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DOE OSTI2023

A superconducting nanowire binary shift register

We present a design for a superconducting nanowire binary shift register, which stores digital states in the form of circulating supercurrents in high-kinetic-inductance loops. Adjacent superconducting loops are connected with nanocryotrons, three-terminal electrothermal switches, and fed with an alternating two-phase clock to synchronously transfer the digital state between the loops. A two-loop serial-input shift register was fabricated with thin-film NbN and a bit error rate of less than 10 –4 was achieved, when operated at a maximum clock frequency of 83 MHz and in an out-of-plane magnetic field of up to 6 mT. A shift register based on this technology offers an integrated solution for low-power readout of superconducting nanowire single photon detector arrays and is capable of interfacing directly with room-temperature electronics and operating unshielded in high magnetic field environments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

The Atacama Cosmology Telescope: delensed power spectra and parameters

We present ΛCDM cosmological parameter constraints obtained from delensed microwave background power spectra. Lensing maps from a subset of DR4 data from the Atacama Cosmology Telescope (ACT) are used to undo the lensing effect in ACT spectra observed at 150 and 98 GHz. At 150 GHz, we remove the lensing distortion with an effective efficiency of 30% (TT), 30% (EE), 26% (TE) and 20% (BB); this results in detections of the delensing effect at 8.7σ (TT), 5.1σ (EE), 2.6σ (TE), and 2.4σ (BB) significance. The combination of 150 and 98 GHz TT, EE, and TE delensed spectra is well fit by a standard ΛCDM model. We also measure the shift in best-fit parameters when fitting delensed versus lensed spectra; while this shift does not inform our ability to measure cosmological parameters, it does provide a three-way consistency check among the lensing inferred from the best-fit parameters, the lensing in the CMB power spectrum, and the reconstructed lensing map. This shift is predicted to be zero when fitting with the correct model since both lensed and delensed spectra originate from the same region of sky. Furthermore, fitting with a ΛCDM model and marginalizing over foregrounds, we find that the shift in cosmological parameters is consistent with zero. Our results show that gravitational lensing of the microwave background is internally consistent within the framework of the standard cosmological model.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

It's only natural: Plant respiration in unmanaged systems

Abstract Respiration plays a key role in the terrestrial carbon cycle and is a fundamental metabolic process in all plant tissues and cells. We review respiration from the perspective of plants that grow in their natural habitat and how it is influenced by wide-ranging elements at different scales, from metabolic substrate availability to shifts in climate. Decades of field-based measurements have honed our understanding of the biological and environmental controls on leaf, root, stem, and whole-organism respiration. Despite this effort, there remain gaps in our knowledge within and across species and ecosystems, especially in more challenging-to-measure tissues like roots. Recent databases of respiration rates and associated leaf traits from species representing diverse biomes, plant functional types, and regional climates have allowed for a wider-lens view at modeling this important CO2 flux. We also re-analyze published data sets to show that maximum leaf respiration rates (R max) in species from around the globe are related both to leaf economic traits and environmental variables (precipitation and air temperature), but that root respiration does not follow the same latitudinal trends previously published for leaf data. We encourage the ecophysiological community to continue to expand their study of plant respiration in tissues that are difficult to measure and at the whole plant and ecosystem levels to address outstanding questions in the field.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

What Shapes Transportation Charging Infrastructure Availability? Evidence from Tennessee

This study examines how community, travel, and freight characteristics relate to public charging infrastructure availability across Tennessee ZIP codes. We link Alternative Fuels Data Center station locations with traffic, socioeconomic, demographic, commuting, and freight employment data to build a ZIP code-level dataset. Ordinary least squares regression captures variation in chargers per 10,000 residents (R2=0.311). Quantile regressions at the 25th, 50th, and 75th percentiles, with pseudo R2 values up to 0.099, show that the determinants of infrastructure availability differ across low-, medium-, and high-availability areas. Percent female, percent car commuters, average household size, and median age are negatively associated with charging availability across much of the distribution. Truck traffic is positively associated only in lower-availability ZIP codes, while vehicle miles traveled shifts from a negative association at the lower end of the distribution to a positive association at the upper end. The results provide insight into how public charging deployment aligns with community characteristics, mobility demand, and freight activity across Tennessee. Future work can distinguish charger types and power levels, incorporate land-use and temporal rollout patterns, and examine how charging infrastructure needs differ across urban and rural contexts.

