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DOE OSTI2024

Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research

Introduction The agriculture genomics community has numerous data submission standards available, but the standards for describing and storing single-cell (SC, e.g., scRNA- seq) data are comparatively underdeveloped. Methods To bridge this gap, we leveraged recent advancements in human genomics infrastructure, such as the integration of the Human Cell Atlas Data Portal with Terra, a secure, scalable, open-source platform for biomedical researchers to access data, run analysis tools, and collaborate. In parallel, the Single Cell Expression Atlas at EMBL-EBI offers a comprehensive data ingestion portal for high-throughput sequencing datasets, including plants, protists, and animals (including humans). Developing data tools connecting these resources would offer significant advantages to the agricultural genomics community. The FAANG data portal at EMBL-EBI emphasizes delivering rich metadata and highly accurate and reliable annotation of farmed animals but is not computationally linked to either of these resources. Results Herein, we describe a pilot-scale project that determines whether the current FAANG metadata standards for livestock can be used to ingest scRNA-seq datasets into Terra in a manner consistent with HCA Data Portal standards. Importantly, rich scRNA-seq metadata can now be brokered through the FAANG data portal using a semi-automated process, thereby avoiding the need for substantial expert curation. We have further extended the functionality of this tool so that validated and ingested SC files within the HCA Data Portal are transferred to Terra for further analysis. In addition, we verified data ingestion into Terra, hosted on Azure, and demonstrated the use of a workflow to analyze the first ingested porcine scRNA-seq dataset. Additionally, we have also developed prototype tools to visualize the output of scRNA-seq analyses on genome browsers to compare gene expression patterns across tissues and cell populations. This JBrowse tool now features distinct tracks, showcasing PBMC scRNA-seq alongside two bulk RNA-seq experiments. Discussion We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem based on Findable, Accessible, Interoperable, and Reusable (FAIR) SC principles to facilitate SC-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species.

Genetics & Heredity↗

DOE OSTI2025

Single-nuclei transcriptome analysis of IgM+ cells isolated from channel catfish (Ictalurus punctatus) spleen

Catfish production is the primary aquaculture sector in the United States, and the key cultured species is channel catfish (Ictalurus punctatus). The major causes of production losses are pathogenic diseases, and the spleen, an important site of adaptive immunity, is implicated in these diseases. To examine the channel catfish immune system, single-nuclei transcriptomes of sorted and captured IgM + cells were produced from adult channel catfish. Three channel catfish (~1 kg) were euthanized, the spleen dissected, and the tissue dissociated. The lymphocytes were isolated using a Ficoll gradient and IgM + cells were then sorted with flow cytometry. The IgM + cells were lysed and single-nuclei libraries generated using a Chromium Next GEM Single Cell 3’ GEM Kit and the Chromium X Instrument (10x Genomics) and sequenced with the Illumina NovaSeq X Plus sequencer. The reads were aligned to theI. punctatusreference assembly (Coco_2.0) using Cell Ranger, and normalization, cluster analysis, and differential gene expression analysis were carried out with Seurat. Across the three samples, approximately 753.5 million reads were generated for 18,686 cells. After filtering, 10,637 cells remained for the cluster analysis. The cluster analysis identified 16 clusters which were classified as B cells (10,276), natural killer-like (NK-like) cells (178), T cells or natural killer cells (45), hematopoietic stem and progenitor cells (HSPC)/megakaryocytes (MK) (66), myeloid/epithelial cells (40), and plasma cells (32). The B cell clusters were further defined as different populations of mature B cells, cycling B cells, and plasma cells. The plasma cells highly expressedighmand we demonstrated that the secreted form of the transcript was largely being expressed by these cells. This atlas provides insight into the gene expression of IgM + immune cells in channel catfish. The atlas is publicly available and could be used garner more important information regarding the gene expression of splenic immune cells.

