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Microbial community data from throughfall exclusion experiment: Metadata, SI, community composition, LefSe, and FunGuilR data tables from PARCHED Panama tropical forest soils, 2024-2025

Soil contains more carbon (C) than terrestrial vegetation and the atmosphere combined, with some of the largest terrestrial C stocks in tropical rainforests. Soil microbes decompose organic matter, playing a vital role in the storage or loss of soil C. With climate change, drought conditions are predicted to increase in many tropical regions, including both chronic drying and extended drought, potentially influencing these processes. This project explored the effects of chronic and seasonal drying on soil microbial communities across four distinct tropical forests in a long-term drying experiment. We investigated the effects of a chronic drying manipulation on soil microbial community abundance and variation across different forests and seasons. We also compared findings with previously published data from these forests after short-term drying. This project used soils from a long-term drying experiment established in 2018 across four seasonal lowland forests in Panama. Soils were collected from 0 – 10 cm depths during three seasonal periods in control and drying plots in 2024 and 2025 from a total of 32 plots (n = 4 per forest per treatment). The forests varied in baseline rainfall and soil fertility. We calculated alpha and beta diversity indices and compared taxonomic community composition. We found significant biogeographic variation in microbial diversity and taxonomy, with significant differences across the forests and significant effects of the drying treatment. Metadata and sample IDs are within Metadata_16S.csv and Metadata_ITS.csv. Relative abundance tables of every sample at every season are shown in the Excel workbooks 16S Relative Abundance.xlsx and ITS Relative Abundance.xlsx. They are then also shown in CSV files by each taxonomic level. Linear discriminant analysis effect size (LefSe) tables are shown for the full 16S and ITS datasets (n = 96), subsets for every site at every season (n = 8), and then for the forests with each plot merged by season (n = 8). FunGuildR data table of ITS data is uploaded.

Bacteria↗

Machine learning models for rat multigeneration reproductive toxicity prediction

Reproductive toxicity is one of the prominent endpoints in the risk assessment of environmental and industrial chemicals. Due to the complexity of the reproductive system, traditional reproductive toxicity testing in animals, especially guideline multigeneration reproductive toxicity studies, take a long time and are expensive. Therefore, machine learning, as a promising alternative approach, should be considered when evaluating the reproductive toxicity of chemicals. We curated rat multigeneration reproductive toxicity testing data of 275 chemicals from ToxRefDB (Toxicity Reference Database) and developed predictive models using seven machine learning algorithms (decision tree, decision forest, random forest, k-nearest neighbors, support vector machine, linear discriminant analysis, and logistic regression). A consensus model was built based on the seven individual models. An external validation set was curated from the COSMOS database and the literature. The performances of individual and consensus models were evaluated using 500 iterations of 5-fold cross-validations and the external validation data set. The balanced accuracy of the models ranged from 58% to 65% in the 5-fold cross-validations and 45%–61% in the external validations. Prediction confidence analysis was conducted to provide additional information for more appropriate applications of the developed models. The impact of our findings is in increasing confidence in machine learning models. We demonstrate the importance of using consensus models for harnessing the benefits of multiple machine learning models (i.e., using redundant systems to check validity of outcomes). While we continue to build upon the models to better characterize weak toxicants, there is current utility in saving resources by being able to screen out strong reproductive toxicants before investing in vivo testing. The modeling approach (machine learning models) is offered for assessing the rat multigeneration reproductive toxicity of chemicals. Our results suggest that machine learning may be a promising alternative approach to evaluate the potential reproductive toxicity of chemicals.

consensus model↗

Coolant Pump Predictive Data Analytics from Signatures Generated by the Recursive Short Time Fast Fourier Transform

