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KS-TmG.2.0

Soil samples were collected in triplicate in the Fall of 2017 across three grassland locations having differences in historical annual precipitation. For each of the three field site soil collections, one deeply sequenced composite metagenome (> 1 terabase) was obtained and individually sequenced in replicate to provide three additional terabase metagenomes for replicate statistical comparison in addition to screening for viral soil contigs for assessing the impact of historical annual precipitation. This data package provides new knowledge of viral types, abundances, diversity, and auxiliary metabolic genes (AMGs) in grassland soils for predicting viral response to changes in their environment.

59 BASIC BIOLOGICAL SCIENCES↗

WA-TmG.2.0

Soil samples were collected in triplicate in the Fall of 2017 across three grassland locations having differences in historical annual precipitation. For each of the three field site soil collections, one deeply sequenced composite metagenome (> 1 terabase) was obtained and individually sequenced in replicate to provide three additional terabase metagenomes for replicate statistical comparison in addition to screening for viral soil contigs for assessing the impact of historical annual precipitation. This data package provides new knowledge of viral types, abundances, diversity, and auxiliary metabolic genes (AMGs) in grassland soils for predicting viral response to changes in their environment.

59 BASIC BIOLOGICAL SCIENCES↗

E-Labs - Learning with Authentic Data

the success teachers have had providing an opportunity for students to: • Organize and conduct authentic research. • Experience the environment of scientific collaborations. • Possibly make real contributions to a burgeoning scientific field. We've created projects that are problem-based, student driven and technology dependent. Students reach beyond classroom walls to explore data with other students and experts and share results, publishing original work to a worldwide audience. Students can discover and extend the research of other students, modeling the processes of modern, large-scale research projects. From start to finish e-Labs are student-led, teacher-guided projects. Students need only a Web browser to access computing techniques employed by professional researchers. A Project Map with milestones allows students to set the research plan rather than follow a step-by-step process common in other online projects. Most importantly, e-Labs build the learning experience around the students' own questions and let them use the very tools that scientists use. Students contribute to and access shared data, most derived from professional research databases. They use common analysis tools, store their work and use metadata to discover, replicate and confirm the research of others. This is where real scientific collaboration begins. Using online tools, students correspond with other research groups, post comments and questions, prepare summary reports, and in general participate in the part of scientific research that is often left out of classroom experiments. Teaching tools such as student and teacher logbooks, pre- and post-tests and an assessment rubric aligned with learner outcomes help teachers guide student work. Constraints on interface designs and administrative tools such as registration databases give teachers the "one-stop-shopping" they seek for multiple e-Labs. Teaching and administrative tools also allow us to track usage and assess the impact on student learning.

Bardeen, Marjorie G.↗

Response to Andrew Fowlie’s Comments

This Letter to the Editor of Harvard Data Science Review is a rejoinder to a Letter to the Editor by Andrew Fowlie, titled “Comment on Reproducibility and Replication of Experimental Particle Physics Results”.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A methodology to develop multi-physics dynamic fuel cell system models validated with vehicle realistic drive cycle data

Fuel cell (FC) technology has been identified as a technically attractive solution to decarbonize the transportation sector, especially for heavy-duty vehicles. In this context, the industry and the scientific community are in need of advanced fuel cell systems (FCS) models that are able to replicate real -world operating conditions. Due to the scarcity of said models in the open literature, this study aimed to develop a comprehensive methodology to calibrate and validate multi -physics dynamic FCS models. Therefore, the key contribution of this paper is the detailed description of the calibration process for each component and the calibration order. The specific focus here was to accurately describe the behavior of the FC stack as well as the cathode, anode, and cooling circuits of the balance of plant. The model was calibrated with the aid of experimental data from a Toyota Mirai FC electric vehicle, which was predominantly retrieved from the vehicle's Controller Area Network (CAN) bus system thereby negating the need for major intrusion into the powertrain system. The validation process was deemed successful with the model being able to truthfully replicate the characteristics of the FC vehicle operated on the World-wide harmonized Light duty Test Cycle (WLTC) 3b and US06 driving cycle. The time -resolved physical parameters such as the cathode pressure, mass flow, or the FC stack temperature were captured with high fidelity, while the overall performance parameters such as the H2 consumption in the stack and the system, and the compressor energy consumption were predicted accurately with a deviation lower than 0.47%, 1.75% and 1.89% with respect to the experimental data, respectively.

