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Data from: Lowland Tropical Forests Remain a Methane Sink Under Warming and Long-Term Hurricane Disturbance Recovery

The repository folder contains spreadsheets and script for soil greenhouse gas (GHG) fluxes, soil moisture, soil temperature, air temperature, and precipitation measurements collected from the Tropical Responses to Altered Climate Experiment (TRACE) at the Sabana Research Field Station, El Yunque National Forest (USDA Forest Service; 18°19′28.74″ N, 65°43′50.09″ W) — an open-air field warming experiment located in a lowland tropical forest in Puerto Rico within the Luquillo Experimental Forest (LEF) — six to seven years after Hurricanes Irma and Maria (2017). All spreadsheets for soil and air microclimate data, as well as soil greenhouse gas data, are included as csv files. Air temperature data are also included as Excel spreadsheets (.xlsx). The script is built in R Studio, which is the only software required to run data analysis. This dataset is associated with the manuscript “Larocca Conte G ; Zuvela L ; Cruz-Pérez R ; Barreto-Vélez T ; Becerra-Santillan N ; Campbell S ; Chu H ; Dam T ; Grullón-Penkova I ; Kleit M ; Ortiz-Iglesias D ; Rubio-Lebrón L ; Cavaleri M ; Reed S ; Sihi D ; Wood T ; O'Connell C., 2026. Lowland Tropical Forests Remain a Methane Sink Under Warming and Long-Term Hurricane Disturbance Recovery. Agricultural and Forest Meteorology. In review". The dataset was used to test the effect of warming on soil CH4 dynamics following long-term legacy effects of hurricane disturbance. The dataset includes: - An overall README file in word and pdf format describing methodology and spreadsheets’ structure. - Continuous measurements of soil temperature and moisture from January 2023 to July 2024 measured with Campbell CS655 probes (“TRACE_soil_temperature_and_moisture_2023_cleaned(in).csv” and “TRACE_soil_temperature_and_moisture_2024_cleaned. csv”). - Air temperature data measured with a HOBO MX23O1A data logger (“Hobo air temperature 2023 Sep 2024” and “Hobo air temperature 2023 Sep 2024” – “CSV FILES folders”). - Precipitation data from a nearby weather tower downloaded from González et al. (2025; “sabana_2020-2025.csv”). - Soil CH4 and CO2 effluxes measured intermittently in two summer campaigns (June – August 2023 and June – July 2024) with a LI-COR 8200-01S Portable Smart Chamber coupled with a LI-COR LI-7810 CH4/ CO2/H2O Trace Gas Analyzer (“23_24COMBO2.0.csv”). - R markdown script for data analysis (“Trace new_PLOTS.Rmd”).

54 ENVIRONMENTAL SCIENCES

Automated ICRF heating surrogate modeling via machine learning

This work introduces automated machine learning workflows that address critical bottlenecks in surrogate model development for Ion Cyclotron Range of Frequencies (ICRF) heating applications. The automated framework includes data analysis tools that transform raw datasets into actionable insights in seconds, replacing weeks of manual exploratory effort and ensuring consistent, reproducible dataset characterization. By integrating advanced hyperparameter optimization (HPO) methods including Bayesian optimization via BoTorch and Tree-structured Parzen Estimators (TPE), the framework significantly reduces model development time from weeks to hours, decreasing computational cost and required expertise, while enabling high-accuracy surrogate models. Compared to traditional hyperparameter scanning (HPS) techniques such as methodical, randomized, and grid searches, HPO methods achieve superior convergence and predictive performance, even when compared to already well-tuned reference models. On NSTX High Harmonic Fast Wave (HHFW) heating datasets, both Random Forest Regressor (RFR) and neural network surrogates demonstrate improved accuracy, achieving R 2 values beyond 0.97 and 0.98, respectively. The results show that while HPO gains are modest for robust architectures like RFR, they become essential for more sensitive models such as neural networks, highlighting the trade-offs across optimization strategies. Through automated workflows that eliminate manual hyperparameter tuning and require minimal ML expertise, this work enables widespread adoption of high-fidelity surrogate models across the fusion community for real-time plasma control, uncertainty quantification, rapid experimental scenario development, and integrated system optimization.