Although a nuclear reactor is a hostile environment for sensors and signal transmissions, the reactor core is amenable to acoustic communication. An acoustic measurement infrastructure installed at the Advanced Test Reactor (ATR) nozzle trench area records acoustic signals that can capture reactor operating states. The distinct states produce unique signatures that can be identified and tracked using data processing and data analytics. The infrastructure relies on acoustic transmission through ATR in-pile structural components, piping, and coolant that transmit acoustically modified signals generated by the coolant pumps. This paper will discuss results from using the Recursive Short Time Fast Fourier Transform (RSTFFT) technique used to process acoustic signals and provide signatures that are identified and monitored by analytics. The RSTFFT is applied to ATR data to understand the vibration levels and signatures for different operating regimes as displayed by the spectrogram. The combination of coolant pumps for normal and high-power operation generate unique signatures. These acoustic signatures are used to develop machine learning approaches to automatically classify operating regimes. Two machine-learning models, Support Vector Machines and Linear Discriminant Analysis, were developed to classify two event classes. Class 1 is a normal steady-state operation, and Class 2 is any event that is due to start up, shut down, or other actions. Both types of machine learning models had over a 96% prediction accuracy for the two classes. These results lay the foundation for predictive analytic frameworks that can be leveraged by ATR to optimize operations and maintenance.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

High dimensional binary classification under label shift: phase transition and regularization

Label Shift has been widely believed to be harmful to the generalization performance of machine learning models. Researchers have proposed many approaches to mitigate the impact of the label shift, e.g., balancing the training data. However, these methods often consider the underparametrized regime, where the sample size is much larger than the data dimension. The research under the overparametrized regime is very limited. Here, to bridge this gap, we propose a new asymptotic analysis of the Fisher Linear Discriminant classifier for binary classification with label shift. Specifically, we prove that there exists a phase transition phenomenon: Under certain overparametrized regime, the classifier trained using imbalanced data outperforms the counterpart with reduced balanced data. Moreover, we investigate the impact of regularization to the label shift: The aforementioned phase transition vanishes as the regularization becomes strong.

binary classification↗

A protein scaffold enables hydrogen evolution for a Ni-bisdiphosphine complex

We find that an artificial metalloenzyme acting as a functional biomimic of hydrogenase enzymes was activated by assembly via covalent attachment of the molecular complex, [Ni(PN glycine P) 2 ] 2- , within a structured protein scaffold. Electrocatalytic H2 production was observed from pH 3.0 to 10.0 for the artificial enzyme, while no electrocatalytic activity was observed for similar [Ni(PNP) 2 ] 2+ systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Data supporting manuscript from L. Sheneman, G. Stephanopoulos, A.E. Vasdekis titled "Deep learning classification of lipid droplets in quantitative phase images" as currently under review at PLOS ONE. This includes: 1) raw and binary labeled Quantitative Phase Images (QPI) of Y. lipolytica cells used in the analyses described within the manuscript. 2) various derived data including classifier scores, etc.

Data supporting manuscript from L. Sheneman, G. Stephanopoulos, A.E. Vasdekis titled "Deep learning classification of lipid droplets in quantitative phase images" as currently under review at PLOS ONE. This includes: 1) raw and binary labeled Quantitative Phase Images (QPI) of Y. lipolytica cells used in the analyses described within the manuscript. 2) various derived data including classifier scores, etc.

ANN↗

Functional Principal Component Analysis of Radio–Optical Reference Frame Tie

The Gaia optical reference frame is intrinsically undefined with respect to global orientation and spin, so it needs to be anchored in the radio-based International Celestial Reference Frame (ICRF) to provide a referenced and quasi-inertial celestial coordinate system. The link between the two fundamental frames is realized through two samples of distant extragalactic sources, mostly active galactic nuclei and quasars, but only the smaller sample of radio-loud ICRF sources with optical counterparts is available to determine the mutual orientation. The robustness of this link can be mathematically formulated in the framework of functional principal component analysis using a set of vector spherical harmonics to represent the differences in celestial positions of the common objects. The weakest eigenvectors are computed, which describe the greatest deficiency of the link. The deficient or poorly determined terms are specific vector fields on the sphere that carry the largest errors of absolute astrometry using Gaia in reference to the ICRF. This analysis provides guidelines for the future development of the ICRF maximizing the accuracy of the link over the entire celestial sphere. A measure of the robustness of a least-squares solution, which can be applied to any linear model fitting problem, is introduced to help discriminate between reference frame tie models of different degrees.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Kinetic Separation of Siloxanes in Metal–Organic Frameworks

