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At least 217 records · Page 12

Integration of ultra-low coverage whole-genome sequences for reconstructing the evolutionary history of Galapagos giant tortoises

Genomic data from contemporary and historical samples often need to be coupled for evolutionary reconstructions of multitaxon complexes. However, the genetic data recovered from historical samples may result only in ultra-low coverage whole-genome sequences (ulcWGS; <0.15× depth), leading to inaccurate evolutionary inferences given a preponderance of missing data. Using the Galapagos giant tortoise radiation as a study system (Chelonoidis spp., composed of 13 extant and four extinct lineages), we assembled a novel methodological pipeline that removes potential noise introduced by the missing data and enhances the evolutionary signal from ulcWGS samples. We leveraged existing tools for phylogenomic placement (EPA-ng), population genomic structure (smartsnp) and admixture (Admixfrog, NGSadmix) to demonstrate that the evolutionary history of samples can be uncovered with sequencing depths as low as 0.008–0.139×. Importantly, these approaches do not use genotype imputation of the ulcWGS samples, which would require extensive reference datasets. Our application to two cases of extinct lineages of Galapagos giant tortoises, with and without references from the same lineage, demonstrates the general value of the approach. We confirm where the extinct lineages from San Cristóbal and Santa Fe islands fit into the Galapagos giant tortoise radiation, and that these lineages were evolutionarily distinct entities.

ancient DNA↗

Building thermal load prediction through shallow machine learning and deep learning

Building thermal load prediction informs the optimization of cooling plant and thermal energy storage. Physics-based prediction models of building thermal load are constrained by the model and input complexity. In this study, we developed 12 data-driven models (7 shallow learning, 2 deep learning, and 3 heuristic methods) to predict building thermal load and compared shallow machine learning and deep learning. The 12 prediction models were compared with the measured cooling demand. It was found XGBoost (Extreme Gradient Boost) and LSTM (Long Short Term Memory) provided the most accurate load prediction in the shallow and deep learning category, and both outperformed the best baseline model, which uses the previous day's data for prediction. Then, we discussed how the prediction horizon and input uncertainty would influence the load prediction accuracy. Major conclusions are twofold: first, LSTM performs well in short-term prediction (1 h ahead) but not in long term prediction (24 h ahead), because the sequential information becomes less relevant and accordingly not so useful when the prediction horizon is long. Second, the presence of weather forecast uncertainty deteriorates XGBoost's accuracy and favors LSTM, because the sequential information makes the model more robust to input uncertainty. Training the model with the uncertain rather than accurate weather data could enhance the model's robustness. Finally, our findings have two implications for practice. First, LSTM is recommended for short-term load prediction given that weather forecast uncertainty is unavoidable. Second, XGBoost is recommended for long term prediction, and the model should be trained with the presence of input uncertainty.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Kinetic, metabolic, and statistical analytics: addressing metabolic transport limitations among organelles and microbial communities

Microbial organisms engage in a variety of metabolic interactions. A crucial part of these interactions is the exchange of molecules between different organelles, cells, and the environment. The main forces mediating this metabolic exchange are transporters. This transport can be difficult to measure experimentally because several transport mechanisms remain opaque. However, theoretical calculations about the inputs and outputs of cells via metabolic exchanges have enabled the successful inference of the workings of intra-organismal and inter-organismal systems. Kinetic, metabolic, and statistical modeling approaches in combination with omics data are enhancing our knowledge and understanding about metabolic exchange and mass resource allocation. Furthermore, this model-driven analytics approach can guide effective experimental design and yield new insights into biological function and control.

59 BASIC BIOLOGICAL SCIENCES↗

An experimental study on dehumidification and regeneration performance of a new nonporous membrane-based heat and mass exchanger using an ionic liquid desiccant