Sanchez-Villar, Alvaro [Princeton Plasma Physics L

Robust Automatic EXAFS First-Shell Fits

Extended X-ray absorption fine structure (EXAFS) is a widely used technique for atomic structure determination. Fourier transformation connects EXAFS in k space and R space. However, determining the appropriate k-range for the transformation can be challenging, but critical for the first-shell fit. In this study, we present an automatic method to determine the k-range using the Larch package and a Python program. The first step is to estimate spectral noise across a series of k-ranges with a fixed minimum value and identify the optimal maximum value in the k-range (k max ). The k max is determined by an empirical noise threshold that marks the point where the noise level in the Fourier transformed spectrum changes dramatically. Using the obtained k max value, the first shell is modeled to determine the minimum k value (k min ) by optimizing the background function through alignment of the spectrum with theory. The optimal k min corresponds to the point of the minimum R-factor, which quantifies the difference between the experimental and fitted spectrum. Our method was tested on various typical datasets and yielded suitable k-ranges for Fourier transformation and accurate first-shell fits. This approach helps avoid unreliable, irreproducible data analysis, especially for noisy data from diluted samples, and enables robust automatic first-shell EXAFS fitting.

EXAFS analysis

AI Model Benchmarking for Nonproliferation Applications: Steel Thread Benchmarking Task Force Technical Report (Rev. 2)

Steel Thread is a NA-22 venture that seeks to build trustworthy, reliable AI models that can be used in a wide variety of nonproliferation tasks. A key aspect of building these models is developing appropriate benchmarks and evaluation methods, which will enable the venture to identify and adapt models to provide the most value in the nonproliferation domain. Benchmarks must be relevant to key tasks in this domain, such as question answering, information retrieval, document summarization and classification, consensus analysis, and image and data analysis. This report 1) provides an overview of benchmark design, evaluation, and challenges; 2) reviews a variety of open benchmarks, with a focus on language models and tasks; and 3) identifies benchmarks that are most relevant to Steel Thread. This report is intended to serve as a basis for further efforts to classify and evaluate benchmarks and their correlation with success on nonproliferation-specific tasks. The Steel Thread venture has defined benchmarks to be a particular combination of a dataset (or datasets) and a metric (or metrics) conceptualized as representing one or more specific tasks or sets of abilities for a specific modality. It is adopted by a research community as a shared framework for comparing methods.1 It includes 1) Data: Labeled (a designated subset not used for training, which could be all the data), 2) Metric: A way to quantify performance, 3) Task/Ability: What the benchmark is testing, 4) Protocol: A structured and repeatable evaluation process, 5) Baseline/Reference Model: For comparison; could be statistical, rule-based, SME-derived, or another model, and 6) Maintenance Plan: to update with new information over time; important for long-term utility. For further clarity, the definition includes what a benchmark, in this context, is not. It is not a corpus of training data, specific to a model (it is intended to apply to a range of models), a universal evaluation of performance, a guarantee that the ‘top’ model on the leaderboard will be the best fit for every specific use case, an all-encompassing proof of a model’s universal quality, nor is it a one-size-fits-all measure of success. It does not cover every real-world constraint (like operational, ethical, or cost considerations), a systems integration test, or a unit test. This definition was inspired by and resulted from discussions within the Steel Thread Benchmarking Task Force. This group was formed to define what we would mean as a benchmark within Steel Thread but persisted as the need to develop a thorough understanding of the large and expanding existing benchmarking space. This technical report is a result of the group’s divide and conquer approach to exploring this space. The release of benchmarks might not be progressing as quickly as model development, but it is moving very fast, as many benchmarks quickly become saturated, when state-of-the-art models score so close to the benchmark’s ceiling that their results are virtually indistinguishable. At that point, the test no longer differentiates between new systems, so researchers usually stop reporting scores as the benchmark no longer informs about improvements from the next generation of models. In the OpenAI announcement of GPT-5, they reported results on six flagship public benchmarks (AIME 2025, SWE-bench Verified, Aider Polyglot, MMMU, HealthBench Hard, GPQA) but the full system-card covers roughly thirty-five separate evaluations, comprising hundreds of test task items in total. There have been some efforts to summarize benchmarks in specific fields, like for text-to-image generation, but these surveys have had a narrow methodology scope. Therefore, a comprehensive survey of all benchmarks or even all benchmarks that could be relevant to Steel Thread is outside of the scope of this report. We chose some specific benchmarks to investigate in detail.