We present an in silico assessment of metal–organic frameworks (MOFs) for the kinetic separation of linear and cyclic siloxanes. We employed molecular dynamics simulations investigating both rigid and flexible 1D MOF frameworks to identify a specific range of pore parameters that enables the diffusion of linear siloxanes but leads to slow diffusion of cyclic siloxanes. We then extended our analysis to flexible 3D MOFs to select adsorbents for the kinetic separation of cyclic and linear siloxanes. Based on synthesizability metrics we identified four 3D MOFs capable of discriminating between cyclic and linear siloxanes. One of the MOFs with structure code WIYFAM stood out with the ability to distinguish between cyclic and linear siloxanes and facilitate the diffusion of all linear siloxanes investigated in this study. One of the other MOFs, IRMOF-6, is found to be capable of not only discriminating between cyclic and linear siloxanes, but even between shorter and longer linear siloxanes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nickel Isonicotinate Framework with Optimal Pore Structure for Complete Discrimination of Hexane Isomers

Efficient separation of physicochemically similar alkanes is of vital importance. Adsorptive separation utilizing porous materials such as metal–organic frameworks with tunable pore structure and surface functionality represents an energy-efficient technology. In this study, we demonstrate successful separation of alkanes with varying degree of branching using a microporous nickel isonicotinate framework, Ni(4-PyC) 2 . Its 2-fold interpenetrated diamondoid structure with well-suited pore size enables selective adsorption of linear and monobranched hexane isomers, while excluding dibranched isomer. Breakthrough experiments validated its capability to completely discriminate all three hexane isomers. Ab initio calculations combined with in situ infrared spectroscopic analysis unveiled the nature of host–guest interactions and differences in the binding energies and diffusion barriers among the isomers. Furthermore, having well-balanced adsorption uptakes (146 and 79 mg g –1 of nHEX and 3MP), high nHEX/DMB uptake ratio (12.2) and fast kinetics, Ni(4-PyC) 2 stands out as a promising adsorbent for complete separation of hexane isomers under ambient conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Kinetic Measurements in Heterogeneous Catalysis

This contribution is about the experimental determination of the rate of a heterogeneous catalytic reaction and the analysis of kinetic data. In this case, the reaction rate can be defined as the frequency at which the closed sequence of elementary steps transforming reactants into products is occurring. However, the rate of chemical reaction is not directly observed; rather, one records the rate of substance change. The rate of chemical reaction is calculated based on the rate of substance change and assumed stoichiometry of the reaction. In order to make this an intensive quantity (i.e., independent of the volume in which the reaction is performed, this frequency is divided by the latter or by a quantity proportional to the latter). As the focus of what follows is on heterogeneously catalyzed reactions this can be the catalyst mass, the catalyst surface area or the total number of active sites present in the reaction volume confined by the walls of a chemical reactor. For example, the rate may be reported as one of the following: Net rate of consumption/production of component i mol m-3 s-1 Net specific rate of consumption/production of component i mol kg-1 s-1 Rate of substance change (per unit volume of catalyst) mol m-3 s-1 Specific reaction rate (per unit mass of catalyst) mol kg-1 s-1 Net rate of consumption/production of component i mol m-2 s-1 The turnover frequency (TOF) is a characteristic originally introduced by Boudart [1] is expressed as TOF=R/G_tot , where R is the steady-state rate of reactant consumption or product generation and G_totis the total areal density of active sites [mol m-2]. The latter is typically taken from experimental chemisorption data obtained at low temperature. The advancement of a chemical reaction leads to changes in the amounts of reactants and products which, for a stoichiometric single reaction, are connected by the stoichiometric coefficients. In many cases, for the sake of simplicity, we will assume that the investigated reaction proceeds according to a single reaction pathway, so that the net production rate of a reaction component is directly proportional to the reaction rate and that the latter equals the net production rate of any of the involved components when divided by the appropriate stoichiometric coefficient. For complex stoichiometric reactions the net production rates of the involved components are linear combinations of the reaction rates. Different goals for kinetic measurements can be formulated: Catalyst testing, i.e., obtaining the kinetic dependences for the development and discrimination of efficient catalytic materials. Precise kinetic characterization of active materials via high-throughput screening is a part of such activity. Detailed kinetics, i.e., revealing the detailed mechanism of complex catalytic reaction via systematic kinetic studies, both steady-state and non-steady-state Industrial kinetics, i.e., obtaining data and relationships for describing and predicting the behaviour of catalytic reactors and processes at industrial scale Finally, mathematical modeling and analysis where kinetic measurements provide data for understanding complex kinetic phenomena, e.g., oscillations, non-linear self-organization, etc.