As a promising alternative to inefficient vapor-compression-based air conditioning, liquid desiccant dehumidification uses a liquid desiccant in contact with the humid air absorbing the moisture. However, it has not gained much market share due to the issues related to the carryover, corrosion, fouling, and crystallization of liquid desiccant. The research has developed a new membrane-based exchanger, which uses a non-corrosive ionic liquid desiccant and nonporous tubular membranes to address these issues. As the second generation of the prototype, the new exchanger was tested at various operating conditions. According to the experimental data, when it is used in the dehumidification loop, the new membrane-based exchanger achieves a specific vapor transportation rate of 778.6 g/(h–m 2 ) and an average water vapor flux of 0.316 g/(h-m 2 -Pa), which is a significant improvement compared with the previous designs using nonporous membranes. It also achieved a comparable or even better dehumidification performance compared with the dehumidifiers that use porous membrane and conventional liquid desiccants. However, the regeneration performance is not as good as its dehumidification. It is mainly caused by the high operating temperature required in the regeneration loop. The experimental data and findings provide first-hand experimental data and enhance the understanding of advanced membrane-based ionic liquid desiccant systems.

42 ENGINEERING↗

Simulation of a TRISO MiniFuel irradiation experiment with data-informed uncertainty quantification

An irradiation experiment using tristructural isotropic (TRISO) fuel particles and the miniature fuel (MiniFuel) irradiation vehicle was performed in Oak Ridge National Laboratory’s High Flux Isotope Reactor (HFIR) to support development of the Kairos Power fluoride salt–cooled, high-temperature reactor (KP-FHR). Here, this paper describes modeling predictions of temperatures and fuel burnup for the as-built experiment. An uncertainty quantification (UQ) analysis was performed to determine the effect of TRISO particle volume and position on the temperature predictions at various fuel heat generation rates (HGRs). This UQ study utilized fuel kernel position and volume measurements previously collected using X-ray computed tomography (XCT) techniques and Monte Carlo sampling methods to generate fuel compact cases that were then analyzed using a finite element thermal model. The UQ analysis indicated that uncertainty in calculated temperatures caused by varying TRISO particle arrangement is relatively small, even at high fuel HGR. Final predictions of particle temperatures throughout the irradiation are shown to be relevant to KP-FHR normal and off-normal operating conditions and to previous TRISO irradiation experiments. The combination of XCT with UQ analyses will inform post-irradiation examination (PIE) of the irradiated fuel compacts, and these analyses can be used to develop fuel performance models for coated particle fuel forms. Both PIE of separate-effects irradiation data and enhanced fuel performance modeling support accelerated qualification of TRISO fuels for a broad range of advanced reactor applications. The novel approach demonstrated here of measuring TRISO particle configurations with XCT methods and generating representative fuel compacts for finite element modeling and UQ analysis could be leveraged by the broader particle fuel community in the development of other TRISO fuel experiments in which these variables may have a significant impact on key outcomes.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Conversion of real-world aluminum scrap streams into high-performance Al–Mg–Si–Cu automotive alloys using shear assisted processing and extrusion

The conversion of post-consumer aluminum (Al) scrap into usable Al alloys without adding primary Al is challenging because of excess impurities. In this work, >99% post-consumer Twitch, used beverage cans (UBCs), and remelt scrap ingots (RSIs) were used as feedstock materials. As-cast and solution heat-treated feedstock billets were extruded using Shear Assisted Processing and Extrusion (ShAPE) at ~510°C, followed by press quenching. To explore the development of the microstructure, texture, and underlying mechanisms and how they contribute to the overall strengthening in as-extruded and artificially aged samples, scanning electron microscopy (SEM) and electron backscatter diffraction (EBSD) were used to collect microstructure and texture data. The enhanced strength and ductility were corroborated with the microstructural features and crystallographic texture. Simple shear $\textrm{A}/\bar{\textrm{A}}$, $\textrm{A}_1^*/\textrm{A} _2^*$ texture components along with weak $\textrm{C}$ and $\textrm{B}/\bar{\textrm{B}}$ texture components were formed during extrusion; the texture was strengthened after heat treatment. The refined second-phase particles helped to retain the deformed microstructure and texture. The contributions of dislocation and precipitate strengthening were maximized when billets were solution-heat-treated prior to extrusion. This is attributed to the formation of effective supersaturated solid solutions during the ShAPE process, which precipitate out during the peak age treatment. Overall, the highest yield strength of 305 MPa, ultimate tensile strength of 350 MPa, and elongation of 12% were achieved in artificially aged samples, which are comparable to those of Al 6082-T6.