Calderón, Oriana [University of Tennessee, Knoxvil↗

DOE OSTI2022

The miniJPAS survey quasar selection – I. Mock catalogues for classification

In this series of papers, we employ several machine learning (ML) methods to classify the point-like sources from the miniJPAS catalogue, and identify quasar candidates. Since no representative sample of spectroscopically confirmed sources exists at present to train these ML algorithms, we rely on mock catalogues. In this first paper, we develop a pipeline to compute synthetic photometry of quasars, galaxies, and stars using spectra of objects targeted as quasars in the Sloan Digital Sky Survey . To match the same depths and signal-to-noise ratio distributions in all bands expected for miniJPAS point sources in the range 17.5 ≤ r < 24, we augment our sample of available spectra by shifting the original r-band magnitude distributions towards the faint end, ensure that the relative incidence rates of the different objects are distributed according to their respective luminosity functions, and perform a thorough modelling of the noise distribution in each filter, by sampling the flux variance either from Gaussian realizations with given widths, or from combinations of Gaussian functions. Finally, we also add in the mocks the patterns of non-detections which are present in all real observations. Although the mock catalogues presented in this work are a first step towards simulated data sets that match the properties of the miniJPAS observations, these mocks can be adapted to serve the purposes of other photometric surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Genomic fingerprints of the world’s soil ecosystems

Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes—more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Packages of Distributed Energy Technologies Demonstrating Demand Flexibility at Community Scale

The combination of increased electric load growth across all sectors, deferred electrical infrastructure investment, and other factors resulting in variable electric power supply, has created technical challenges to maintaining a resilient and reliable grid. Many federal, regional, and local efforts are in play to modernize the electric grid, including advancing building technologies and distributed energy resources (DERs) that are utilizing smarter controls to become responsive to both occupant and grid needs. This report reviews ten pilot projects demonstrating how groups of buildings combined with behind-the-meter (BTM) DERs such as electric vehicle (EV) charging, battery storage, flexible HVAC and domestic hot water systems, and photovoltaic systems can reliably and cost effectively provide grid services. Each of the ten pilot projects aim to deliver both energy efficiency and demand flexibility (DF) while supporting load growth. The ten demonstration teams are piloting flexible DER packages across diverse communities of residential and commercial buildings to address a variety of regional grid needs. The outcomes of these pilot projects will be used to inform future scaling through utility program development. This paper characterizes the ten teams, showcasing the decision-making process used by each group to develop their packages (Section 2), the grid services they plan to deliver (Section 3), the types of DER packages selected for deployment within building sectors (Section 4) and trends between building sector, DER types, and grid services In order to achieve community scale benefits, the pilot projects must utilize aggregated control mechanisms for coordinating buildings and DERs together. Several types of coordinated control architectures have evolved amongst the teams, influenced by use type, existing market conditions, and integration type. Three coordinated controls architectures have been characterized, highlighting their use cases, benefits, challenges, and tradeoffs in their design. These insights can aid utilities, control vendors, and developers in scaling community-level energy systems (Paul, 2024). Ultimately, the technology packages selected by the ten teams will be coordinated to provide power system services, also known as grid services. Insights from these demonstrations will be useful for grid operators, regulators, aggregators and other stakeholders as they look to deploy demand flexible resources as grid services in the future. The grid services that each team is targeting for demonstration are described in Section 3 and Section 4. Methods for evaluating the grid services have been described in the paper Metrics for Evaluating Grid Service Provision from Communities of Grid-interactive and Efficient Buildings and other DER (MacDonald, 2023). To identify technology packages for demonstration, Section 2 shows that project teams used a range of analysis approaches, including building energy modeling, AMI data analysis, cost-benefit frameworks, and utility pilot data. Some teams emphasized technical modeling to quantify grid impacts and demand reduction potential, while others prioritized economic evaluations, stakeholder input, or exploratory pilots to inform deployment decisions. This diversity reflects the need to tailor selection methods to project goals, available data, and organizational context. Section 5 discusses trends between the DER technologies deployed and the grid service provisions from each team. Residential buildings (multifamily and single family) lean towards technologies that enhance energy efficiency (e.g. weatherization upgrades, smart thermostats) and onsite power generation integration (e.g. solar PV). Commercial building demonstrations prioritize technologies that ensure operational reliability (e.g. battery storage) and centralized energy management systems and optimization solutions. Teams that are deploying controllable storage-based technologies are more likely to provide grid services that require a near real-time response. Teams incorporating load shifting technologies like smart thermostats with HEMs are likely to include energy markets participation and customer bill management offerings. Campus demonstrations are adopting diverse sets of DERs to emphasize renewable generation, paired with centralized control. This section also describes technologies that were considered during project planning but ultimately excluded from final deployment. These demonstrations reveal that effective DER package design should be tailored to building type, customer segment, and construction vintage. Multifamily buildings benefit from centralized HVAC upgrades and supervisory controls, while single-family homes are well-suited for individualized technologies like solar, storage, and smart home energy monitors. Commercial and campus settings prioritize EMIS integration and load optimization. New construction enables cost-effective integration of DER-ready infrastructure, whereas retrofits require deployments aligned with owner and tenant value streams. For utility program planners, early coordination with developers and building owners, paired with segmented and modular program offerings, can improve adoption, scalability, and grid impact.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2022

