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At least 19 records

Deciphering Microbial Metal Toxicity Responses using RB-TnSeq and Activity-Based Metabolomics

To uncover metal toxicity targets and defense mechanisms of the facultative anaerobe Pantoea sp. strain MT58 (MT58), we used a multiomic strategy combining two global techniques, random bar code transposon site sequencing (RB-TnSeq) and activity-based metabolomics. MT58 is a metal-tolerant Oak Ridge Reservation (ORR) environmental isolate that was enriched in the presence of metals at concentrations measured in contaminated groundwater at an ORR nuclear waste site. The effects of three chemically different metals found at elevated concentrations in the ORR contaminated environment were investigated: the cation Al 3+ , the oxyanion CrO 4 2- , and the oxycation UO 2 2+ . Both global techniques were applied using all three metals under both aerobic and anaerobic conditions to elucidate metal interactions mediated through the activity of metabolites and key genes/proteins. These revealed that Al 3+ binds intracellular arginine, CrO 4 2- enters the cell through sulfate transporters and oxidizes intracellular reduced thiols, and membrane-bound lipopolysaccharides protect the cell from UO 2 2+ toxicity. In addition, the Tol outer membrane system contributed to the protection of cellular integrity from the toxic effects of all three metals. Likewise, we found evidence of regulation of lipid content in membranes under metal stress. Individually, RB-TnSeq and metabolomics are powerful tools to explore the impact various stresses have on biological systems. In this work, we show that together they can be used synergistically to identify the molecular actors and mechanisms of these pertubations to an organism, furthering our understanding of how living systems interact with their environment.

59 BASIC BIOLOGICAL SCIENCES↗

New Techniques and Data for Understanding the Global Soil Respiration Flux

Abstract Soil respiration ( R s ; the soil surface‐to‐atmosphere CO 2 flux) has been measured in the field for decades, but only recently have we begun to assemble and leverage these small‐scale but extensive data. Recently, Zhao et al. (2017, https://doi.org/10.1002/2016ef000480 ) applied a novel artificial neural network model to the problem of estimating the global R s flux and understanding its variations between regions and biomes. Their results point to a convergence in estimates of global R s , and the power of leveraging the long record of observed R s in global ecosystems, but also to uncertainties about soils' response to climate change. It will take a combination of long‐term studies, data syntheses, modeling intercomparisons, and probably a new generation of sampling networks and experiments to fully resolve these questions.

Bond‐Lamberty, Ben↗

Event Horizon Telescope imaging of the archetypal blazar 3C 279 at an extreme 20 microarcsecond resolution

3C 279 is an archetypal blazar with a prominent radio jet that show broadband flux density variability across the entire electromagnetic spectrum. We use an ultra-high angular resolution technique – global Very Long Baseline Interferometry (VLBI) at 1.3 mm (230 GHz) – to resolve the innermost jet of 3C 279 in order to study its fine-scale morphology close to the jet base where highly variable γ-ray emission is thought to originate, according to various models. The source was observed during four days in April 2017 with the Event Horizon Telescope at 230 GHz, including the phased Atacama Large Millimeter/submillimeter Array (ALMA), at an angular resolution of ∼20 μas (at a redshift of z = 0.536 this corresponds to ∼0.13 pc ∼ 1700 Schwarzschild radii with a black hole mass MBH = 8 × 108 M⊙). Imaging and model-fitting techniques were applied to the data to parameterize the fine-scale source structure and its variation. We find a multicomponent inner jet morphology with the northernmost component elongated perpendicular to the direction of the jet, as imaged at longer wavelengths. The elongated nuclear structure is consistent on all four observing days and across different imaging methods and model-fitting techniques, and therefore appears robust. Owing to its compactness and brightness, we associate the northern nuclear structure as the VLBI “core”. This morphology can be interpreted as either a broad resolved jet base or a spatially bent jet. We also find significant day-to-day variations in the closure phases, which appear most pronounced on the triangles with the longest baselines. Our analysis shows that this variation is related to a systematic change of the source structure. Two inner jet components move non-radially at apparent speeds of ∼15 c and ∼20 c (∼1.3 and ∼1.7 μas day−1, respectively), which more strongly supports the scenario of traveling shocks or instabilities in a bent, possibly rotating jet. The observed apparent speeds are also coincident with the 3C 279 large-scale jet kinematics observed at longer (cm) wavelengths, suggesting no significant jet acceleration between the 1.3 mm core and the outer jet. The intrinsic brightness temperature of the jet components are ≲1010 K, a magnitude or more lower than typical values seen at ≥7 mm wavelengths. The low brightness temperature and morphological complexity suggest that the core region of 3C 279 becomes optically thin at short (mm) wavelengths.Key words: galaxies: active / galaxies: jets / galaxies: individual: 3C 279 / techniques: interferometric⋆ The data are only available at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/cat/J/A+A/640/A69 and at https://eventhorizontelescope.org/for-astronomers/data⋆⋆ Deceased.