Al alloy↗

Summertime Continental Shallow Cumulus Cloud Detection Using GOES‐16 Satellite and Ground‐Based Ceilometer at North Alabama

Abstract Accurate simulations of boundary layer cloud processes remain challenging in Earth system modeling. Observations are essential to evaluate and improve models of such processes. This study introduces a comprehensive validation framework for a satellite‐based detection algorithm of continental shallow cumulus (ShCu) clouds during the daytime, which was initially developed using ground‐based observations of stereo cameras at the Department of Energy Atmospheric Radiation Measurement (ARM) Southern Great Plains site (J. Tian et al., 2021, https://doi.org/10.3390/rs13122309 , 2022, https://doi.org/10.1029/2021gl097070 ). To validate this algorithm, the framework employs ground‐based ceilometer measurements from North Alabama (NA) where ShCu populations are prevalent. This study first generates clear‐sky surface reflectance maps at NA and identifies ShCu pixels with a detection threshold using Geostationary Operational Environmental Satellite (GOES) reflectance data. The obtained cloud fractions (CFs) are then compared against CFs from a ground‐based ceilometer, considering factors such as observed area differences, satellite parallax issue, and systematic biases. We found that with a detection threshold (∆R) of 0.05, the ShCu detection algorithm is effective for NA, enabling the reproduction of hourly ShCu CFs using GOES. Our framework is straightforward and easily repeatable to evaluate the effectiveness of a ∆R threshold for detecting ShCu clouds in various geographic regions where ceilometers are deployed. This satellite detection of ShCu provides a crucial regional context for ground‐based measurements, facilitating the tracking of convection initiation and its coupling with land surface conditions. Integrating localized ground‐based and regional satellite data will enhance our ability to conduct thorough studies of cloud morphology and land‐atmosphere interactions in North Alabama.

54 ENVIRONMENTAL SCIENCES↗

Dynamics of episodic supershear in the 2023 M7.8 Kahramanmaraş/Pazarcik earthquake, revealed by near-field records and computational modeling

Abstract The 2023 M7.8 Kahramanmaraş/Pazarcik earthquake was larger and more destructive than what had been expected. Here we analyzed nearfield seismic records and developed a dynamic rupture model that reconciles different currently conflicting inversion results and reveals spatially non-uniform propagation speeds in this earthquake, with predominantly supershear speeds observed along the Narli fault and at the southwest (SW) end of the East Anatolian Fault (EAF). The model highlights the critical role of geometric complexity and heterogeneous frictional conditions in facilitating continued propagation and influencing rupture speed. We also constrained the conditions that allowed for the rupture to jump from the Narli fault to EAF and to generate the delayed backpropagating rupture towards the SW. Our findings have important implications for understanding earthquake hazards and guiding future response efforts and demonstrate the value of physics based dynamic modeling fused with near-field data in enhancing our understanding of earthquake mechanisms and improving risk assessment.

Environmental Sciences & Ecology↗

Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR

The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Center (BRC) program to assist researchers with analyzing the growing body of genome sequence and other omics-related data. In this report, we describe the merger of the PAThosystems Resource Integration Center (PATRIC), the Influenza Research Database (IRD) and the Virus Pathogen Database and Analysis Resource (ViPR) BRCs to form the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) https://www.bv-brc.org/. The combined BV-BRC leverages the functionality of the bacterial and viral resources to provide a unified data model, enhanced web-based visualization and analysis tools, bioinformatics services, and a powerful suite of command line tools that benefit the bacterial and viral research communities.

59 BASIC BIOLOGICAL SCIENCES↗

Constrained GAN-Generated X-Ray CT Data For Self-Supervised And Foundation-Model Segmentation Of Concrete Microstructures

Three-dimensional characterization of materials using X-ray computed tomography (XCT) is challenging due to the complexity of internal structures, noise, and variations in resolution. Traditional computer vision models often struggle to accurately segment these images, particularly in domain-specific applications like materials science. While supervised deep learning approaches have been developed to address the limitations of conventional algorithms, they typically require large amounts of labeled training data and often fail to generalize across different datasets. Self-supervised, few-and zero-shot learning methods have gained prominence in natural image processing and segmentation tasks, but their application to scientific imaging remains limited due to the unique structural complexity, noise, and textural artifacts present in materials science data. In this work, we investigate how domain adaptation, leveraging physics-based and GAN-generated synthetic data, impacts segmentation performance. We introduce a modified Contrastive Unpaired Translation (CUT) model designed to generate realistic labeled data, which can be used for training, pre-training, and fine-tuning segmentation models for real XCT microstructure data. We evaluate the performance of two segmentation approaches: a self-supervised network (SSL-ALPNet) and a foundation model (Segment Anything Model), assessing their improvements when pre-trained and/or fine-tuned on the synthesized data. Our results demonstrate that leveraging synthetic data significantly enhances segmentation performance, particularly in challenging materials science applications.