Immunology↗

DOE OSTI2024

In Vitro Antimicrobial Activity of Volatile Compounds from the Lichen Pseudevernia furfuracea (L.) Zopf. Against Multidrug-Resistant Bacteria and Fish Pathogens

Lichens are symbiotic organisms with unique secondary metabolism. Various metabolites from lichens have shown antimicrobial activity. Nevertheless, very few studies have investigated the antimicrobial potential of the volatile compounds they produce. This study investigates the chemical composition and antimicrobial properties of volatile compounds from Pseudevernia furfuracea collected in two regions of Morocco. Hydrodistillation was used to obtain volatile compounds from samples collected in the High Atlas and Middle Atlas. Gas chromatography–mass spectrometry (GC-MS) analysis identified phenolic cyclic compounds as the primary constituents, with atraric acid and chloroatranol being the most abundant. Additionally, eight compounds were detected in lichens for the first time. The antimicrobial activity of these compounds was assessed using disc diffusion and broth microdilution methods. Both samples demonstrated significant antimicrobial effects against multidrug-resistant human bacteria, reference microorganisms, fish pathogens, and Candida albicans, with minimum inhibitory concentrations (MICs) ranging from 1000 µg/mL to 31.25 µg/mL. This study provides the first report on the volatile compounds from Pseudevernia furfuracea and their antimicrobial effects, particularly against fish pathogens, suggesting their potential as novel antimicrobial agents for human and veterinary use. Further research is warranted to explore these findings in more detail.

Essadki, Yasser (ORCID:0009000648460075)↗

DOE OSTI2020

The Outburst of the Young Star Gaia19bey

We report photometry and spectroscopy of the outburst of the young stellar object Gaia19bey. We have established the outburst light curve with archival Gaia “G,” ATLAS “Orange,” Zwicky Transient Facility r-band, and Pan-STARRS “rizy”-filter photometry, showing an outburst of ~4 yr duration, longer than typical EX Lupi objects but shorter than FU Orionis objects. Its pre-outburst spectral energy distribution shows a flat far-infrared spectrum, confirming the early evolutionary state of Gaia19bey and its similarity to other deeply embedded young stars experiencing outbursts. A lower limit to the peak outburst luminosity is ~182 L{sub ⊙} at an assumed distance of 1.4 kpc, the minimum plausible distance. Infrared and optical spectroscopy near maximum light show an emission line spectrum, including H i lines, strong red Ca ii emission, other metal emission lines, infrared CO bandhead emission, and a strong infrared continuum. Toward the end of the outburst, the emission lines have all but disappeared and the spectrum has changed into an almost pure continuum spectrum. This indicates a cessation of magnetospheric accretion activity. The near-infrared colors have become redder as Gaia19bey has faded, indicating a cooling of the continuum component. Near the end of the outburst, the only remaining strong emission lines are forbidden shock-excited emission lines. Adaptive optics integral-field spectroscopy shows the H{sub 2} 1–0 S(1) emission with the morphology of an outflow cavity and the extended emission in the [Fe ii] line at 1644 nm with the morphology of an edge-on disk. However, we do not detect any large-scale jet from Gaia19bey.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Visualizing How the Structure of Large-Radius Jets Shapes Their Wakes

The ATLAS collaboration has introduced and implemented a strategy for selecting and analyzing large-radius jets composed of skinny $R=0.2$ subjets in heavy ion collisions at the LHC. We show how measurements of these jets teach us about the resolution length $L_{\rm res}$ of quark-gluon plasma (QGP) and can teach us how jet substructure shapes the wakes that jets excite in the QGP droplets through which they pass. We use Hybrid Model calculations to reproduce measurements of $R_{AA}$ for large-radius jets in PbPb collisions, and study their dependence on the angle between the two skinny subjets involved in the final reclustering step of an $R=1$ jet. We show how these observables can constrain the value of $L_{\rm res}$ and demonstrate that the ATLAS data rule out any picture in which an entire parton shower loses energy coherently as if it were a single entity. Determining the degree to which the QGP can resolve partons within a jet is central to the broader program of using jet quenching measurements to probe QGP. We make further use of this setup by analyzing the response of the medium to the passage of large-radius $R=2$ jets containing two skinny subjets in gamma-jet events. We introduce novel jet-shape observables that allow us to visualize the angular shape of the soft hadrons originating from the wakes that wide jets with two skinny subjets excite in a droplet of QGP, as a function of the angular separation between the subjets. We find that even when they are $\sim 0.8- 1$ radian apart, a single broad wake is produced. Only when the two subjets are even farther apart is the presence of two sub-wakes revealed. We show that the way in which jet structure shapes jet wakes can be visualized with similar clarity in experiments by using only those hadrons with low $p_T$. These observables thus offer a new and distinctive way of seeing jet wakes in heavy ion collision data.