Lopez-Juarez, Marcos↗

Role of the likelihood for elastic scattering uncertainty quantification

In the last decade, uncertainty quantification (UQ) for optical model potentials (OMPs) has become a focal point for nuclear reaction theory, and several competing approaches for OMP UQ have recently been developed. Here, we clarify recent efforts to compare frequentist and Bayesian approaches in the context of OMP UQ [G. B. King et al., Phys. Rev. Lett. 122, 232502 (2019)]. We replicate a portion of that OMP UQ study but use independent statistical tools. Specifically, we compare two methods for OMP parameter inference from elastic scattering data: the Levenberg-Marquardt algorithm for χ 2 minimization on one hand and Markov chain Monte Carlo (MCMC) sampling on the other. Separately, we assess the common practice of using a renormalized likelihood (χ 2 /N), N being the number of data points, instead of the canonical weighted-least-squares likelihood (χ 2 ), as a way of accounting for unknown data correlations. Here, we show that for a generic linear model and for a five-parameter OMP analysis, frequentist and uniform-prior Bayesian approaches recover the same optimum and uncertainty estimates—not systematically larger uncertainties for the Bayesian approach, as was concluded in G. B. King et al., Phys. Rev. Lett. 122, 232502 (2019). Further, we show that if an additional, near-degenerate parameter is introduced into the same OMP analysis such that the parameter posterior becomes non-Gaussian, then covariance-based estimates of uncertainty become unreliable. Finally, we show that regardless of optimization approach, if χ 2 /N is used for the likelihood, the resulting parametric uncertainties increase by $\sqrt{N}$, and that this is responsible for the conclusions drawn in the revisited study. Based on our replication results, we find that a fortuitous cancellation of unreported errors and the renormalization factor can lead to improvement in empirical coverages, as was the case in the original comparative study. We emphasize that developing and applying a realistic likelihood function is an essential task in a UQ analysis, and that several recent UQ studies that employed a renormalized likelihood (i.e., including a 1/N factor) may have yielded unrealistically large uncertainties for elastic-scattering observables. If the parameter posterior deviates from multivariate-normal, a sampling-based approach like MCMC has a clear advantage over methods that assume the Laplace approximation holds. We note that empirical coverage can serve as an important internal check for the analyst whose model or data may have additional, unaccounted-for uncertainties.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Fourier Neural Networks as Function Approximators and Differential Equation Solvers

We present a Fourier neural network (FNN) that can be mapped directly to the Fourier decomposition. The choice of activation and loss function yields results that replicate a Fourier series expansion closely while preserving a straightforward architecture with a single hidden layer. The simplicity of this network architecture facilitates the integration with any other higher-complexity networks, at a data pre- or postprocessing stage. We validate this FNN on naturally periodic smooth functions and on piecewise continuous periodic functions. We showcase the use of this FNN for modeling or solving partial differential equations with periodic boundary conditions. The main advantages of the current approach are the validity of the solution outside the training region, interpretability of the trained model, and simplicity of use.

Fourier decomposition↗

Data-driven Modeling for Grid Edge IBRs: A Digital Twin Perspective of User-Defined Models

Recent events in Odessa have brought attention to the challenges associated with the interaction between Inverter- Based Resources (IBRs) and the transmission and distribution system. The NERC event diagnosis report has highlighted sev- eral issues, emphasizing the need for continuous performance monitoring of these IBRs by system operators. Key areas of concern include the mismatch of control and protection perfor- mance of IBRs between the original equipment manufacturer (OEM)-provided models and field measurements. The inability to replicate the realistic response can result in incorrect reliability and resilience studies. In this paper, we developed an approach on how to emulate the behavior of an IBR using measurement data obtained for system operators to utilize in real-time and long- term planning. Two experiments are conducted in the phasor domain and electromagnetic transients (EMT) domain to emulate the behavior for grid forming and grid following inverters under various operating conditions and the effectiveness of the proposed model is demonstrated in terms of accuracy and ease of utilizing user-defined models (UDMs)

Mahapatra, Kaveri [BATTELLE (PACIFIC NW LAB)]↗

The intermediate filament network protein, vimentin, is required for parvoviral infection