97 MATHEMATICS AND COMPUTING

Influence of Alkyne Precursor Structure on Carbon Nanotube Chiral Distribution: Data-Dense Analysis Across Multiple Catalyst Types

Carbon nanotubes (CNTs) are a desirable material in the field of optoelectronics and semiconductors due to electronic properties (e.g., bandgap) that are dependent upon their chirality, defined by their diameter and lattice angle. Unfortunately, industrial-scale syntheses have yet to realize growth of a single desired chirality and instead rely on postsynthetic separation techniques to refine a chiral mixture, which increases process complexity and cost. Here, we studied the influence of precursor structure on chiral distribution, using a series of terminal alkyne precursors (acetylene, methylacetylene, vinylacetylene, 1-butyne, two enantiomers of 3-butyn-2-ol and a racemic mixture thereof) to grow CNTs across five transition-metal catalysts (Fe, FeMo, and three proportions of CoMo). Multiwavelength Raman spectroscopy on 5,145 spots (5 catalysts, 7 precursors, 3 lasers, and 49 distinct substrate locations on each) determined that acetylene grew the smallest diameter CNTs, while vinylacetylene produced fewer subnanometer CNTs. Though precursor structure did not dictate a uniform chiral shift, it was shown to broaden or narrow chiral distribution, while catalyst structure played a dominant role. In conclusion, this is consistent with metal-precursor binding occurring through unsaturated bonds in the hydrocarbons via the alkyne polymerization mechanism.

Carbon nanotubes

Performance Analysis of Data Processing in Distributed File Systems with Near Data Processing

In the era of big data, the escalating volume and velocity of data generation pose significant challenges in data processing. Traditional systems like Spark and Hadoop manage the increasing amount and velocity of data by improving data placement and processing speeds. However, they face inherent limitations due to the essential data movement required for processing. In this paper, we explore the Skyhook framework, a novel extension of the Ceph distributed system, which significantly reduces the need for data movement. We present an extensive case study using the Skyhook framework, applying it with the TPC-H and K-means clustering algorithms. More specifically, we leverage the TPC-H benchmark to distinguish between CPU-intensive and I/O-intensive tasks. We explore the integration of K-means clustering into SQL, coupled with a near-data processing system to offload the computational burden of the K-means clustering algorithm to storage nodes. We conduct a comprehensive performance evaluation of distributed data processing applications across three processing approaches: traditional layout (baseline), optimized layout, and near-data processing. Additionally, we introduce the use of the FIO tool to simulate real-world system workloads, enabling the measurement of performance metrics such as average latency and CPU utilization. Our research is a significant advance in understanding how to optimize data processing systems to meet the demands of the modern data landscape.

Hou, Shiyue

Analyzing Multifaceted Scientific Data with Topological Analytics (Final Technical Report)

This final technical report describes the activities undertaken through Department of Energy, Office of Science, Advanced Scientific Computing Research Early Career award DE-SC-0019039, “Analyzing Multifaceted Scientific Data with Topological Analytics." This report summarizes contributions made toward the research of visualization, machine learning, and topological data analysis of complex simulation data.

97 MATHEMATICS AND COMPUTING

M3AS-25IN1002073: Analysis of data from irradiation testing of printed strain gauges in prototypic nuclear environments

Advancement in additively manufactured strain gauges help address critical technology gaps to accurately monitor real-time materials behavior in reactor experiments. This is critical as it provides data to inform predictive models and simulations that enhance the development of reactors and fuel cycle systems. In this report, additively manufactured strain gauges are exposed to a neutron irradiation environment at the Ohio State University Research Reactor. This report goes over a 2-week campaign for neutron irradiating printed resistive strain gauges and capacitive strain gauges. These results complement the prior separate effects (i.e., mechanical strain, temperature, etc.) testing that were performed on these additive manufactured sensors and presented in prior milestone reports. These results also help progress our understanding of their usage in harsh environment applications. The outcome of developing advanced sensing and instrumentation capabilities plays an important role in increasing the safety, reliability, and energy efficiency of both next-generation and existing nuclear reactors.

36 - MATERIALS SCIENCE

Reliable Integration of AI Data Centers at Scale – Analysis, Modeling and Synthetic Data Generation

This report analyzes the power consumption of large dynamic digital loads using the open-source MIT supercloud and SURF datasets. With an emphasis on the MIT data, we calculate important power consumption characteristics to help system operators improve generation planning and resource allocation. We also introduce a rudimentary model for generating synthetic load profiles.