FOS: Physical sciences↗

DOE OSTI2020

HL-LHC Computing Review: Common Tools and Community Software

Common and community software packages, such as ROOT, Geant4 and event generators have been a key part of the LHC's success so far and continued development and optimisation will be critical in the future. The challenges are driven by an ambitious physics programme, notably the LHC accelerator upgrade to high-luminosity, HL-LHC, and the corresponding detector upgrades of ATLAS and CMS. In this document we address the issues for software that is used in multiple experiments (usually even more widely than ATLAS and CMS) and maintained by teams of developers who are either not linked to a particular experiment or who contribute to common software within the context of their experiment activity. We also give space to general considerations for future software and projects that tackle upcoming challenges, no matter who writes it, which is an area where community convergence on best practice is extremely useful.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

The Composite Spectrum of QSO Absorption Line Systems in DESI DR2

We present details regarding the construction of a composite spectrum of quasar (QSO) absorption line systems. In this composite spectrum we identify more than 70 absorption lines, and observe oxygen and hydrogen emission features at a higher signal-to-noise ratio than in any previous study. As the light from a distant quasar travels towards an observer, it may interact with the circumgalactic medium environment of an intervening galaxy, forming absorption lines. In order to maximize the signal of these absorption lines, we have selected a sample of 238,838 quasar spectra from the second data release of the Dark Energy Spectroscopic Instrument (DESI), each identified to have absorption lines resulting from such an interaction. By stacking these spectra in the restframe of the absorption, and calculating a median composite spectrum, we are able to isolate and enhance these absorption lines. We provide a full atlas of all detected absorption and emission lines as well as their fit centroids and equivalent width values. This atlas should aid in future studies investigating the compositions and physical conditions of these absorbers.

Napolitano, Lucas [Wyoming U.] (ORCID:000000025166↗

DOE OSTI2020

Design of Stand-Alone Cryomodule based on Superconducting Quarter-Wave Resonator

Present superconducting accelerators require a central refrigeration system and piping to distribute liquid helium and nitrogen. Stand-alone cryocooler-based systems are of significant interest both to scientific and industrial customers, as they allow applications at facilities where no cryogenic equipment and expertise exists, where it is undesirable to develop additional cryogenic systems, or where a mobile system that can be transported between beamlines or facilities is required. The technical challenge of this approach is to minimize the heat losses to the liquid helium so that commercially available, self-contained cryocoolers are able to handle the thermal load. This paper presents an improved design for a stand-alone quarter-wave resonator (QWR) cryomodule a based on commercially available cryocoolers. This cryomodule has a particular application in the ATLAS intensity upgrade project where it will house a 72.75 MHz QWR for beam energy adjustments to experimental areas, where no helium cryogenic systems exist. The described cryomodule may also be the critical part of a turnkey system with application to material processing, semiconductor manufacturing, food irradiation and homeland security. The development of low heat loss peripheral components reduces cost and widens applicability of the system. We will discuss the cryomodule and RF coupler designs, including numerical thermal and structural analyses.

43 PARTICLE ACCELERATORS↗

DOE OSTI2021

Dynamic Distribution of High-Rate Data Processing from CERN to Remote HPC Data Centers

The prompt reconstruction of the data recorded from the Large Hadron Collider (LHC) detectors has always been addressed by dedicated resources at the CERN Tier-0. Such workloads come in spikes due to the nature of the operation of the accelerator and in special high load occasions experiments have commissioned methods to distribute (spill-over) a fraction of the load to sites outside CERN. The present work demonstrates a new way of supporting the Tier-0 environment by provisioning resources elastically for such spilled-over workflows onto the Piz Daint Supercomputer at CSCS. Furthermore, this is implemented using containers, tuning the existing batch scheduler and reinforcing the scratch file system, while still using standard Grid middleware. ATLAS, CMS and CSCS have jointly run selected prompt data reconstruction on up to several thousand cores on Piz Daint into a shared environment, thereby probing the viability of the CSCS high performance computer site as on demand extension of the CERN Tier-0, which could play a role in addressing the future LHC computing challenges for the high luminosity LHC.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Proposal to search for long-lived neutral particles in CERN service shafts