Intermediate filaments (IFs) have recently been shown to serve novel roles during infection by many viruses. Here we have begun to study the role of IFs during the early steps of infection by the parvovirus minute virus of mice (MVM). We found that during early infection with MVM, after endosomal escape, the vimentin IF network was considerably altered, yielding collapsed immunofluorescence staining near the nuclear periphery. Furthermore, we found that vimentin plays an important role in the life cycle of MVM. The number of cells, which successfully replicated MVM, was reduced in infected cells in which the vimentin network was genetically or pharmacologically modified; viral endocytosis, however, remained unaltered. Perinuclear accumulation of MVM-containing vesicles was reduced in cells lacking vimentin. Our data suggests that vimentin is required for the MVM life cycle, presenting possibly a dual role: (1) following MVM escape from endosomes and (2) during endosomal trafficking of MVM. - Highlights: • MVM infection changes the distribution of the vimentin network to perinuclear regions. • Disrupting the vimentin network with acrylamide decreases MVM replication. • MVM replication is significantly reduced in vimentin-null cells. • Distribution of MVM-containing vesicles is affected in MVM infected vimentin-null cells.

60 APPLIED LIFE SCIENCES↗

An Open Combinatorial Diffraction Dataset Including Consensus Human and Machine Learning Labels with Quantified Uncertainty for Training New Machine Learning Models

Modern machine learning and autonomous experimentation schemes in materials science rely on accurate analysis of the data ingested by these models. Unfortunately, accurate analysis of the underlying data can be difficult, even for domain experts, complicating the training of the models intended to drive experiments. This is especially true when the goal is to identify the presence of weak signatures in diffraction or spectroscopic datasets. In this work, we examine a set of as-obtained diffraction data that track the phase transition from monoclinic to tetragonal in a Nb-doped VO2 film as a function of temperature and dopant concentration. We then task a set of domain experts and a set of machine learning experts with identifying which phase is present in each diffraction pattern manually and algorithmically, respectively; in both cases, the labels can vary dramatically, especially at the phase boundaries. We use the mode of the labels and the Shannon entropy as a method to capture, preserve and propagate consensus labels and their variance. Further we use the expert labels as a benchmark and demonstrate the use of Shannon entropy weighted scoring to test the performance of machine learning generated labels. Finally, we propose a material data challenge centered around generating improved labeling algorithms. This real-world dataset curated with expert labels can act as test bed for new algorithms. The raw data, annotations and code used in this study are all available online at data.gov and the interested reader is encouraged to replicate and improve the existing models

97 MATHEMATICS AND COMPUTING↗

GreenThrift: Optimizing Carbon and Cost for Flexible Residential Loads

Reducing buildings’ carbon emissions is an important sustainability challenge. While scheduling flexible building loads has been previously used for a variety of grid and energy optimizations, carbon footprint reduction using such flexible loads poses new challenges since such methods need to balance both energy and carbon costs while also reducing user inconvenience from delaying such loads. This paper highlights the potential conflict between electricity prices and carbon emissions and the resulting trade-offs in carbon-aware and cost-aware load scheduling. To address this trade-off, we propose GreenThrift, a home automation system that leverages the scheduling capabilities of smart appliances and knowledge of future carbon intensity and cost to reduce both the carbon emissions and costs of flexible energy loads. At the heart of GreenThrift is an optimization technique that automatically computes schedules based on user configurations and preferences. We evaluate the effectiveness of GreenThrift using real-world carbon intensity data, electricity prices, and load traces from multiple locations and across different scenarios and objectives. Our results show that GreenThrift can replicate the offline optimal and retains 97% of the savings when optimizing the carbon emissions. Moreover, we show how GreenThrift can balance the conflict between carbon and cost and retain 95.3% and 85.5% of the potential carbon and cost savings, respectively.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

An automated multiplexed turbidometric and data collection system for measuring growth kinetics of anaerobes dependent on gaseous substrates

Standard methods of monitoring the growth kinetics of anaerobic microorganisms are generally impractical when there is a protracted or indeterminate period of active growth, and when high numbers of samples or replications are required. As part of our studies of the adaptive evolution of a simple anaerobic syntrophic mutualism, requiring the characterization of many isolates and alternative syntrophic pairings, here we developed a multiplexed growth monitoring system using a combination of commercially available electronics and custom designed circuitry and materials. This system automatically monitors up to 64 sealed, and as needed pressurized, culture tubes and reports the growth data in real-time through integration with a customized relational database. The utility of this system was demonstrated by resolving minor differences in growth kinetics associated with the adaptive evolution of a simple microbial community comprised of a sulfate reducing bacterium, Desulfovibrio vulgaris, grown in syntrophic association with Methanococcus maripaludis, a hydrogenotrophic methanogen.

