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WA-Omic_LA.1.0 - Quantitative Lipidomics, Metabolomics, and Sequencing (16S/ITS) Publication Data DOI Package

Corresponding Data Publication: "Rapid remodeling of the soil lipidome in response to a drying-rewetting event." This study reveals specific changes in lipids and metabolites that are indicative of stress adaptation, substrate use, and cellular recovery during soil drying and subsequent rewetting. Drought induced nutrient limitation was reflected in the lipidome and polar metabalome, both of which rapidly shifted (within hours) upon rewet. Reduced nutrient access in dry soil caused the replacement of glycerophospholipids with phosphorus-free lipids and impeded resource-expensive osmolyte accumulation. Elevated levels of ceramides and lipids with long chain polyunsaturated fatty acids, in dry soil suggests that lipids play an important role in fungal drought tolerance. Increasing abundance of bacterial glycerophospholipids and triacylglycerols with fatty acids typical of bacteria and polar metabolites suggest metabolic recovery in representative bacteria once the environmental conditions are conducive for growth. These results underscore the importance of the soil lipidome as a robust indicator of microbial community responses, especially at the short time scales of cell-environment reactions. Data package contents reported here are the first version and contain pre- and post-processed data acquisition and subsequent downstream analysis files using various data source instrument method techniques and Mass Spectroscopy (MS) EMSL capabilities. This publication data package DOI is a comprehensive high-throughput multi-omics data lifecycle collection containing processed data method metadata. Support files include additional data download “Read Me” file containing data descriptor information and data source application ontologies (see data dictionary). Reported data download contents are structured for compliance with project data sharing guidelines, community standards initiatives, and sponsor stakeholder policies supporting FAIR data principles. For increased data availability and interoperability, GC-MS/LC-MS mass spectrometry datasets (Thermo .raw ) were deposited at the MassIVE database repository under the related data accession MSV000086931 and can be accessed by using the API. Statistical data processing software, analysis tools, and data workflows are listed below corresponding to the host repository long-term location.

Amplicon sequencing 16S ITS LC-MS/MS lipidomics mu↗

Scaling Ensembles of Data-Intensive Quantum Chemical Calculations for Millions of Molecules

Deep learning models are efficient computational tools that can accelerate the inverse design of molecules with desired functional properties by generating predictions at a fraction of the time required by traditional quantum chemical approaches. To ensure that a model maintains accuracy and transferability across broad regions of the chemical space explored during the inverse design, it must be trained on massively large volumes of simulation data. This requires running large-scale ensemble quantum chemical calculations on high-performance computing (HPC) systems for data collection. However, the efficient execution of such large ensemble calculations and the management of large volumes of output data require tools that can judiciously utilize computational resources and manage metadata overhead on the file system. Therefore, we present a high-performance, scalable, ensemble management framework for performing data-intensive quantum chemical electronic structure calculations for organic molecules. This framework provides abstractions to plug different ab initio, first principles, and first principles-based semi-empirical methods and executes them efficiently at large scale on HPC systems. It dynamically distributes tasks to resources and uses tiered storage for managing large collections of files. We employed this framework to process over ten million organic molecules and generate open-source datasets that provide UV-vis absorption spectra by running time-dependent density-functional tight-binding calculations. It is the largest database containing molecular optical spectra that were simulated with quantum chemical methods in a consistent manner.

Mehta, Kshitij↗

A 5G Enabled Adaptive Computing Workflow for Greener Power Grid

5G wireless technology can deliver higher data speeds, ultra low latency, more reliability, massive network capacity, increased availability, and a more uniform user experience to users. It brings additional power to help address the challenges brought by renewable integration and decarbonization. In this paper, a 5G enabled adaptive computing workflow tool has been presented that consists of various computing resources, such as 5G equipment, edge computing, cluster, Graphics processing unit (GPU) and cloud computing, with two examples showing technical feasibility for edge-grid-cloud interaction for real-time monitoring, security assessment, and forecasting. Benefiting from the high data transmission speed and massive connection capability of 5G, the workflow shows its potential to seamlessly integrate various applications at distributed and/or centralized locations to build more complex and powerful functions, with better flexibility.