Long-lived particles are predicted by many extensions of the Standard Model and have been gaining interest in recent years. In this paper the original proposal is presented for AN Underground Belayed In-Shaft (ANUBIS) detector that substantially extends the sensitivity to particle lifetimes by instrumenting the existing service shafts above the ATLAS or CMS experiments with tracking stations. For scenarios with electrically neutral long-lived particles with 𝑚 ≳ 1~GeV produced at the electroweak scale and above, the lifetime reach is increased by 2-3 orders of magnitude compared to currently operating and approved future experiments at the LHC. Here, the original ANUBIS detector design proposal is outlined along with the projected costs.

ANUBIS↗

DOE OSTI2022

The VMM3a ASIC

The VMM3a is a custom low-noise Application Specific Integrated Circuit. It is intended to be used in the front end readout electronics of both the Micromegas and sTGC detectors of the ATLAS New Small Wheels upgrade project at CERN. It is fabricated in the 130 nm GlobalFoundries 8RF-DM process. Here, the 64 channels with highly configurable parameters, although designed for a specific project, can meet the processing needs of signals from various detector types in several other applications. In this note, the VMM3a, which is the production version of the VMM family, will be presented along with the features incorporated and its performance.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Expansion of Machine-Learning Method for Classifying Neutron Resonances

The understanding of astrophysics processes and the performance of nuclear reactors and other nuclear systems depend on a precise description of the neutron interaction cross sections for materials and nuclei present in these environments. At low neutron energies, these cross sections exhibit resonance structure represented by sharp enhancements when the neutron energy is sufficiently close to excited levels in a compound nucleus. Such resonances can be characterized by their quantum numbers relative to angular momenta, which are often deduced in an ad hoc and irreproducible manner from the shape of the cross sections. The correct assignment of the quantum numbers of neutron resonances is therefore of paramount importance. To address this we have developed a machine-learning method to automate the identification and correction of these spin assignments. The algorithm is trained from simulated data, generated from statistical properties of resonance data for a given nucleus, to mimic the errors found in real data. In this project we describe five independent approaches to further develop and expand the applicability of the machine-learning spin classifier: i) Feature impact; ii) Integration with the Atlas; iii) Training optimization; iv) Spacings systematics; and v) Validation with polarized data. The premises, methods, results, and future perspectives are discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

Exploiting the Higgs Boson for Discovery

This document summarizes the research program of Prof. Meyer within the ATLAS Collaboration during the period of August 1, 2021 to March 31, 2023. In particular, the recently discovered Higgs boson was used as a probe to learn more about the fundamental particles that make up the universe and the forces that govern them. The group performing this work was composed of one postdoc, one graduate student, and one high-school student. Products include one publication, one public note that is being prepared for journal submission, and three public presentations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Redefining Net-Zero Water for Resilient Aquifers