59 BASIC BIOLOGICAL SCIENCES↗

COMPASS-FME Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) Experiment Tree Inventory

This is the tree inventory (diameter, species, and live/dead status) data from the Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) experimental site. This manipulative, ecosystem-scale TEMPEST experiment is part of the COMPASS-FME (Coastal Observations, Mechanisms, and Predictions Across Systems and Scales: Field Measurements and Experiments; see https://compass.pnnl.gov/FME/COMPASSFME) project. It addresses the potential for freshwater and estuarine-water disturbance events to alter tree function, species composition, and ecosystem processes in a deciduous coastal forest in eastern Maryland, USA. The experiment uses a large-unit (2000 m2), un-replicated experimental design, with three 50 m × 40 m plots serving as control, freshwater, and estuarine-water treatments.This dataset includes:- An overall dataset README file.- The tree inventory data in both "wide" and "long" forms. These contain the same information but are structured differently, with the former more useful for human viewers and the latter more amenable for programmatic analyses.- A key to the species/genus codes used, which follow the U.S. Department of Agriculture's PLANTS schema (https://plants.usda.gov/).- A copy of the R code used to generate the wide- and long-form data files.All files are comma-separated value (CSV) and no special software is required to read them.

54 ENVIRONMENTAL SCIENCES↗

Evaluation of CMIP5 continental precipitation simulations relative to satellite-based gauge-adjusted observations

Numerous studies have emphasized that climate simulations are subject to various biases and uncertainties. The objective of this study is to cross-validate 34 Coupled Model Intercomparison Project Phase 5 (CMIP5) historical simulations of precipitation against the Global Precipitation Climatology Project (GPCP) data, quantifying model pattern discrepancies and biases for both entire data distributions and their upper tails. The results of the Volumetric Hit Index (VHI) analysis of the total monthly precipitation amounts show that most CMIP5 simulations are in good agreement with GPCP patterns in many areas, but that their replication of observed precipitation over arid regions and certain sub-continental regions (e.g., northern Eurasia, eastern Russia, central Australia) is problematical. Overall, the VHI of the multi-model ensemble mean and median also are superior to that of the individual CMIP5 models. However, at high quantiles of reference data (e.g., the 75th and 90th percentiles), all climate models display low skill in simulating precipitation, except over North America, the Amazon, and central Africa. Analyses of total bias (B) in CMIP5 simulations reveal that most models overestimate precipitation over regions of complex topography (e.g. western North and South America and southern Africa and Asia), while underestimating it over arid regions. Also, while most climate model simulations show low biases over Europe, inter-model variations in bias over Australia and Amazonia are considerable. The Quantile Bias (QB) analyses indicate that CMIP5 simulations are even more biased at high quantiles of precipitation. Lastly, we found that a simple mean-field bias removal improves the overall B and VHI values, but does not make a significant improvement in these model performance metrics at high quantiles of precipitation.

54 ENVIRONMENTAL SCIENCES↗

Boosting to Amplify Signal with Isobaric Labeling (BASIL) Strategy for Comprehensive Quantitative Phosphoproteomic Characterization of Small Populations of Cells

Comprehensive phosphoproteomic analysis of small populations of cells remains a daunting task due primarily to the insufficient MS signal intensity from low concentrations of enriched phosphopeptides. Isobaric labeling has a unique multiplexing feature where the “total” peptide signal from all channels (or samples) triggers MS/MS fragmentation for peptide identification while the reporter ions provide quantitative information. In light of this feature, we tested the concept of using a “boosting” sample (e.g., a biological sample mimicking the study samples but available in much larger quantity) in multiplexed analysis to enable sensitive and comprehensive quantitative phosphoproteomic measurements with <100,000 cells. This simple Boosting to Amplify Signal with Isobaric Labeling (BASIL) strategy increased the overall number of quantifiable phosphorylation sites more than 4-fold. Good reproducibility in quantification was demonstrated with a median CV of 15.3% and Pearson correlation coefficient of 0.95 from biological replicates. A proof-of-concept experiment demonstrated the ability of BASIL to distinguish acute myeloid leukemia cells based on the phosphoproteome data. Moreover, in a pilot application, this strategy enabled quantitative analysis of over 20,000 phosphorylation sites from human pancreatic islets treated with interleukin-1ß and interferon-gamma. Together, this signal boosting strategy provides an attractive solution to comprehensive and quantitative phosphoproteome profiling of relatively small populations of cells where traditional phosphoproteomic workflows provide insufficient sensitivity.