79 ASTRONOMY AND ASTROPHYSICS↗

In Situ Determination of Thermoelastic Properties of Magnesite at High Pressure and Temperature With Implications to Seismic Detectability of Moderately Carbonated Lithologies in the Earth's Mantle

Abstract Subduction of carbonate‐bearing oceanic plates into Earth's interior recycles carbon from the surface to the deep mantle. The subducted carbonates can significantly affect mantle properties and dynamics. Magnesite is recognized as one of the major potential carbon hosts in the deep mantle because of its stability up to deep lower mantle conditions. However, despite many previous studies on the equation of state and elastic properties of magnesite, large discrepancies still exist for its elastic moduli and their pressure and temperature derivatives. Here we report in situ density and elastic wave velocity measurements on a natural magnesite at simultaneous high pressure‐temperature conditions up to ∼8 GPa–1073 K in a multi‐anvil apparatus using ultrasonic and synchrotron X‐ray techniques. Global fitting of the data set to finite strain equations yieldsK S0 = 114.0 ± 1.2 GPa, = 4.9 ± 0.3, = (−0.019 ± 0.002) GPa/K,G 0 = 68.6 ± 0.4 GPa,G′ = 1.6 ± 0.1, and = (−0.018 ± 0.001) GPa/K. Compared to other major upper mantle and transition zone minerals, magnesite has intermediateV P , the lowestV S , and the lowest density. Thus, magnesite possesses higherV P /V S ratio than other mantle minerals in normal mantle regions, whereas this feature is less pronounced in subduction zone environments. Modeling of the velocity profiles of carbonated lithologies along different geotherms suggests that moderately‐enriched magnesite domains are unlikely to be detected seismically in the Earth's mantle.

Geochemistry & Geophysics↗

Calibration of reactive burn and Jones-Wilkins-Lee parameters for simulations of a detonation-driven flow experiment with uncertainty quantification

Here, uncertainties in the explosive-specific parameters of the Jones-Wilkins-Lee (JWL) equation of state (EOS) are carefully considered in hydrodynamic simulations of an explosive experiment to minimize the error in the flow prediction. Experimental data of the leading shock position in the transverse direction over time serves as the prediction metric for quantifying simulation prediction error. The uncertainty quantification technique, global sensitivity analysis, is utilized to determine the JWL parameters to which the transverse shock propagation is most sensitive. A polynomial response surface (PRS) is constructed in the space of the most influential JWL parameters, and the point of minimum error between the experimental data and the PRS yields calibrated JWL parameters for the experimental flow. The simulation results following the parameter calibration show good agreement with the experimental data. It was found that two significant parameters, the heat release per unit mass of reactant Q and JWL model exponent R 1 are strongly related, which makes it difficult to identify accurate values.

36 MATERIALS SCIENCE↗

Global Optimization of Chemical Cluster Structures: Methods, Applications, and Challenges

Chemical clusters are relevant to many applications in catalysis, separations, materials, and energy sciences. Experimentally, the structure of clusters is difficult to determine, but it is very important in understanding their chemistry and properties. Computational methods can be used to examine cluster structure, however finding the most stable structure is not simple, particularly as the cluster size increases. Global optimization techniques have long been used to tackle the problem of the most stable structure, but such approaches would have to look for a global minimum, while sampling local minima over the whole potential energy surface as well. In this review, the state-of-the-art theory of global optimization theory is summarized. First, the definition, significance, relation to experiments, and a brief history of global optimization is presented. We then discuss, in more detail, three versatile global optimization methods: the basin hopping, the artificial bee colony algorithm, and the genetic algorithm. We close with some representative application examples of global optimization of clusters since 2016 and the challenges, open questions and opportunities in this field.