Groundwater has long been a critical source of potable water, supplying one-third of all global water withdrawals and providing strategic reserves in times of drought (Konikow, 2012; Famiglietti, 2014). The risk in relying on groundwater is that it is often pumped at rates far greater than it can be naturally replenished. With increasing population and a changing climate, the depletion of potable water supplies has become an ever-growing concern (Srinivasan et al., 2012). Recently, the concept of “resilience” has been applied to groundwater, leaving many questions to be explored in terms of what resilience should mean for aquifers (Foster and MacDonald, 2014; Grönwall and Oduro-Kwarteng, 2017). The term is commonly used to indicate resilience to impacts of climate change specifically, but here we consider resilience in the context of more general water insecurity. Relatedly, the concept of “sustainable yield” has emerged in an attempt to determine a metric that can ensure the long-term resilience of groundwater systems, but the definition is fraught with inherent uncertainties and its quantification poses challenges (Rudestam and Langridge, 2014; Grönwall and Oduro-Kwarteng, 2017). At the heart of these concepts is a focus on sustainable management of aquifers. A sustainable approach to managing groundwater resources usually involves balancing long-term abstraction with the long-term recharge taking into account the needs for environmental flows and implementing drought-preparedness measures (Robins et al. 2006; Foster and MacDonald, 2014). At a high level, a sustainable balance of groundwater abstraction versus aquifer recharge may be considered “Net Zero” (NZ) or “Net Positive” (NP) in cases where recharge is equal to or in excess of abstraction, respectively. However, NZ/NP water management programs that address these concerns have varied definitions of compliance, which include considerations for the application at hand (ILFI, 2020; USGBC, 2020). Locations with high risk of low or poor water supply may be particularly interested in pursuing NZ/NP water. The AQUEDUCT Water Risk Atlas (World Resources Institute, 2019) indicates long-term availability, providing risk levels for quantity and quality of water at specific locations across the globe, for existing and predicted future conditions. This paper follows the U.S. Department of Energy (DOE) Federal Energy Management Program (FEMP) NZ water definition adopted by the U.S. Army for use at their installations, including Army Reserve Centers (ARCs). This definition also relates to the U.S. Army’s current focus on water resilience, which includes short-term and long-term availability of water resources.

net zero water, HUC12, Saipan, American Samoa, Mau↗

DOE OSTI2022

Development of a prediction model for radiotherapy response among patients with head and neck squamous cell carcinoma based on the tumor immune microenvironment and hypoxia signature

Abstract Introduction The immune system and hypoxia are major factors influencing radiosensitivity in patients with different cancer types. This study aimed at developing a model to predict radiotherapy response in patients with head and neck squamous cell carcinoma (HNSCC) based on the tumor immune microenvironment and hypoxia signature. Materials and Methods We first evaluated the hypoxia status and tumor immune microenvironment in the Cancer Genome Atlas (TCGA) cohort by using transcriptomic data. Differentially expressed genes (DEGs) were identified between the “high immunity and low hypoxia” and “low immunity and high hypoxia” groups and those DEGs significantly associated with disease‐specific survival in the univariate Cox regression analysis were selected as the prognostic DEGs. We selected the immune hypoxia–related genes (IHRGs) by intersecting prognostic DEGs with immune and hypoxia gene sets. We used the IHRGs to train a multivariate Cox regression model in the TCGA cohort, based on which we calculated the IHRG prognostic index (IHRGPI) for each patient and validated its efficacy in predicting radiotherapy response in the Gene Expression Omnibus cohorts. Furthermore, we explored potential mechanisms and effective combinational treatment strategies for different IHRGPI groups. Results Five IHRGs were used to construct the IHRGPI, which was used to dichotomize the cohorts. The patients with lower IHRGPI showed a better radiotherapy response across different cohorts and endpoints, including overall survival, progression‐free survival, and recurrence‐free survival ( p < 0.05). Patients with higher IHRGPI showed greater hypoxia and lesser immune cell infiltration. A lower IHRGPI indicated a better immunotherapy response, while a higher IHRGPI indicated a better chemotherapy response. Conclusions IHRGPI is promising for predicting radiotherapy response and guiding combinational treatment strategies in patients with HNSCC.

Zhu, Guang‐Li↗

DOE OSTI2023

Implementation and verification of a user-defined element (UEL) for coupled thermal-hydraulic-mechanical-chemical (THMC) processes in saturated geological media