5G technology, computational workflow, edge comput↗

Multi defect detection and analysis of electron microscopy images with deep learning

Electron microscopy is widely used to explore defects in crystal structures, but human detecting of defects is often time-consuming, error-prone, and unreliable, and is not scalable to large numbers of images or real-time analysis. In this work, we discuss the application of machine learning approaches to find the location and geometry of different defect clusters in irradiated steels. We show that a deep learning based Faster R-CNN analysis system has a performance comparable to human analysis with relatively small training data sets. Furthermore, this study proves the promising ability to apply deep learning to assist the development of automated microscopy data analysis even when multiple features are present and paves the way for fast, scalable, and reliable analysis systems for massive amounts of modern electron microscopy data.

36 MATERIALS SCIENCE↗

MassiveGNN: Efficient Training via Prefetching for Massively Connected Distributed Graphs

Graph Neural Networks (GNN) are indispensable in learning from graph-structured data, yet their rising computational costs, especially on massively connected graphs, pose significant challenges in terms of execution performance. To tackle this, distributed-memory solutions such as partitioning the graph to concurrently train multiple replicas of GNNs are in practice. However, approaches requiring a partitioned graph usually suffer from communication overhead and load imbalance, even under optimal partitioning and communication strategies due to irregularities in the neighborhood minibatch sampling. This paper proposes practical trade-offs for improving the sampling and communication overheads for representation learn- ing on distributed graphs (using popular GraphSAGE architecture) by developing a parameterized prefetch and eviction scheme on top of the state-of-the-art Amazon DistDGL distributed GNN framework, demonstrating about 15–40% improvement in end-to-end training performance on the NERSC Perlmutter supercomputer for various OGB datasets.

Machine Leanring, high performance comptuing, grap↗

Advanced Computing, Data Science, and Artificial Intelligence Research Opportunities for Energy-Focused Transportation Science

The Energy Efficient Mobility Systems (EEMS) technology landscape is complex and rapidly evolving, which provides both tremendous opportunities and formidable challenges. Significant alterations to the mobility landscape are underway due to the advent of vehicle and infrastructure connectivity, autonomous driving, and rapid passenger- and freight-vehicle electrification. Advanced computing will play an increasingly important role in enabling the EEMS program to understand and identify the most important levers to improve the energy productivity of future integrated mobility systems. It is also driving new approaches to mobility and the research to unlock an affordable, efficient, safe, and accessible transportation future. Driving much of this change is the collection, analysis, and strategic use of massive amounts of diverse, complex data from infrastructure and vehicles with on-board sensors and data storage and transmission capabilities. Diverse and representative data are key to implementing approaches to maximize mobility energy productivity. While high-fidelity modeling of integrated transportation networks has strengthened our understanding of dynamic movement and behavior patterns, existing tools must be expanded beyond their current focus. This work necessitates data infrastructure investments (e.g., secure-streaming data platforms driven by ubiquitous sensors and video analytics) as well as investments in critical capabilities for large-scale automated analysis and organization using modern machine learning, statistics, and artificial intelligence. Other chief needs include agile, large-scale storage that can be quickly searched and queried for relevant data to support validation and model development, data-sharing agreements, and formatting standards for key data types. The future of public transit must be explored in greater detail, research must inform design, and opportunities must be identified for improving the mobility productivity of public transit in both urban and rural America.

33 ADVANCED PROPULSION SYSTEMS↗

Data compression and covariance matrix inspection: Cosmic shear

Covariance matrices are among the most difficult pieces of end-to-end cosmological analyses. In principle, for two-point functions, each component involves a four-point function, and the resulting covariance often has hundreds of thousands of elements. We investigate various compression mechanisms capable of vastly reducing the size of the covariance matrix in the context of cosmic shear statistics. This helps identify which of its parts are most crucial to parameter estimation. We start with simple compression methods, by isolating and “removing” 200 modes associated with the lowest eigenvalues, then those with the lowest signal-to-noise ratio, before moving on to more sophisticated schemes like compression at the tomographic level and, finally, with the massively optimized parameter estimation and data compression (MOPED). We find that, while most of these approaches prove useful for a few parameters of interest, like Ω m , the simplest yield a loss of constraining power on the intrinsic alignment (IA) parameters as well as S 8 . For the case considered—cosmic shear from the first year of data from the Dark Energy Survey—only MOPED was able to replicate the original constraints in the 16-parameter space. Finally, we apply a tolerance test to the elements of the compressed covariance matrix obtained with MOPED and confirm that the IA parameter A IA is the most susceptible to inaccuracies in the covariance matrix.