97 MATHEMATICS AND COMPUTING

Asymptotic inconsistency of the cumulative algorithm for laser-induced damage probability analysis

The “cumulative algorithm” is a data analysis method that has been proposed to provide an objective, nonparametric determination of laser-induced damage probability as a function of fluence from experimental data that contain both damaged sites and undamaged sites (i.e., 1-on-1 or S-on-1 testing protocols). In this work, the limitations of this approach are explored by considering the asymptotic limit of a large number of test sites. It is shown that the cumulative algorithm does not converge to the true probability distribution and significantly underestimates the damage probability near the damage onset. Here, based on the results of this work, the cumulative algorithm is not recommended for accurate estimation of damage probability.

Computational methods

Physics-guided dual implicit neural representations for source separation

Significant challenges exist in efficient data analysis of most advanced experimental and observational techniques because the collected signals often include unwanted contributions, such as background and signal distortions, that can obscure the physically relevant information of interest. To address this, we have developed a self-supervised machine-learning approach for source separation using a dual implicit neural representation framework that jointly trains two neural networks: one for approximating distortions of the physical signal of interest and the other for learning the effective background contribution. Our method learns directly from the raw data by minimizing a reconstruction-based loss function without requiring labeled data or pre-defined dictionaries. We demonstrate the effectiveness of our framework by considering a challenging case study involving large-scale simulated, as well as experimental, momentum-energy-dependent inelastic neutron scattering data in a four-dimensional parameter space, characterized by heterogeneous background contributions and unknown distortions to the target signal. The method is found to successfully separate physically meaningful signals from a complex or structured background even when the signal characteristics vary across all four dimensions of the parameter space. An analytical approach that informs the choice of the regularization parameter is presented. Our method offers a versatile framework for addressing source separation problems across diverse domains, ranging from superimposed signals in astronomical measurements to structural features in biomedical image reconstructions.

47 OTHER INSTRUMENTATION

Data for Spatial Analysis of Cell Patterning to Aid Genetic and Phenotypic Understanding of Grass Stomatal Density: A Case Study in Maize

Biological processes involve complex hierarchies where composite traits result from multiple component traits. However, holistically understanding of how sets of component traits interact to underpin genotype-to-phenotype relationships is generally lacking. Stomatal density (SD) is a tractable model system for exploring how high-throughput phenotyping (HTP) data could be exploited by a new spatial analysis approach to better understand a developmentally and functionally important trait. SD is a composite trait, resulting from various components related to cell identity and size, which are themselves governed by a series of spatio-developmental processes. Data from 192 recombinant inbred lines of maize [Zea mays (L.)] were analyzed by a new stomatal patterning phenotype (SPP) to (1) describe the average spatial probability distribution of the nearest neighboring stomata; (2) derive a core set of component traits related to cell size, cell packing, and positional probabilities; (3) build a structural equation model of component traits underlying SD; and (4) identify stomatal patterning quantitative trait loci (QTL). The core set of SPP-derived traits explained 74% of the variation in SD. Analyzing SPP component traits allowed some loci previously identified as generic SD QTL to be recognized as specific to lateral versus longitudinal elements of stomatal patterning. Therefore, this study highlights how novel insights can be gained by decomposing a composite trait (e.g., SD) into a set of component traits that were present in HTP data but not previously exploited.

AI/ML

Autonomous phase mapping of gold nanoparticles synthesis with differentiable models of spectral shape

Autonomous experimentation–or self-driving labs–offers a systematic approach to accelerate materials discovery by integrating automated synthesis, characterization, and data-driven decision-making. We present a closed-loop workflow for the on-demand synthesis and structural characterization of colloidal gold nanoparticles, enabling direct mapping from composition to nanoscale structure. Our framework leverages differentiable models of spectral shape to address two central tasks in self-driving labs: (a) phase mapping, or identifying compositional regions with distinct structural behavior; and (b) material retrosynthesis, or optimizing compositions for target structure. Using functional data analysis, we develop a data-driven model with generative pre-training, active learning, and high-throughput experiments to predict spectral responses across composition space. We demonstrate the approach on seed-mediated growth of gold nanoparticles, showcasing its ability to extract design rules, reveal secondary interactions, and efficiently navigate morphology space. Gradient-based optimization of the models enables inverse design, making this a unified platform.