Efficient and accurate modeling of the coupled thermal-hydraulic-mechanical-chemical (THMC) processes in various rock formations is indispensable for designing energy geo-structures such as underground repositories for high-level nuclear wastes. Here, this work focuses on developing and verifying an implicit finite element solver for generic coupled THMC problems in geological settings. Starting from the mass, momentum, and energy balance laws, a specialized set of governing equations and a thermoporoelastic constitutive model is derived. This system is then solved by an implicit finite element (FE) scheme. Specifically, the residuals and the Jacobians are scripted in a user-defined element (UEL) subroutine which is then combined with the general-purpose FE software Abaqus Standard to solve initial-boundary value problems. Considering the complexity of the system, the UEL development follows a stepwise manner by first solving the coupled hydraulic-mechanical (HM) and thermal-hydraulic-mechanical (THM) equations before moving on to the full THMC problem. Each implementation step consists of at least one verification test by comparing computed results with closed-form analytical solutions to ensure that the various coupling effects are correctly realized. To demonstrate the robustness of the algorithm and to validate the UEL, a three-dimensional case study is performed with reference to the in-situ heating test of ATLAS at Belgium in 1980s. A hypothetical radionuclide leakage event is then simulated by activating the chemical-concentration degree of freedom and prescribing a constant high concentration at the heater's surface. The model predicts a limited contaminated regime after six years considering both diffusion and advection effects on species transport.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2026

RCSB protein data Bank: Next‐generation advanced search for exploration of experimental structures and computed structure models

Abstract The Protein Data Bank (PDB), established in 1971, is the primary global, open‐access archive for experimentally determined 3D macromolecular structures (proteins, RNA, DNA). The research‐focused RCSB.org web‐portal provides access to these data alongside more than one million machine‐learning‐predicted structure models, greatly expanding the available structural landscape. Rapid growth of both experimental and computational structures has increased the need for powerful yet accessible search tools that serve a broad and diverse scientific community. Herein, we describe a redesigned RCSB Protein Data Bank RCSB.org Advanced Search capability that supports intuitive discovery of 3D structures through a unified interface. This interface integrates annotation‐, sequence‐, and 3D structure‐based searches, embeds an interactive 3D viewer, and incorporates curated biological knowledge, such as catalytic site definitions from Mechanism and Catalytic Site Atlas and ligand‐guided structural motifs, for constructing geometry‐driven queries. A new Chemical Search tool allows definition of chemical queries via an integrated drawing tool or standard identifiers, seamlessly combining them with annotation filters. By allowing query definition directly within spatial and chemical contexts, these search interfaces reduce the need for detailed knowledge of residue numbering, chain identifiers, or external cheminformatics software. This capability enables efficient exploration of structures, chemical diversity, and structure–function relationships across all life domains. The redesigned interfaces can be accessed directly at rcsb.org/search/advanced for Advanced Search and rcsb.org/search/chemical for Chemical Search.

Rose, Yana [Research Collaboratory for Structural ↗

DOE OSTI2021

Genomic variation within the maize stiff-stalk heterotic germplasm pool

The stiff-stalk heterotic group in Maize (Zea mays L.) is an important source of inbreds used in U.S. commercial hybrid production. Founder inbreds B14, B37, B73, and, to a lesser extent, B84, are found in the pedigrees of a majority of commercial seed parent inbred lines. We created high-quality genome assemblies of B84 and four expired Plant Variety Protection (ex-PVP) lines LH145 representing B14, NKH8431 of mixed descent, PHB47 representing B37, and PHJ40, which is a Pioneer Hi-Bred International (PHI) early stiff-stalk type. Sequence was generated using long-read sequencing achieving highly contiguous assemblies of 2.13-2.18 Gbp with N50 scaffold lengths >200 Mbp. Inbred-specific gene annotations were generated using a core five-tissue gene expression atlas, whereas transposable element (TE) annotation was conducted using de novo and homology-directed methodologies. Compared with the reference inbred B73, synteny analyses revealed extensive collinearity across the five stiff-stalk genomes, although unique components of the maize pangenome were detected. Comparison of this set of stiff-stalk inbreds with the original Iowa Stiff Stalk Synthetic breeding population revealed that these inbreds represent only a proportion of variation in the original stiff-stalk pool and there are highly conserved haplotypes in released public and ex-Plant Variety Protection inbreds. Despite the reduction in variation from the original stiff-stalk population, substantial genetic and genomic variation was identified supporting the potential for continued breeding success in this pool. The assemblies described here represent stiff-stalk inbreds that have historical and commercial relevance and provide further insight into the emerging maize pangenome.

59 BASIC BIOLOGICAL SCIENCES↗