdenum alloy as the fuel and could be operated in steady-state or burst modes. The HPRR has recently been the object of an investigation to create a criticality benchmark. Such benchmarks are very important, as they are used primarily to show the accuracy of newly developed modeling codes and to help experimental validation and reactor licensing. The evaluated experiments considered in this paper were carried out between 1974 and 1986 from various HPRR activities such as steady-state subcritical, steady-state critical, and burst prompt super-critical operations of the reactor for dosimetry, irradiation, or training purposes. By using the HPRR experimental logbook information and the as-built drawings of the critical assembly, a highly detailed model of the HPRR was created with SCALE 6.2.4/KENO-VI, and a first version of a critical benchmark of the HPRR was developed following the International Criticality Safety Benchmark Evaluation Project (ICSBEP) guidelines for thorough description and uncertainty/sensitivity quantification. Unfortunately, in most of the evaluated experiments, the obtained difference between calculated and experimental k eff is around 1,000 pcm, corresponding to a relative error of approximately 1%, beyond the quality standards of the ICSBEP recommending a relative error below 0.1%. Moreover, the derived experimental uncertainty is high, around 4% relative, mainly due to the U-Mo fuel density uncertainty, but also from numerous other factors. For these reasons, the creation of a valuable critical benchmark from HPRR operation data is thus far compromised. In this paper, the different steps of the experiments’ evaluation are summarized, and the reasons for the experimental/calculation discrepancies and potential ways to solve them are explored. This paper also aims to remind us always to exercise considerable care when performing experimental work, and to record all the data possible for potential future uses.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Characterizing climate pathways using feature importance on echo state networks

The 2022 National Defense Strategy of the United States listed climate change as a serious threat to national security. Climate intervention methods, such as stratospheric aerosol injection, have been proposed as mitigation strategies, but the downstream effects of such actions on a complex climate system are not well understood. The development of algorithmic techniques for quantifying relationships between source and impact variables related to a climate event (i.e., a climate pathway) would help inform policy decisions. Data-driven deep learning models have become powerful tools for modeling highly nonlinear relationships and may provide a route to characterize climate variable relationships. In this paper, we explore the use of an echo state network (ESN) for characterizing climate pathways. ESNs are a computationally efficient neural network variation designed for temporal data, and recent work proposes ESNs as a useful tool for forecasting spatiotemporal climate data. However, ESNs are noninterpretable black-box models along with other neural networks. The lack of model transparency poses a hurdle for understanding variable relationships. We address this issue by developing feature importance methods for ESNs in the context of spatiotemporal data to quantify variable relationships captured by the model. We conduct a simulation study to assess and compare the feature importance techniques, and we demonstrate the approach on reanalysis climate data. In the climate application, we consider a time period that includes the 1991 volcanic eruption of Mount Pinatubo. This event was a significant stratospheric aerosol injection, which acts as a proxy for an anthropogenic stratospheric aerosol injection. Furthermore, we are able to use the proposed approach to characterize relationships between pathway variables associated with this event that agree with relationships previously identified by climate scientists.

black-box models↗

Exploring Tradeoffs in Federated Learning on Serverless Computing Architectures

Federated learning is driving the development of new techniques to efficiently and securely use data across multiple sites while using diverse resources. One of these techniques is the use of the serverless computing paradigm to abstract away resource specific configurations, allowing federated learning across heterogeneous environments. However, deploying federated learning across edge resources, the cloud, and traditional HPC sites will require specialized approaches in order to best account for the weaknesses and strengths of each resource. In this work, we explore the new tradeoffs presented by managing a federated learning task across heterogeneous resources and demonstrate these tradeoffs with experiments using a serverless federated learning framework.

Baughman, Matt↗

Particle Track Classification Using Quantum Associative Memory (Final Technical Report)

This project explored the use of quantum-assisted algorithms for pattern matching in sub-atomic physics experiments. Pattern matching algorithms are commonly employed to prune data of random noise and to help discriminate between signals generated by particle tracks of interest and signals generated by background events. The quantum-assisted algorithms explored in this project were based on an Ising formulation of quantum associative model (QAMM) recall and quantum content-addressable memory (QCAM) recall. The recall is performed by comparing a probe pattern with those stored in a library of patterns encoded in the QAMM/QCAM model. The classification accuracy of QAMM and QCAM recall was determined as a function of detector resolution, noise, and efficiency and pattern density, where pattern density is defined as the ratio of the number of reference signal patterns encoded in the library to each pattern’s length. We found that QAMM achieved high classification accuracy when applied to datasets with low pattern density. QCAM achieved high classification accuracy for datasets with high pattern density and was found to be more robust to detector noise. The project methodology and results are described in detail in our arXiv preprint (arXiv:2011.11848) . This project was conducted by scientists at the Johns Hopkins University Applied Physics Laboratory and Oak Ridge National Laboratory from August 2018 to August 2020 and was supported by DOE grant DE-SC0019497.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Mitigating the optical depth degeneracy using the kinematic Sunyaev-Zel’dovich effect with CMB-S4 data