36 MATERIALS SCIENCE↗

An Artificial Neural Network System for Photon-Based Active Interrogation Applications

Active interrogation (AI) is a promising technique to detect shielded special nuclear materials (SNMs). At the University of Michigan, we are developing a photon-based AI system that uses bremsstrahlung radiation from an electron linear accelerator (linac) as an ionizing source and stilbene organic scintillating detectors for neutron detection. Stilbene scintillators are sensitive to fast neutrons and photons and have excellent pulse shape discrimination (PSD) capabilities. The traditional charge integration (CI) method commonly used for PSD analysis eliminates piled-up pulses and relies on a particle discrimination line to separate neutrons and photons. The presence of the intense photon flux during AI creates a significant number of piled-up events in the stilbene scintillator, thereby posing a great challenge to the traditional CI method. Identifying true single neutron pulses becomes challenging due to the presence of a pile-up cloud and overlapping neutron, photon and pile-up clouds in the PSD analysis. To mitigate the effect of pulse pile up and identify true single neutron pulses from stilbene scintillators, an artificial neural network (ANN) system is developed. The developed ANN system identifies single neutron pulses and neutron-photon combinations from piled-up events. The results obtained from a 252Cf measurement in the presence of the intense photon flux show that the developed ANN system outperforms the traditional CI method. Since many piled-up events lie above the particle discrimination line, they get misclassified as neutrons by the traditional CI method resulting in 25% overestimation of the net neutron count rate during the linac pulse. The overall net neutron count rate (single and restored neutrons) during the linac pulse, estimated by the ANN system is 60% of the ground truth. Energy spectroscopy of the ANN attributed single neutron pulses further provides evidence on the detection of prompt fission neutrons from the 252Cf fission source.

42 ENGINEERING↗

Near-infrared chemical abundances of stars in the Sculptor dwarf galaxy

Owing to the recent identification of major substructures in our Milky Way (MW), the astronomical community has started to reevaluate the importance of dissolved and existing dwarf galaxies. In this work, we investigate up to 13 elements in 43 giant stars of the Sculptor dwarf galaxy (Scl) using high-signal-to-noise-ratio near-infrared (NIR) APOGEE spectra. Thanks to the strong feature lines in the NIR, we were able to determine high-resolution O, Si, and Al abundances for a large group of sample stars for the first time in Scl. By comparing the [α/Fe] (i.e., O, Mg, Si, Ca, and Ti) of the stars in Scl, Sagittarius, and the MW, we confirm the general trend that less massive galaxies tend to show lower [α/Fe]. The low [Al/Fe] (~ - 0.5) in Scl demonstrates the value of this ratio as a discriminator with which to identify stars born in dwarf galaxies (from MW field stars). A chemical-evolution model suggests that Scl has a top-light initial mass function (IMF), with a high-mass IMF power index of ~ - 2.7, and a minimum Type Ia supernovae delay time of ~100 Myr. Furthermore, a linear regression analysis indicates a negative radial metallicity gradient and positive radial gradients for [Mg/Fe] and [Ca/Fe], in qualitative agreement with the outside-in formation scenario.