79 ASTRONOMY AND ASTROPHYSICS↗

Automatic detection of cataclysmic variables from SDSS images

Abstract Investigating rare and new objects have always been an important direction in astronomy. Cataclysmic variables (CVs) are ideal and natural celestial bodies for studying the accretion process of semi-detached binaries with accretion processes. However, the sample size of CVs must increase because a lager gap exists between the observational and the theoretical expanding CVs. Astronomy has entered the big data era and can provide massive images containing CV candidates. CVs as a type of faint celestial objects, are highly challenging to be identified directly from images using automatic manners. Deep learning has rapidly developed in intelligent image processing and has been widely applied in some astronomical fields with excellent detection results. YOLOX, as the latest YOLO framework, is advantageous in detecting small and dark targets. This work proposes an improved YOLOX-based framework according to the characteristics of CVs and Sloan Digital Sky Survey (SDSS) photometric images to train and verify the model to realise CV detection. We use the Convolutional Block Attention Module to increase the number of output features with the feature extraction network and adjust the feature fusion network to obtain fused features. Accordingly, the loss function is modified. Experimental results demonstrate that the improved model produces satisfactory results, with average accuracy (mean average Precision at 0.5) of 92.0%, Precision of 92.9%, Recall of 94.3%, and $F1-score$ of 93.6% on the test set. The proposed method can efficiently achieve the identification of CVs in test samples and search for CV candidates in unlabeled images. The image data vastly outnumber the spectra in the SDSS-released data. With supplementary follow-up observations or spectra, the proposed model can help astronomers in seeking and detecting CVs in a new manner to ensure that a more extensive CV catalog can be built. The proposed model may also be applied to the detection of other kinds of celestial objects.

Astronomy & Astrophysics↗

DART-PFLOTRAN: An ensemble-based data assimilation system for estimating subsurface flow and transport model parameters

Ensemble-based Data Assimilation (EDA), based on the Monte Carlo approach, has been effectively applied to estimate model parameters through inverse modeling in subsurface flow and transport problems. However, implementation of EDA approach involves a complicated workflow that include setting up and executing ensemble forward model simulations, processing observations and model simulation results for parameter updates, and repeat for sequential or iterative EDA. To facilitate the management of such workflow and lower the barriers for adopting EDA-based parameter estimation in subsurface science, we develop a generic software frame-work linking the Data Assimilation Research Testbed (DART) with a massively parallel subsurface FLOw and TRANsport code PFLOTRAN. The new DART-PFLOTRAN leverages both the core data assimilation engines in DART and the computational power afforded by PFLOTRAN. In addition to the standard smoother and filtering options, DART-PFLOTRAN enables an iterative EDA workflow based on the Ensemble Smoother for Multiple Data Assimilation method (ES-MDA) to improve estimation accuracy for nonlinear forward problems. Here, we verify the implementation of ES-MDA in DART-PFLOTRAN using two synthetic cases designed to estimate static permeability and dynamic exchange fluxes across the riverbed, respectively, from continuous temperature measurements made across a depth profile. One-dimensional hydro-thermal simulations are performed in both cases to relate temperature responses with the parameters of interest. In the case of estimating dynamic parameters, we demonstrate the flexibility of DART-PFLOTRAN in automating sequential ES-MDA workflow, which will significantly reduce the time researchers spend on managing complex workflows in similar applications. Both studies yield accurate estimations of the parameters compared to their synthetic truth, while ES-MDA leads to more accurate estimation when a high level of nonlinearity exist between observed responses and unknown parameters. With a code base in Python and Fortran, DART-PFLOTRAN paves the way for applications in large-scale subsurface inverse modeling by automating the complex workflow of sequential ES-MDA that can be executed on various computing platforms.