Global optimization, Chemical clusters, Artificial↗

P-Mart: Interactive Analysis of Ion Abundance Global Proteomics Data

The use of mass-spectrometry-based techniques for global protein profiling of biomedical or environmental experiments has become a major focus in research centered on biomarker discovery; however, one of the most important issues recently highlighted in the new era of omics data generation is the ability to perform analyses in a robust and reproducible manner. This has been hypothesized to be one of the issues hindering the ability of clinical proteomics to successfully identify clinical diagnostic and prognostic biomarkers of disease. P-Mart (https://pmart.labworks.org) is an interactive web-based software environment that enables domain scientists to perform quality-control processing, statistics, and exploration of large-complex proteomics data sets without requiring statistical programming. P-Mart is developed in a manner that allows researchers to perform analyses via a series of modules, explore the results using interactive visualization, and finalize the analyses with a collection of output files documenting all stages of the analysis and a report to allow reproduction of the analysis.

59 BASIC BIOLOGICAL SCIENCES↗

Local and Global Sensitivity Analysis of a Reactive Transport Model Simulating Floodplain Redox Cycling

Reactive transport models (RTMs) are essential tools that simulate the coupling of advective, diffusive, and reactive processes in the subsurface, but their complexity makes them difficult to understand, develop and improve without accompanying statistical analyses. Although global sensitivity analysis (SA) can address these issues, the computational cost associated with most global SA techniques limits their use with RTMs. In this study, we apply distance-based generalized sensitivity analysis (DGSA), a novel and computationally efficient method of global SA, to a floodplain-scale RTM and compare DGSA results to those from local SA. Our test case focuses on the impact of 17 uncertain environmental parameters on spatially and temporally variable redox conditions within a floodplain aquifer. The input parameters considered include flow and diffusion rates, geochemical reaction rates, and the spatial distribution of sediment facies. Sensitivity was evaluated for three distinct components of the model response, encompassing both multidimensional and categorical output. Parameter rankings differ between local SA and DGSA, due to nonlinear effects of individual parameters and interaction effects between parameters. DGSA results show that fluid residence time, which is controlled by aquifer permeability, generally exerts a stronger control on redox conditions than do geochemical reaction rates. Sensitivity indices also demonstrate that sulfate reduction is key for establishing and maintaining reducing conditions throughout the aquifer. Furthermore, these results provide insights into the key drivers of heterogeneous redox processes within floodplain aquifers, as well as the main sources of uncertainty when modeling complex subsurface systems.

54 ENVIRONMENTAL SCIENCES↗

A User-Friendly GUI Tool for Automated Microstructural Analysis of Fiber-Reinforced Composites and Porous Structures

Understanding and quantifying microstructural features such as fiber orientation and porosity is critical for predicting the mechanical behavior and performance of fiber-reinforced polymer composites. Traditional manual analysis is time-consuming, subjective, and unsuitable for high-throughput datasets. We present a graphical user interface (GUI) application that automates the analysis of microscopy images to extract key microstructural metrics, including fiber orientation tensors, fiber orientation distribution, porosity and pore size distribution. The app integrates multiple image segmentation techniques including global and local thresholding, clustering, and region-based approaches, offering flexibility for different types of image qualities and features. Users can load microstructural images, select regions of interest and segmentation techniques tailored to their image dataset. It also addresses a critical challenge in fiber orientation analysis: the ambiguities caused by touching, overlapping, or partially cut fibers. It supports autorun examples for standardized workflows, enabling reproducible analysis and facilitating training and benchmarking. This tool significantly reduces manual intervention, enhances consistency, and accelerates data generation for structure–property modeling, process optimization, and digital materials research. The tool is intended for use by materials scientists, engineers, and researchers engaged in composite characterization, quality control, and machine learning-based microstructural studies.