Nonlocal subpicosecond delay metrology using spectral quantum interference

Precise knowledge of position and timing information is critical to support elementary protocols such as entanglement swapping on quantum networks. While approaches have been devised to use quantum light for such metrology, they largely rely on time-of-flight (ToF) measurements with single-photon detectors and, therefore, are limited to picosecond-scale resolution owing to detector jitter. In this work, we demonstrate an approach to distributed sensing that leverages phase modulation to map changes in the spectral phase to coincidence probability, thereby overcoming the limits imposed by single-photon detection. By extracting information about the joint biphoton phase, we measure a generalized delay—the difference in signal–idler arrival, relative to local radio frequency (RF) phase modulation. For nonlocal ranging measurements, we achieve (2$σ$) precision of ±0.04 ps and for measurements of the relative RF phase, (2$σ$) precision of ±0.7°. We complement this fine timing information with ToF data from single-photon time-tagging to demonstrate absolute measurement of time delay. By relying on off-the-shelf telecommunications equipment and standard quantum resources, this approach has the potential to reduce overhead in practical quantum networks.

42 ENGINEERING↗

DOE OSTI2024

A mechanistic interpretation of Nelson curves for PVP failures under high temperature hydrogen attack

As an empirically established design criterion, Nelson curves that relate the service temperature and the allowable hydrogen partial pressure have been developed and utilized for more than sixty years in pressure vessels and piping (PVP) safety design. Despite a relatively clear thermodynamic understanding of the high-temperature-hydrogen-attack (HTHA) problem, the detailed fracture process on the microstructural length scales, however, remains elusive, and a quantitative assessment of the PVP lifetime under HTHA from the available creep fracture dataset is still not possible. This work develops a microstructure-informed and micromechanics-based model by incorporating a synergy between hydrogen transport and intergranular-cavity-based fracture process. Based on the available creep lifetime data of C-0.5Mo steels, we are able to calibrate material constitutive parameters, and then conduct nonlinear finite element simulations that reveal a real-time stress-induced hydrogen diffusional transport along grain boundaries, coupled with a microstructure-explicit failure process, from which Nelson curves can be computed. Such failure analyses allow us to delineate two distinct regimes on the Nelson curves, i.e., dislocation-creep-controlled or grain boundary diffusion-assisted cavity growth. More importantly, we found that a small change of the pipe thickness and applied stresses can significantly shift these lifetime curves. However, these two parameters are usually not provided in Nelson curves, thus limiting their usage in material selection and safety design. In conclusion, this discrepancy can clearly be mitigated by extensive parametric studies from our micromechanical modeling/simulation framework.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Temperature-dependent calibration procedures for the silicon photomultiplier readout of the cosmic ray veto detector for the Mu2e experiment