97 MATHEMATICS AND COMPUTING↗

Functional characterization of prokaryotic dark matter: the road so far and what lies ahead

Eight-hundred thousand to one trillion prokaryotic species may inhabit our planet. Yet, fewer than two-hundred thousand prokaryotic species have been described. This uncharted fraction of microbial diversity, and its undisclosed coding potential, is known as the “microbial dark matter” (MDM). Next-generation sequencing has allowed to collect a massive amount of genome sequence data, leading to unprecedented advances in the field of genomics. Still, harnessing new functional information from the genomes of uncultured prokaryotes is often limited by standard classification methods. These methods often rely on sequence similarity searches against reference genomes from cultured species. This hinders the discovery of unique genetic elements that are missing from the cultivated realm. It also contributes to the accumulation of prokaryotic gene products of unknown function among public sequence data repositories, highlighting the need for new approaches for sequencing data analysis and classification. Increasing evidence indicates that these proteins of unknown function might be a treasure trove of biotechnological potential. Here, we outline the challenges, opportunities, and the potential hidden within the functional dark matter (FDM) of prokaryotes. We also discuss the pitfalls surrounding molecular and computational approaches currently used to probe these uncharted waters, and discuss future opportunities for research and applications.

59 BASIC BIOLOGICAL SCIENCES↗

Constraints on millicharged particles from cosmic-ray production

We study cosmic-ray-atmosphere collisions as a permanent production source of exotic millicharged particles (MCPs) for all terrestrial experiments. [MCPs are also known as charged massive particles (CHAMPs).] Based on data from Super-K, this allows us to derive new limits on MCPs that are competitive with, or improve, the currently leading bounds from accelerator-based searches for masses up to 1.5 GeV. In models where a subdominant component of dark matter (DM) is fractionally charged, these constraints probe parts of the parameter space that is inaccessible for conventional direct-detection DM experiments, independently of assumptions about the DM abundance.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Dynamical Packing in the Habitable Zone: The Case of Beta CVn

Uncovering the occurrence rate of terrestrial planets within the habitable zone (HZ) of their host stars has been a particular focus of exoplanetary science in recent years. The statistics of these occurrence rates have largely been derived from transiting planet discoveries, and have uncovered numerous HZ planets in compact systems around M-dwarf host stars. Here we explore the width of the HZ as a function of spectral type, and the dynamical constraints on the number of stable orbits within the HZ for a given star. We show that, although the Hill radius for a given planetary mass increases with larger semimajor axis, the width of the HZ for earlier-type stars allows for more terrestrial planets in the HZ than late-type stars. In general, dynamical constraints allow ∼6 HZ Earth-mass planets for stellar masses ≳0.7M {sub ⊙}, depending on the presence of farther out giant planets. As an example, we consider the case of Beta CVn, a nearby bright solar-type star. We present 20 yr of radial velocities (RV) from the Keck/High Resolution Echelle Spectrometer (HIRES) and Automated Planet Finder (APF) instruments and conduct an injection-recovery analysis of planetary signatures in the data. Our analysis of these RV data rule out planets more massive than Saturn within 10 au of the star. These system properties are used to calculate the potential dynamical packing of terrestrial planets in the HZ and show that such nearby stellar targets could be particularly lucrative for HZ planet detection by direct imaging exoplanet missions.

79 ASTRONOMY AND ASTROPHYSICS↗

Inferring Type II-P Supernova Progenitor Masses from Plateau Luminosities

Abstract Connecting observations of core-collapse supernova explosions to the properties of their massive star progenitors is a long-sought, and challenging, goal of supernova science. Recently, Barker et al. presented bolometric light curves for a landscape of progenitors from spherically symmetric neutrino-driven core-collapse supernova (CCSN) simulations using an effective model. They find a tight relationship between the plateau luminosity of the Type II-P CCSN light curve and the terminal iron-core mass of the progenitor. Remarkably, this allows us to constrain progenitor properties with photometry alone. We analyze a large observational sample of Type II-P CCSN light curves and estimate a distribution of iron-core masses using the relationship of Barker et al. The inferred distribution matches extremely well with the distribution of iron-core masses from stellar evolutionary models and namely, contains high-mass iron cores that suggest contributions from very massive progenitors in the observational data. We use this distribution of iron-core masses to infer minimum and maximum masses of progenitors in the observational data. Using Bayesian inference methods to locate optimal initial mass function parameters, we find M min = 9.8 − 0.27 + 0.37 and M max = 24.0 − 1.9 + 3.9 solar masses for the observational data.