The epoch of reionization is one of the major phase transitions in the history of the universe, and is a focus of ongoing and upcoming cosmic microwave background (CMB) experiments with improved sensitivity to small-scale fluctuations. Reionization also represents a significant contaminant to CMB-derived cosmological parameter constraints, due to the degeneracy between the Thomson-scattering optical depth, $\tau$, and the amplitude of scalar perturbations, $A_s$. This degeneracy subsequently hinders the ability of large-scale structure data to constrain the sum of the neutrino masses, a major target for cosmology in the 2020s. In this work, we explore the kinematic Sunyaev-Zel'dovich (kSZ) effect as a probe of reionization, and show that it can be used to mitigate the optical depth degeneracy with high-sensitivity, high-resolution data from the upcoming CMB-S4 experiment. We discuss the dependence of the kSZ power spectrum on physical reionization model parameters, as well as on empirical reionization parameters, namely $\tau$ and the duration of reionization, $\Delta z$. We show that by combining the kSZ two-point function and the reconstructed kSZ four-point function, degeneracies between $\tau$ and $\Delta z$ can be strongly broken, yielding tight constraints on both parameters. We forecast $\sigma(\tau) = 0.003$ and $\sigma(\Delta z) = 0.25$ for a combination of CMB-S4 and Planck data, including detailed treatment of foregrounds and atmospheric noise. The constraint on $\tau$ is nearly identical to the cosmic-variance limit that can be achieved from large-angle CMB polarization data. The kSZ effect thus promises to yield not only detailed information about the reionization epoch, but also to enable high-precision cosmological constraints on the neutrino mass.

79 ASTRONOMY AND ASTROPHYSICS↗

FAIRLinked: Data FAIRification Tools for Materials Data Science

FAIRLinked is a software package created to support the FAIRification of materials science data, ensuring proper alignment with FAIR principles: Findable, Accessible, Interoperable, and Reusable. It is built to be compatible with MDS-Onto, an ontology designed to capture the semantics of various types of materials data, enabling integration and sharing across different research workflows. The package is subdivided into three subpackages: InterfaceMDS, RDFTableConversion, and QBWorkflow. The first subpackage, InterfaceMDS allows users to search for terms using either string search or various filters, explore different domains and subdomains, and add terms to MDS-Onto. RDFTableConversion is used for serialization and deserialization of data from CSV into JSONLDs and vice versa in a way that captures the semantics of the data using MDS-Onto. Lastly, QBWorkflow is a serialization and deserialization workflow that incorporates RDF Data Cube vocabulary, useful for working with multidimensional datasets. By offering these packages, FAIRLinked lowers the barrier of creating FAIR, machine-actionable data for researchers in the materials science community.

FAIR↗

Single‐Cell Nanodroplet Processing Proteomics Pipeline for Analysis of Human‐Derived Microglia

Single-cell omics tools provide unique insights into heterogeneous cell populations and their responses to stimuli. For example, single-cell RNA sequencing has identified several transcriptionally distinct populations of microglia, which are resident immune cells of the central nervous system (CNS) that are responsive to CNS injury, infection, and neurodegeneration. To date, single-cell studies of microglia have focused on RNA-sequencing or cytometry by time of flight (CyTOF), which provide indirect readouts of protein abundance or quantification of a limited number of targets. Herein, we present a workflow based on FACS-assisted isolation, cryopreservation, and nanodroplet-based processing for single-cell mass spectrometry proteomics analysis of the postmortem human brain cortex-derived microglia. From a single microglial cell, 1039 proteins could be identified on average. As a proof-of-principle, we applied single-cell proteomics for exploring the heterogeneity of brain microglia at the cellular level. This pilot proteomics data partially recapitulates the prior microglia subtypes. Specifically, we determined that mitochondrial proteins, in particular members of NADH dehydrogenase (Complex I), cytochrome b-c1 (Complex III), cytochrome c oxidase (Complex IV), F1-ATPase (Complex V), and Na+/K+-ATPase complex, drive variation across microglia. This pipeline offers the potential for identifying functionally and analytically relevant protein targets for microglia in Alzheimer's disease and other neurological disorders.

59 BASIC BIOLOGICAL SCIENCES↗

Naturally light Dirac and pseudo-Dirac neutrinos from left-right symmetry

We develop a class of left-right symmetric theories based on the gauge group SU(3) c x SU(2) L x SU(2) R x U(1) with a generalized seesaw mechanism for generating the charged fermion masses. Neutrinos are naturally Dirac particles in this setup with their small masses arising from two-loop quantum corrections. We evaluate these two-loop diagrams exactly and analyze the flavor structure of the lepton sector. We find excellent fits to neutrino oscillation data, independent of the right-handed gauge symmetry breaking scale. We also explore the possibility that neutrinos are pseudo-Dirac particles in this framework, with the tiny mass splittings between active and sterile neutrinos arising from Planck-induced corrections and find possible realizations. These models can be tested in the near future with precision cosmological measurements of ΔN eff in CMB which is predicted to be ≃ 0.14. This class of models allows for a solution to the strong CP problem via parity symmetry without the need for an axion.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