36 MATERIALS SCIENCE

EMPHATIC Silicon Strip Detector Efficiencies

EMPHATIC is an experiment at Fermilab which aims to reduce current neutrino flux uncertainties. This report discusses the limitations current neutrino flux uncertainties places on large scale neutrino experiments, provides background on the EMPHATIC experiment, and details the project of determining the efficiency of the Silicon Strip Detectors (SSDs) used in EMPHATIC. As part of the data analysis process and in order to increase the accuracy of EMPHATIC’s simulations a representation of efficiency of each SSD is required. To achieve this a data-driven analysis was performed on EMPHATIC's collected data using the Root and Art frameworks. Visual and numerical representations of efficiency were determined. The average efficiency over all SSDs is 98.58\%, however this number deflated as it includes known bad channels.

Olson, Virginia [Illinois U., Urbana (main)]

Determining the Efficiency of EMPHATICs Silicon Strip Detectors (SSDs)

EMPHATIC is an experiment at Fermilab which aims to reduce current neutrino flux uncertainties. This report discusses the limitations current neutrino flux uncertainties places on large scale neutrino experiments, provides background on the EMPHATIC experiment, and details the project of determining the efficiency of the Silicon Strip Detectors (SSDs) used in EMPHATIC. As part of the data analysis process and in order to increase the accuracy of EMPHATIC’s simulations a representation of efficiency of each SSD is required. To achieve this a data-driven analysis was performed on EMPHATIC's collected data using the Root and Art frameworks. Visual and numerical representations of efficiency were determined. The average efficiency over all SSDs is 98.58\%, however this number deflated as it includes known bad channels.

Olson, V. [Illinois U., Urbana (main)]

Radio Afterglow Detection and AI-driven Response (RADAR): A Federated Framework for Gravitational-wave Event Follow-up

The landmark detection of both gravitational waves (GWs) and electromagnetic (EM) radiation from the binary neutron star merger GW170817 has spurred efforts to streamline the follow-up of GW alerts in current and future observing runs of ground-based GW detectors. Within this context, the radio band of the EM spectrum presents unique challenges. Sensitive radio facilities capable of detecting the faint radio afterglow seen in GW170817, and with sufficient angular resolution, have small fields of view compared to typical GW localization areas. Additionally, theoretical models predict that the radio emission from binary neutron star mergers can evolve over weeks to years, necessitating long-term monitoring to probe the physics of the various postmerger ejecta components. These constraints, combined with limited radio observing resources, make the development of more coordinated follow-up strategies essential—especially as the next generation of GW detectors promises a dramatic increase in detection rates. Here, we present RADAR, a framework designed to address these challenges by promoting community-driven information sharing, federated data analysis, and system resilience, while integrating AI methods for both GW signal identification and radio data aggregation. We show that it is possible to preserve data rights while sharing models that can help design and/or update follow-up strategies. We demonstrate our approach through a case study of GW170817, and discuss future directions for refinement and broader application.

Gravitational waves

Validating the galaxy and quasar catalog-level blinding scheme for the DESI 2024 analysis

In the era of precision cosmology, ensuring the integrity of data analysis through blinding techniques is paramount — a challenge particularly relevant for the Dark Energy Spectroscopic Instrument (DESI). DESI represents a monumental effort to map the cosmic web, with the goal to measure the redshifts of tens of millions of galaxies and quasars. Given the data volume and the impact of the findings, the potential for confirmation bias poses a significant challenge. To address this, we implement and validate a comprehensive blind analysis strategy for DESI Data Release 1 (DR1), tailored to the specific observables DESI is most sensitive to: Baryonic Acoustic Oscillations (BAO), Redshift-Space Distortion (RSD) and primordial non-Gaussianities (PNG). We carry out the blinding at the catalog level, implementing shifts in the redshifts of the observed galaxies to blind for BAO and RSD signals and weights to blind for PNG through a scale-dependent bias. We validate the blinding technique on mocks as well as on data by applying a second blinding layer to perform a series of sanity checks; the latter allows probing complexities in real data not captured in mocks. We find that the blinding strategy alters the data vector in a controlled way, and the BAO and RSD analysis choices are robust to blinding. The successful validation of the blinding strategy paves the way for the unblinded DESI DR1 analysis, alongside future blind analyses with DESI and other surveys.

79 ASTRONOMY AND ASTROPHYSICS