79 ASTRONOMY AND ASTROPHYSICS↗

Star–Galaxy Image Separation with Computationally Efficient Gaussian Process Classification

Abstract We introduce a novel method for discerning optical telescope images of stars from those of galaxies using Gaussian processes (GPs). Although applications of GPs often struggle in high-dimensional data modalities such as optical image classification, we show that a low-dimensional embedding of images into a metric space defined by the principal components of the data suffices to produce high-quality predictions from real large-scale survey data. We develop a novel method of GP classification hyperparameter training that scales approximately linearly in the number of image observations, which allows for application of GP models to large-size Hyper Suprime-Cam Subaru Strategic Program data. In our experiments, we evaluate the performance of a principal component analysis embedded GP predictive model against other machine-learning algorithms, including a convolutional neural network and an image photometric morphology discriminator. Our analysis shows that our methods compare favorably with current methods in optical image classification while producing posterior distributions from the GP regression that can be used to quantify object classification uncertainty. We further describe how classification uncertainty can be used to efficiently parse large-scale survey imaging data to produce high-confidence object catalogs.

79 ASTRONOMY AND ASTROPHYSICS↗

Prediction challenge: First principles simulation of the ultrafast electron diffraction spectrum of cyclobutanone

Computer simulation has long been an essential partner of ultrafast experiments, allowing the assignment of microscopic mechanistic detail to low-dimensional spectroscopic data. However, the ability of theory to make a priori predictions of ultrafast experimental results is relatively untested. Herein, as a part of a community challenge, we attempt to predict the signal of an upcoming ultrafast photochemical experiment using state-of-the-art theory in the context of preexisting experimental data. Specifically, we employ ab initio Ehrenfest with collapse to a block mixed quantum–classical simulations to describe the real-time evolution of the electrons and nuclei of cyclobutanone following excitation to the 3s Rydberg state. The gas-phase ultrafast electron diffraction (GUED) signal is simulated for direct comparison to an upcoming experiment at the Stanford Linear Accelerator Laboratory. Following initial ring-opening, dissociation via two distinct channels is observed: the C3 dissociation channel, producing cyclopropane and CO, and the C2 channel, producing CH2CO and C2H4. Direct calculations of the GUED signal indicate how the ring-opened intermediate, the C2 products, and the C3 products can be discriminated in the GUED signal. We also report an a priori analysis of anticipated errors in our predictions: without knowledge of the experimental result, which features of the spectrum do we feel confident we have predicted correctly, and which might we have wrong?

Chemistry↗

Hierarchical Model Reduction Driven by Machine Learning for Parametric Advection-Diffusion-Reaction Problems in the Presence of Noisy Data

Abstract We propose a new approach to generate a reliable reduced model for a parametric elliptic problem, in the presence of noisy data. The reference model reduction procedure is the directional HiPOD method, which combines Hierarchical Model reduction with a standard Proper Orthogonal Decomposition, according to an offline/online paradigm. In this paper we show that directional HiPOD looses in terms of accuracy when problem data are affected by noise. This is due to the interpolation driving the online phase, since it replicates, by definition, the noise trend. To overcome this limit, we replace interpolation with Machine Learning fitting models which better discriminate relevant physical features in the data from irrelevant unstructured noise. The numerical assessment, although preliminary, confirms the potentialities of the new approach.

97 MATHEMATICS AND COMPUTING↗

Sampling-based Sublinear Low-rank Matrix Arithmetic Framework for Dequantizing Quantum Machine Learning

We present an algorithmic framework for quantum-inspired classical algorithms on close-to-low-rank matrices, generalizing the series of results started by Tang’s breakthrough quantum-inspired algorithm for recommendation systems [STOC’19]. Motivated by quantum linear algebra algorithms and the quantum singular value transformation (SVT) framework of Gilyén et al. [STOC’19], we develop classical algorithms for SVT that run in time independent of input dimension, under suitable quantum-inspired sampling assumptions. Our results give compelling evidence that in the corresponding QRAM data structure input model, quantum SVT does not yield exponential quantum speedups. Since the quantum SVT framework generalizes essentially all known techniques for quantum linear algebra, our results, combined with sampling lemmas from previous work, suffice to generalize all prior results about dequantizing quantum machine learning algorithms. In particular, our classical SVT framework recovers and often improves the dequantization results on recommendation systems, principal component analysis, supervised clustering, support vector machines, low-rank regression, and semidefinite program solving. We also give additional dequantization results on low-rank Hamiltonian simulation and discriminant analysis. Our improvements come from identifying the key feature of the quantum-inspired input model that is at the core of all prior quantum-inspired results: ℓ 2 -norm sampling can approximate matrix products in time independent of their dimension. We reduce all our main results to this fact, making our exposition concise, self-contained, and intuitive.