79 ASTRONOMY AND ASTROPHYSICS↗

Scalable edge clustering of dynamic graphs via weighted line graphs

Timestamped relational datasets consisting of records (or connections) between pairs of entities are ubiquitous in network science. For applications like peer-to-peer communication, email, various social network interactions, and computer network security, it is useful to organize these records into groups based on how and when they are occurring. Weighted line graphs offer a natural way to model how records are related in such datasets but for large real-world graph topologies, building and utilizing the line graph is prohibitively expensive. Here, we present the framework to cluster the edges of a dynamic graph via the associated line graph that contains two major contributions. The first is a method to work with the line graph implicitly and the second is a distributed scale implementation of an agglomerative hierarchical graph clustering algorithm. We outline a novel hierarchical dynamic graph edge clustering approach that efficiently breaks massive relational datasets into small sets of edges containing events at various timescales. This is in stark contrast to traditional graph clustering algorithms that prioritize highly connected (clique-like) community structures. Our approach relies on constructing a sufficient subgraph of a weighted line graph and applying a hierarchical agglomerative clustering. This approach is related to scalable techniques from spatial clustering, nonlinear-dimension reduction, topological data analysis, and draws particular inspiration from HDBSCAN. As an edge clustering, this method yields an overlapping node clustering. Our algorithm is parallelizable and we demonstrate efficient clustering of a billion-scale, real-world dynamic graph into small edge sets that correlate in topology and time. The entire clustering process for a graph with tens of billions of edges takes just a few minutes of run time on 256 nodes of a distributed compute environment. We argue how the output of the edge clustering is useful for a multitude of data visualization and powerful machine learning tasks, both involving the original massive dynamic graph data and metadata associated with the nodes and edges. Finally, we describe how this approach can be extended to dynamic hypergraphs and dynamic graphs/hypergraphs with unstructured data living on vertices and edges.

Data Analysis↗

Cosmological implications of photon-flux upper limits at ultrahigh energies in scenarios of Planckian-interacting massive particles for dark matter

Here using the data of the Pierre Auger Observatory, we report on a search for signatures that would be suggestive of super-heavy particles decaying in the Galactic halo. From the lack of signal, we present upper limits for different energy thresholds above ≳10 8 GeV on the secondary by-product fluxes expected from the decay of the particles. Assuming that the energy density of these super-heavy particles matches that of dark matter observed today, we translate the upper bounds on the particle fluxes into tight constraints on the couplings governing the decay process as a function of the particle mass. Instantons, which are nonperturbative solutions to Yang-Mills equations, can give rise to decay channels otherwise forbidden and transform stable particles into metastable ones. Assuming such instanton-induced decay processes, we derive a bound on the reduced coupling constant of gauge interactions in the dark sector: α X ≲ 0.09, for 10 9 ≲ M X /GeV < 10 19 . Conversely, we obtain that, for instance, a reduced coupling constant α X = 0.09 excludes masses M X ≳ 3 x 10 13 GeV . In the context of dark matter production from gravitational interactions alone during the reheating epoch, we derive constraints on the parameter space that involves, in addition to M X and α X , the Hubble rate at the end of inflation, the reheating efficiency, and the nonminimal coupling of the Higgs with curvature.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Dark Energy Survey Year 3 results: Constraints on extensions to Λ CDM with weak lensing and galaxy clustering