Chawla, Komal [ORNL] (ORCID:0000000190327565)↗

Assessing Effects of Climate Change on Legacy Waste at the Enewetak Atoll

The Republic of the Marshall Islands (RMI) is in the central Pacific Ocean ~4,500 km west of Hawaii. The Enewetak Atoll, located in the northwest part of the RMI, was the site for 43 nuclear weapon tests between 1948 and 1958. Fallout and deposition from the tests contaminated the island surfaces, lagoon waters and sediment, and nearby ocean waters at the atoll. In the 1970s, a cleanup effort collected radioactive waste and placed it in the Cactus Crater on Runit Island (also called the Runit Dome). In December 2021, Congress directed the U.S. Department of Energy to study the impacts of climate change on the Runit Dome nuclear waste disposal site. Pacific Northwest National Laboratory (PNNL) assembled a multidisciplinary team of climate scientists, ocean modelers, environmental scientists, and health physicists to assess the likely effects of remaining radionuclides at the Enewetak Atoll. PNNL’s approach focused on effects of tropical cyclones that were postulated to mobilize and transport contaminated lagoon sediments and result in human and biota exposure. PNNL’s study estimated (1) the radionuclide source term, (2) the effects of climate change on severe storms, (3) mobilization and transport of radionuclides, and (4) radiation dose to humans and biota. Radionuclides in the lagoon and/or ocean waters of the Enewetak Atoll were characterized by the U.S. Atomic Energy Commission (AEC) in 1972, Woods Hole Oceanographic Institution in 2015, and Lawrence Livermore National Laboratory in 2018. The RMI Nationwide Radiological Study was conducted in the early 1990s for radionuclides remaining in island soils. The 1972 AEC survey remains the most comprehensive source of radionuclide data on lagoon sediments. Climate change modeling at a regional scale in the central Pacific Ocean is limited. PNNL climate scientists simulated severe historical storms postulated to occur both in a recent climate (2015) and in the future (2090) using the Advanced Research Weather Research and Forecasting (WRF-ARW) model, employing a pseudo-global-warming technique. A postulated complete, future failure of the Runit Dome was also considered. PNNL developed a high-resolution regional ocean hydrodynamics model covering the entire RMI extended economic zone using the Finite Volume Coastal Ocean Model (FVCOM). The FVCOM model was run using global reanalysis data for current climate and WRF-ARW simulation for the future climate. PNNL also developed a radionuclide fate and transport model using the FVCOM Integrated Compartment Model (FVCOM-ICM) to simulate the current and future mobilization and transport of radionuclides sorbed to lagoon sediments and the exchange of radionuclides between the water and sediment. FVCOM-ICM-predicted radionuclide concentrations were then used to estimate radiation dose to humans and biota at all islands of the Enewetak Atoll. Under current climate conditions, annual radiation exposures for the southern islands including Enewetak (Fred) and Medren (Elmer) were below the current U.S. standards. Radiation doses were somewhat elevated starting at Runit Island northward and westward to Enjebi Island (Janet). The islands in the northwest quadrant, particularly Bokoluo (Alice) and Bokombako (Belle), remain relatively contaminated. The islands in the southwestern quadrant have low contamination. The highest contribution to radiation doses comes from consumption of locally grown foods. Two radionuclides, 90Sr and 137Cs, contributed the greatest fraction for most terrestrial foods. In current climate conditions, the storms temporarily increased radionuclide concentrations in the lagoon waters, increasing the radiation dose slightly. In future conditions, doses are expected to be smaller, primarily because of the radioactive decay of the shorter-lived radioisotopes of 90Sr and 137Cs. This could make all islands in the far northwest of the atoll – except Bokombako (Belle) and perhaps Bokoluo (Alice) – suitable for residency. For the f

Prasad, Rajiv↗

A Bi-Level Formulation And Solution Method For The Integration Of Process Design And Scheduling