Computer Science↗

Discrimination of Hexane Isomers by Temperature Swing Adsorption in a Rigid Aluminum Metal–Organic Framework

The efficient separation of alkane isomers with similar physicochemical properties remains a persistent challenge for the petrochemical industry. Adsorptive separation using metal− organic frameworks (MOFs) offers an energy-efficient alternative to conventional distillation. Herein, we report temperature swing discrimination of hexane isomers with different degrees of branching using MIL-120, a rigid aluminum pyromellitate-based MOF. MIL-120 features uniform one-dimensional channels with an aperture of ∼5.5 Å. At 30 °C, it selectively adsorbs linear and monobranched hexanes while excluding the dibranched isomer. Upon heating to 120 °C, both mono- and dibranched isomers are completely excluded, whereas linear hexane remains strongly adsorbed. Breakthrough experiments validate the temperature swing separation performance. Adsorption heat analysis combined with ab initio calculations provides a quantitative measure of distinct differences in adsorption enthalpies, binding energies, and diffusion barriers responsible for the observed separation efficiency, highlighting the potential of this MOF for efficient separation of alkane isomers via temperature swing adsorption.

Adsorption↗

Field Test Report Neutron Scintillator Array Dry Storage Cask Scanner FY2024

During two weeks of Field Testing at the Idaho National Laboratory INTEC Cask Farm in July and August 2024, the LLNL Dry Storage Cask Scanner Array was lifted on top of an MC-10 dry storage fuel cask and operated to acquire neutron and gamma-ray data from the 24 fuel bundle positions. Neutron and gamma-ray data acquisition scans across the top of the cask of varying dwell times were performed July 15-18, 2024 and August 19-22, 2024 to evaluate the ability of the scanner data to reveal asymmetries in the fuel positions that reflect asymmetries in the MC-10 cask fuel bundle loading. The MC-10 cask 24 position fuel bundle loading at the INTEC Cask Farm is well documented, including the locations of six empty fuel bundle positions. This loading presents an opportunity to test the ability of the scanner system to detect diversion of spent fuel bundles as well as to validate the MC-10 cask MCNP modeling. The cask scanner array consists of six Stilbene crystal scintillator detectors and a linear actuator frame that moves the six detectors across the MC-10 dry storage cask to obtain data above each of the 24 fuel bundle positions. The detectors are connected to a pulse-shape discrimination data acquisition system capable of generating separate neutron and gamma-ray spectra for each detector and for each scan position. From the prior single detector Field Test in 2021 and iteration with MCNP modeling, the neutron and gamma-ray data were analyzed in multiple energy regions to identify an analysis method that would provide the strongest and most consistent signature of the asymmetric MC-10 cask fuel loading1 . From both the 2021 Field Test and the current Field Test results, the neutron capture gamma-ray count rate around 2.2 MeV provides the strongest signature of the asymmetric MC-10 cask fuel loading and has qualitative agreement with MCNP calculations. Counting all gamma-rays produces a similar signature. Neutrons emerging from the cask top are moderated and captured by the hydrogen in the polyethylene moderator and scintillator detector, producing a 2.2 MeV gamma ray which is seen in the scintillator gamma-ray spectrum. The count rate in the 2.2 MeV gamma-ray region is ~50 c/s, which is ~1000x higher than the ~0.05 n/s rate in the > 4MeV neutron region, and ~50x greater than the ~1 n/s rate in the neutrons > 500 keV region. Analysis of the 2.2 MeV neutron-capture Compton-scattered gamma-rays produces a statistically significant signature of the INTEC Cask Farm MC-10 asymmetric fuel loading. MCNP simulations indicate that the average neutron energy spectrum offers the potential to detect a large asymmetry from several missing bundles as well as individual missing fuel bundles. Testing this feature will require measurements on a cask with single missing elements.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