The cosmic ray veto detector for the Mu2e experiment consists of scintillation bars embedded with wavelength-shifting fibers and read out by silicon photomultipliers (SiPMs). Here, in this manuscript, the calibration procedures of the SiPMs are described including corrections for the temperature dependence of their light yield. These corrections are needed as the SiPMs are not kept at a constant temperature due to the complexity and cost of implementing a cooling system on such a large detector. Rather, it was decided to monitor the temperature to allow the appropriate corrections to be made. The SiPM temperature dependence has been measured in a dedicated experiment and the calibration procedures were validated with data from production detectors awaiting installation at Fermilab.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

Hot droughts in the Amazon provide a window to a future hypertropical climate

Tropical forests represent the warmest and wettest of Earth’s biomes, but with continued anthropogenic warming, they will be pushed to climate states with no current analogue. Droughts in the tropics are already becoming more intense as they occur at successively higher temperatures. Here, in this study, we synthesize multiple datasets to assess the effects of hot droughts on a central Amazon forest. First, a more than 30-year record of annually resolved forest demographic data from a selective logging experiment showed higher tree mortality during intense droughts, particularly among fast-growing pioneer species with low wood density. Second, analysis of ecophysiological field measurements from the 2015 and 2023 El Niño droughts identified a soil moisture threshold beyond which transpiration rates rapidly declined. As rainless days beyond this threshold continued, drought conditions intensified, increasing the potential for tree mortality from hydraulic failure and carbon starvation. Third, analyses from the Coupled Model Intercomparison Project Phase 6 demonstrated that under high-emission scenarios, a large area of tropical forest will shift to a hotter ‘hypertropical’ climate by 2100. Last, under a hypertropical climate, temperature and moisture conditions during typical dry season months will more frequently exceed identified drought mortality thresholds, elevating the risk of forest dieback. Present-day hot droughts are harbingers of this emerging climate, offering a window for studying tropical forests under expected extreme future conditions.

drought↗

DOE OSTI2025

Slow ferromagnetic fluctuations in the kagome metal Sc 3 ⁢ Mn 3 ⁢Al 7 ⁢ Si 5 revealed by 27 Al NMR

Static and dynamical magnetic and electronic properties of the kagome metal Sc 3 ⁢Mn 3 ⁢ Al 7⁢ Si 5 have been investigated by 27 Al nuclear magnetic resonance (NMR) measurements. Two distinct 27 Al -NMR signals with two different values of quadrupolar frequencies of 𝜈 Q = 1.55(2) and 1.07(2) MHz are observed, which are assigned to Al(1) and Al(2), respectively. From the detailed NMR spectrum measurements under three different magnetic field directions and the density functional theory calculations, the principal axes of the electric field gradient for each Al site have been determined. The temperature dependence of Knight shift (𝐾) shows a similar temperature dependence of the DC magnetic susceptibility 𝜒 except for the low-temperature region below ∼50 K where 𝐾 is almost constant while 𝜒 keeps increasing, which suggests that the increase in 𝜒 at low temperatures is not intrinsic. 27 Al spin-lattice relaxation rate divided by temperature (1/𝑇 1 ⁢𝑇) is found to be constant, confirming the metallic state of Sc 3 ⁢Mn 3 ⁢ Al 7⁢ Si 5 from a microscopic point of view. Based on a Korringa ratio analysis using the 𝑇 1 and 𝐾 data, ferromagnetic fluctuations are found to dominate in Sc 3 ⁢Mn 3 ⁢ Al 7⁢ Si 5 . In conclusion, these fluctuations are suggested to be very slow with frequencies on the order of kilohertz or lower.