Design and operation decisions of manufacturing plants can often be expressed within a hierarchical structure, where optimal decisions at lower operating level provide constraints for the decision raking at a higher decision level. In this work, we are addressing the case of a hierarchical design and scheduling optimization problem. The integration of design and scheduling decisions can play a big role in designing economically profitable plants and improving their operational performance. This problem can be expressed as a bi-level problem, where design related decisions occur at the upper level and operational scheduling decisions at the lower level. Since discrete decisions are involved in both optimization levels, the resulting formulation typically corresponds to bi-level mixed-integer programming problems (B-MIP). The solution of B-MIP problems is very challenging, and typically requires the use of global optimization techniques, with many algorithms not able to guarantee feasibility. To overcome the challenges in solving this class of problems we propose the use of a multi-parametric based algorithm for the solution of bi-level mixed-integer linear and quadratic programming problems, capable of providing the exact and global solution. The main idea of this approach is to treat the lower scheduling problem as a multi-parametric programming problem in which the design decisions are considered as parameters. Here, the resulting parametric solutions can then be substituted into the upper level design problem, which can be solved as a set of single-level deterministic programming problems. Through the developed formulation and algorithm we are able to supply the decision makers with the exact solution of the integrated design and scheduling problem.

42 ENGINEERING↗

Predicting temperature-dependent ultimate strengths of body-centered-cubic (BCC) high-entropy alloys

This paper presents a bilinear log model, for predicting temperature-dependent ultimate strength of high-entropy alloys (HEAs) based on 21 HEA compositions. We consider the break temperature, T break , introduced in the model, an important parameter for design of materials with attractive high-temperature properties, one warranting inclusion in alloy specifications. For reliable operation, the operating temperature of alloys may need to stay below T break . We introduce a technique of global optimization, one enabling concurrent optimization of model parameters over low-temperature and high-temperature regimes. Furthermore, we suggest a general framework for joint optimization of alloy properties, capable of accounting for physics-based dependencies, and show how a special case can be formulated to address the identification of HEAs offering attractive ultimate strength. We advocate for the selection of an optimization technique suitable for the problem at hand and the data available, and for properly accounting for the underlying sources of variations.

36 MATERIALS SCIENCE↗

An Evaluation of Dynamical Downscaling Methods Used to Project Regional Climate Change

In the past decade, dynamical downscaling using “pseudo-global-warming” (PGW) techniques has been applied frequently to project regional climate change. Such techniques generate signals by adding mean global climate model (GCM)-simulated climate change signals in temperature, moisture, and circulation to lateral and surface boundary conditions derived from reanalysis. An alternative to PGW is to downscale GCM data directly. This technique should be advantageous, especially for simulation of extremes, since it incorporates the GCM's full spectrum of changing synoptic-scale dynamics in the regional solution. Here, we test this assumption, by comparing simulations in Europe and Western North America. We find that for warming and changes in temperature extremes, PGW often produces similar results to direct downscaling in both regions. For mean and extreme precipitation changes, PGW generally also performs surprisingly well in many cases. Moisture budget analysis in the Western North America domain reveals why. Large fractions of the downscaled hydroclimate changes arise from mean changes in large-scale thermodynamics and circulation, that is, increases in temperature, moisture, and winds, included in PGW by design. The one component PGW may have difficulty with is the contribution from changes in synoptic-scale variability. When this component is large, PGW performance could be degraded. Global analysis of GCM data shows there are regions where it is large or dominant. Hence, our results provide a road map to identify, through GCM analyses, the circumstances when PGW would not be expected to accurately regionalize GCM climate signals.

54 ENVIRONMENTAL SCIENCES↗

Benchmarking image processing techniques for porosity measurement in polymer additive manufacturing: Review and experimental analysis

An image processing workflow is proposed for porosity measurement in polymer additive manufacturing. Various techniques, including global and local thresholding, region growing, and K-means clustering, were applied to microscopic images of carbon fiber reinforced acrylonitrile butadiene styrene (CF-ABS) and benchmarked for their ability to accurately measure porosity. Global methods included Otsu, minimum error, iterative, and entropy-based thresholding, while local methods included Niblack, Bernsen, Sauvola, and Bradley-Roth algorithms. Artificial uneven illumination was introduced to test local adaptive thresholds. Results showed significant differences in porosity values across methods. Otsu, region growing, and K-means clustering excelled under uniform illumination, while Sauvola and Bradley-Roth performed better with uneven illumination. Comparison with X-ray computed tomography (XCT) revealed slightly lower porosity values (2.55 %) than optimized methods (2.73–2.79 %) due to XCT's lower resolution excluding smaller pores. While XCT offers finer pore detection, it limits sample volume and underestimates porosity due to spatial variation. Validation using artificial grayscale images with 5 % porosity confirmed that Otsu, Bradley-Roth, region growing, and Sauvola algorithms produced accurate results. Although tested on a single material system, these methods can be adapted to others with optimization. In conclusion, given XCT's high computational and time costs, this study highlights suitable image processing techniques as cost-effective alternatives for porosity analysis in polymer composites.