phosphorylation, phosphoproteomics, pancreatic isl↗

Remote sensing of Pu in uranyl nitrate crystals using reflectance spectroscopy and chemometrics

Remote quantification of Pu(VI) (0–5 mol%) co-crystallized with U in uranyl nitrate hexahydrate (UNH) crystals was achieved in a glove box using reflectance spectroscopy coupled with chemometric modeling. Reflectance spectra were also acquired for Pu(IV) and Np(VI) (0–5 mol%) crystallized with UNH; revealing spectral features consistent with their solution-phase analogs. Principal component analysis revealed Pu(IV/VI) and Np(VI) concentrations as the primary source of variation in the data, informing the development of a supervised partial least squares regression model for Pu(VI). The resulting calibration demonstrated robust performance, with replicate root mean square errors near 10% and quantifiable limits near 0.2 mol% Pu(VI) relative to U. The Pu(VI) remained stable in the crystalline UNH matrix for at least one week with minimal reduction to Pu(IV). Notably, Pu(VI) and Np(VI) incorporation in UNH quenched U(VI) fluorescence while Pu(IV) did not. This study presents a noninvasive, spectroscopic approach for solid-state Pu quantification, with direct implications for material accountability and nuclear nonproliferation monitoring.

Sadergaski, Luke R. [Oak Ridge National Laboratory↗

High-Fidelity Calibration and Characterization of Hyperspectral Computed Tomography System

This document archives the results developed by the Lab Directed Research and Development (LDRD) project sponsored by Sandia National Laboratories (SNL). In this work, a numerical study was performed to show the feasibility of approximating the non-linear operator of SNL's unique high-energy hyperspectral computed tomography system as a sequence of linear operators. The four main results gained from this work include the development of a simulation test-bed using a particle-transport Monte Carlo approach; the demonstration to assemble a linear operator of almost-arbitrary resolution for a given narrow energy window, developing a compression approach to dramatically reduce the size of the linear operator via a spline approach, and the demonstration of using the linear operator to perform processing of x-ray data; in this case, the development of an iterative reconstruction method. This numerical study has indicated that if these results can be replicated on the SNL system, the improved performance could be revolutionary as the method to approximate the nonlinear operator for a hyperspectral CT system is not feasible to perform on a traditional CT system.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

The Hidden Flexibility of the Natural Gas Network for Electric Power Operations: A Case Study of a Near-Miss Winter Event

The U.S. power sector has become increasingly reliant on gas pipeline networks to deliver fuel to natural gas power plants. In addition to supplying relatively low-cost fuel, gas networks offer generators flexibility in their operations through the ability to deliver fuel when needed by using gas storage facilities or linepack if the gas network is at an operating point below its design capacity. However, disruptions or stress events on the gas network - like those occurring in the Northeast and Texas in recent years - can result in limitations on gas availability to generators at times when generation is in short supply. Here we examine a period of stress that occurred in the winter of 2022 in the Western United States. Using data on the region's natural gas pipeline network and electric generators, we build an integrated gas and electric model that closely replicates the actual dispatch of the period. We then evaluate the implications of removing flexibility employed by the gas network operator, which during that period curtailed scheduled gas deliveries to other parties to increase deliveries to natural gas power plants, which requested more gas than initially forecasted. We find that without the flexibility supplied by the gas network operator, there would have been curtailment of gas generation due to gas offtake constraints, requiring the power system operator to redispatch relying on more expensive generation or to potentially shed load. A sensitivity exploring a wind drought further exacerbates the strain, illustrating the potential challenge of managing gas and grid interactions as systems move to higher shares of variable renewable electricity. Based on this example, we discuss potential coordination strategies between the two system operators to ensure that the power system can successfully utilize and rely on the flexibility offered by natural gas networks.

03 NATURAL GAS↗