Ding, Qing-Ping [Ames Laboratory (AMES), Ames, IA ↗

DOE OSTI2025

Optimizing Non-Terrestrial Hybrid RF/FSO Links With Reinforcement Learning: Navigating Through Clouds

In the pursuit of ubiquitous broadband connectivity, there has been a significant shift towards the vertical expansion of communication networks into space, particularly through the exploitation of low Earth orbit (LEO) satellite constellations, which are favored for their relatively low latency. However, this approach faces many challenges that need to be addressed, including atmospheric turbulence, high path loss, and dynamic cloud formations. High-altitude pseudo-satellites (HAPS) have emerged as promising relaying layers between LEO satellites and ground stations, enhancing coverage, latency, and direct terrestrial user connectivity. While radio frequency (RF) bands suffer from congestion and limited bandwidth, free space optical (FSO) communications offer higher data rates, but are susceptible to misalignment and weather-induced signal degradation. To address these challenges, a hybrid RF/FSO approach has been proposed to take advantage of both technologies by dynamic switching between RF and FSO based on propagation channel conditions. This paper introduces a reinforcement learning-based algorithm designed to optimize the trajectory of HAPS, maneuver around cloudy areas, and seamlessly switch between the RF and FSO communication modes to maximize the achievable capacity. The proposed approach aims to maximize system performance by intelligently adapting to environmental conditions and offering a promising solution for next-generation space communication networks.

actor-critic algorithm↗

DOE OSTI2020

Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network

Host-associated microbial communities are shaped by extrinsic and intrinsic factors to the holobiont organism. Environmental factors and microbe-microbe interactions act simultaneously on the microbial community structure, making the microbiome dynamics challenging to predict. The coral microbiome is essential to the health of coral reefs and sensitive to environmental changes. Here, we develop a dynamic model to determine the microbial community structure associated with the surface mucus layer (SML) of corals using temperature as an extrinsic factor and microbial network as an intrinsic factor. The model was validated by comparing the predicted relative abundances of microbial taxa to the relative abundances of microbial taxa from the sample data. The SML microbiome from Pseudodiploria strigosa was collected across reef zones in Bermuda, where inner and outer reefs are exposed to distinct thermal profiles. A shotgun metagenomics approach was used to describe the taxonomic composition and the microbial network of the coral SML microbiome. By simulating the annual temperature fluctuations at each reef zone, the model output is statistically identical to the observed data. The model was further applied to six scenarios that combined different profiles of temperature and microbial network to investigate the influence of each of these two factors on the model accuracy. The SML microbiome was best predicted by model scenarios with the temperature profile that was closest to the local thermal environment, regardless of the microbial network profile. Our model shows that the SML microbiome of P. strigosa in Bermuda is primarily structured by seasonal fluctuations in temperature at a reef scale, while the microbial network is a secondary driver. Coral microbiome dysbiosis (i.e., shifts in the microbial community structure or complete loss of microbial symbionts) caused by environmental changes is a key player in the decline of coral health worldwide. Multiple factors in the water column and the surrounding biological community influence the dynamics of the coral microbiome. However, by including only temperature as an external factor, our model proved to be successful in describing the microbial community associated with the surface mucus layer (SML) of the coral P. strigosa. The dynamic model developed and validated in this study is a potential tool to predict the coral microbiome under different temperature conditions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

On High-Fluence Irradiation Hardening of Nine RPV Surveillance Steels in the UCSB ATR-2 Experiment: Implications for Extended-Life Embrittlement Predictions