Additive manufacturing↗

Direct sensitivity analysis on the parameterization of crystal plasticity models

Various methods for calibrating crystal plasticity finite element (CPFE) models lead to non-unique input parameter values, which subsequently introduce uncertainty in the predicted mechanical response. Sensitivity analysis (SA) conducted on crystal plasticity models is used to identify how variability in these parameters contribute to output uncertainty. Traditional SA on CPFE parameters uses simplified surrogate models to save computational time. However, the accuracy of the surrogate models depends on the quantity of training data used, and any modeling error can propagate into the SA results, potentially affecting their reliability. In this work, the elementary effects test (EET) method, a global SA technique using direct CPFE simulations was employed, and the results obtained were compared with the First Order Second Moment (FOSM) method. ExaConstit, an open-source GPU-enabled CPFE code, was used to perform the simulations and direct SA. The EET method was accurately able to capture the non-linear effects of all the input parameters on the output and is a valuable approach for reliably attributing parameter sensitivities in CPFE models. Based on the results, efficient strategies to perform future parameter calibration and SA are discussed. Additionally, the SA trends observed in different single crystal orientations closely mirrored the activity of the slip systems.

Elementary Effects Test↗

Proposed Critical Thinking Metrics for Power Grid Trainees

The TRS Intro to Critical Thinking for Operational Decision-Making course for power grid operators seeks to help trainees improve their use of critical thinking skills in operation environments. To determine the effectiveness of this training, we have identified 3 categories of evaluation measures: critical thinking metrics, situation awareness (SA) evaluations, and behavioral observations. Critical thinking metrics seek to directly measure trainee’s ability to use critical thinking skills through their verbalized responses to different questions or scenarios. SA will be evaluated during various points throughout simulated exercises completed during the training. SA evaluations aim to determine the level of a trainee’s ability to perceive, comprehend and anticipate events in the operational environment. This construct will be assessed through verbalized responses to questions informed by the Situation Awareness Global Assessment Technique (SAGAT). Behavioral observations capture how trainees use the system, including which simulator displays or windows they use or actions they perform and in what order. These observations help us understand how the critical thinking training may inform operator action. We hypothesize that while these measures are correlated with each other, they provide different perspectives on each trainee’s ability to gain SA and use critical thinking skills in operation environments. By comparing these measures in a pre-assessment and a post-assessment, we can determine how much improvement a trainee gains through the training. These measures may also be used during the training as appropriate. This document specifies these 3 categories of measures, which components of these measures currently seem to be the best candidates to use in the training course, and which parts of the training course is related to each component.

24 POWER TRANSMISSION AND DISTRIBUTION↗

A new mathematical approach to finding global solutions of the magnetic structure determination problem

Abstract Determination of magnetic structure is an important analytical procedure utilized in various fields ranging from fundamental condensed-matter physics and chemistry to advanced manufacturing. It is typically performed using a neutron diffraction technique; however, finding global solutions of the magnetic structure optimization problem represents a significant challenge. Generally, it is not possible to mathematically prove that the obtained magnetic structure is a truly global solution and that no solution exists when no acceptable structure is found. In this study, the global optimization technique called semidefinite relaxation of quadratic optimization, which has attracted much interest in the field of applied mathematics, is proposed to use as a new analytical method for the determination of magnetic structure, followed by the application of polarized neutron diffraction data. This mathematical approach allows avoiding spurious local solutions, decreasing the amount of time required to find a tentative solution and finding multiple solutions when they exist.

97 MATHEMATICS AND COMPUTING↗