We constrain six possible extensions to the Λ cold dark matter (CDM) model using measurements from the Dark Energy Survey’s first three years of observations, alone and in combination with external cosmological probes. The DES data are the two-point correlation functions of weak gravitational lensing, galaxy clustering, and their cross-correlation. We use simulated data vectors and blind analyses of real data to validate the robustness of our results to astrophysical and modeling systematic errors. In many cases, constraining power is limited by the absence of theoretical predictions beyond the linear regime that are reliable at our required precision. The Λ CDM extensions are dark energy with a time-dependent equation of state, nonzero spatial curvature, additional relativistic degrees of freedom, sterile neutrinos with eV-scale mass, modifications of gravitational physics, and a binned σ 8 ( z ) model which serves as a phenomenological probe of structure growth. For the time-varying dark energy equation of state evaluated at the pivot redshift we find ( w p , w a ) = ( - 0.9 9 - 0.17 + 0.28 , - 0.9 ± 1.2 ) at 68% confidence with z p = 0.24 from the DES measurements alone, and ( w p , w a ) = ( - 1.0 3 - 0.03 + 0.04 , - 0. 4 - 0.3 + 0.4 ) with z p = 0.21 for the combination of all data considered. Curvature constraints of Ω k = 0.0009 ± 0.0017 and effective relativistic species N eff = 3.1 0 - 0.16 + 0.15 are dominated by external data, though adding DES information to external low-redshift probes tightens the Ω k constraints that can be made without cosmic microwave background observables by 20%. For massive sterile neutrinos, DES combined with external data improves the upper bound on the mass m eff by a factor of 3 compared to previous analyses, giving 95% limits of ( Δ N eff , m eff ) ≤ ( 0.28 , 0.20 eV ) when using priors matching a comparable Planck analysis. For modified gravity, we constrain changes to the lensing and Poisson equations controlled by functions Σ ( k , z ) = Σ 0 Ω Λ ( z ) / Ω Λ , 0 and μ ( k , z ) = μ 0 Ω Λ ( z ) / Ω Λ , 0 , respectively, to Σ 0 = 0. 6 - 0.5 + 0.4 from DES alone and ( Σ 0 , μ 0 ) = ( 0.04 ± 0.05 , 0.0 8 - 0.19 + 0.21 ) for the combination of all data, both at 68% confidence. Overall, we find no significant evidence for physics beyond Λ CDM .

79 ASTRONOMY AND ASTROPHYSICS↗

Harnessing on-machine metrology data for prints with a surrogate model for laser powder directed energy deposition

In this study, we leverage the massive amount of multi-modal on-machine metrology data generated from Laser Powder Directed Energy Deposition (LP-DED) to construct a comprehensive surrogate model of the 3D printing process. By employing Dynamic Mode Decomposition with Control (DMDc), a data-driven technique, we capture the complex physics inherent in this extensive dataset. This physics-based surrogate model emphasizes thermodynamically significant quantities, enabling us to accurately predict key process outcomes. The model ingests 21 process parameters, including laser power, scan rate, and position, while providing outputs such as melt pool temperature, melt pool size, and other essential observables. Furthermore, it incorporates uncertainty quantification to provide bounds on these predictions, enhancing reliability and confidence in the results. We then deploy the surrogate model on a new, unseen part and monitor the printing process as validation of the method. Our experimental results demonstrate that the predictions align with actual measurements with high accuracy, confirming the effectiveness of our approach. Furthermore, this methodology not only facilitates real-time predictions but also operates at process-relevant speeds, establishing a basis for implementing feedback control in LP-DED.

Digital twins↗

The Stellar Content of H72.97-69.39, a Potential Super Star Cluster in the Making

Young massive clusters and super star clusters (SSCs) represent an extreme mode of star formation. Far-infrared imaging of the Magellanic Clouds has identified one potential embedded SSC, HSO BMHERICC J72.971176-69.391112 (H72.97-69.39 in short), in the southwest outskirts of the Large Magellanic Cloud. We present Gemini Flamingos 2 and GSAOI near-infrared imaging of a 3′ × 3′ region around H72.97-69.39 in order to characterize the stellar content of the cluster. The stellar content is probed down to 1.5 M {sub ⊙}. We find substantial dust extinction across the cluster region, extending up to A {sub K} of 3. Deeply embedded stars are associated with ALMA-detected molecular gas suggesting that star formation is ongoing. The high spatial resolution of the GSAOI data allows identification of the central massive object associated with the {sup 13}CO ALMA observations and detection of fainter low-mass stars around the H30α ALMA source. The morphology of the molecular gas and the nebulosity from adjacent star formation suggest they have interacted covering a region of several parsecs. The total stellar content in the cluster is estimated from the intermediate- and high-mass stellar content to be at least 10,000 M {sub ⊙}, less than R136 with up to 100,000 M {sub ⊙} within 4.7 pc radius, but places it in the regime of an SSC. Based on the extinction determination of individual stars we estimate a molecular gas mass in the vicinity of H72.97-69.39 of 6600 M {sub ⊙}, suggesting more star formation can be expected.

74 ATOMIC AND MOLECULAR PHYSICS↗