Nine archival reactor pressure vessel (RPV) surveillance steels from commercial nuclear power plants were irradiated in the University of California, Santa Barbara Advanced Test Reactor 2 (ATR-2) experiment to evaluate irradiation embrittlement under low-flux surveillance capsule versus higher flux test reactor (ATR-2) conditions. The postirradiation measurements of irradiation hardening, measured as increases in yield stress (Δσy), and corresponding conversions of Δσy to Charpy V-notch 41-J transition temperature shifts (ΔTc) are compared with various embrittlement trend curve (ETC) model predictions for the nine steels. Tensile and converted shear punch and microhardness measurements of Δσy generally show a continuing increase between intermediate and high ATR-2 fluences. The Eason-Odette-Nanstad-Yamamoto and ASTM E900 ETC models underpredict embrittlement at the ATR-2 irradiation condition: irradiation temperature (Ti) of 292°C, neutron fluence (ϕt) of 1.4 × 1020 n/cm2 (E > 1 MeV), and neutron flux (ϕ) of 3.68 × 1012 n/cm2-s. On average, the French FIS and Japanese JAEC ETCs slightly overpredict the ATR-2 data. The increase in Δσy with higher fluence is primarily due to Ni-Mn-Si precipitates, which slowly evolve in both nearly copper-free and copper-bearing steels. Finally, a new Odette-Wells-Almirall-Yamamoto embrittlement model is shown that yields good predictions for the nine steels at high fluences (ϕt > 5.5 × 1019 n/cm2).

Nanstad, Randy K.↗

DOE OSTI2021

Uncontrolled Electric Vehicle Charging Impacts on Distribution Electric Power Systems with Primarily Residential, Commercial or Industrial Loads

An increase in Electric Vehicles (EV) will result in higher demands on the distribution electric power systems (EPS) which may result in thermal line overloading and low voltage violations. To understand the impact, this work simulates two EV charging scenarios (home- and work-dominant) under potential 2030 EV adoption levels on 10 actual distribution feeders that support residential, commercial, and industrial loads. The simulations include actual driving patterns of existing (non-EV) vehicles taken from global positioning system (GPS) data. The GPS driving behaviors, which explain the spatial and temporal EV charging demands, provide information on each vehicles travel distance, dwell locations, and dwell durations. Then, the EPS simulations incorporate the EV charging demands to calculate the power flow across the feeder. Simulation results show that voltage impacts are modest (less than 0.01 p.u.), likely due to robust feeder designs and the models only represent the high-voltage (“primary”) system components. Line loading impacts are more noticeable, with a maximum increase of about 15%. Additionally, the feeder peak load times experience a slight shift for residential and mixed feeders (≈1 h), not at all for the industrial, and 8 h for the commercial feeder.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2023

On High-Fluence Irradiation Hardening of Nine RPV Surveillance Steels in the UCSB ATR-2 Experiment: Implications for Extended-Life Embrittlement Predictions

Nanstad, Randy↗

DOE OSTI2026

scPlantAnnotate: an accurate and robust transformer-based model for plant cell type annotation

Accurate cell type annotation remains a major bottleneck in plant single-cell RNA sequencing (scRNA-seq), where existing tools are often adapted from animal studies and perform sub-optimally on plant data. The lack of plant-specific computational frameworks limits the construction of plant cell atlases and downstream biological discovery. We develop and evaluate scPlantAnnotate, a Transformer-based reference annotation framework tailored for plant scRNA-seq data, and benchmark it against state-of-the-art deep learning and conventional methods across multiple plant species. Species-specific scPlantAnnotate models were trained using curated datasets from Arabidopsis thaliana, Zea mays, Oryza sativa, and Glycine max. We compared scPlantAnnotate with leading baselines under both standard random-split evaluation and a more stringent leave-one-dataset-out setting, which tests robustness to completely unseen datasets and tissue types. scPlantAnnotate consistently outperforms existing approaches across all four species under random-split evaluation. In the leave-one-dataset-out setting for A. thaliana, where performance drops markedly for all methods due to strong batch effects and dataset heterogeneity, scPlantAnnotate nonetheless achieves the highest Accuracy, Macro-F1, Balanced Accuracy, and Macro-AUROC on average and ranks first on most held-out datasets. These results demonstrate improved robustness to dataset shifts, a critical yet underexplored challenge in plant scRNA-seq analysis. A freely accessible web server enables users to annotate their own datasets using pretrained models. scPlantAnnotate provides a plant-specific, Transformer-based framework for single-cell annotation that delivers state-of-the-art performance and enhanced robustness to unseen datasets. By addressing limitations of existing tools and enabling scalable reference-based annotation, scPlantAnnotate supports the development of comprehensive plant cell atlases and facilitates broader use of single-cell genomics in plant biology.

Bioinformatics↗