Ziabari, Amir [ORNL] (ORCID:000000034776457X)↗

A Consensus Equilibrium Approach for 3-D Land Seismic Shots Recovery

Physical and budget constraints often result in inadequate sampling for accurate subsurface imaging. Preprocessing approaches, such as missing trace interpolation, are typically employed to enhance seismic data in such cases. The compressed sensing (CS) framework has been applied for modeling missing seismic data, which is estimated by sparsity-based computational algorithms. While existing work mainly focuses on recovering missing traces resulting from receiver subsampling, source subsampling has greater economical advantages, as sources are more expensive than receivers. Moreover, stronger image models different from sparsity have not been explored for source recovery. This work presents a consensus equilibrium (CE) approach to recover missing seismic shots, which enables to incorporate various regularization operators modeling different data priors. Here, simulation results from a real 3-D land seismic dataset demonstrate that the CE approach provides more accurate estimations of the linear and hyperbolic events in the recovered shots, compared with pure sparsity-based reconstructions.

58 GEOSCIENCES↗

Coordinate-Based Seismic Interpolation in Irregular Land Survey: A Deep Internal Learning Approach

Physical and budget constraints often result in irregular sampling, which complicates accurate subsurface imaging. Preprocessing approaches, such as missing trace or shot interpolation, are typically employed to enhance seismic data in such cases. Recently, deep learning has been used to address the trace interpolation problem at the expense of large amounts of training data to adequately represent typical seismic events. Nonetheless, most research in this area has focused on trace reconstruction, with little attention having been devoted to shot interpolation. Furthermore, existing methods assume regularly spaced receivers/sources failing in approximating seismic data from real (irregular) surveys. This work presents a novel shot gather interpolation approach which uses a continuous coordinate-based representation of the acquired seismic wavefield parameterized by a neural network. The proposed unsupervised approach, which we call coordinate-based seismic interpolation (CoBSI), enables the prediction of specific seismic characteristics in irregular land surveys without using external data during neural network training. Importantly, experimental results on real and synthetic 3-D data validate the ability of the proposed method to estimate continuous smooth seismic events in the time-space and frequency-wavenumber domains, improving sparsity or low-rank-based interpolation methods.

58 GEOSCIENCES↗

adamantine-sim/adamantine

Thermal field simulation of the additive manufacturing process enhanced using data assimilation.

Turcksin, Bruno [Oak Ridge National Lab. (ORNL), O↗

Iterative ML and Experiments for Emerging VOCs

SAND2026-17074O Iterative ML and Experiments for Emerging VOCs is a tool that analyzes and predicts the behaviors of SARS-CoV-2 variants. It processes experimental data on ACE2 (the receptor for the SARS-CoV-2 virus that allows it to infect the cell) and antibody binding using machine learning models, including neural networks, to forecast ACE2 interactions and variant expression. The tool employs transfer learning and global epistasis modeling, integrating public datasets with proprietary data to enhance prediction accuracy. Additionally, it fits concentration-response curves to determine dissociation constants and generates visualizations to support research findings, thereby aiding in the identification of new antibodies for emerging variants of concern. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Sheffield, Thomas [Sandia National Lab. (SNL-NM), ↗

A 15-Year Retrospective on Immersive Visualization Lessons from the Applied Visualization Laboratory

This article shares the experiences of operating an immersive visualization laboratory over a 15-year period. The paper discusses valuable insights into the lessons learned from various projects, including the challenges they faced, such as technical difficulties, user adoption, and opportunities, and practical solutions for overcoming them. One crucial element for successful immersive visualization projects is interdisciplinary collaboration. The paper presents the advantages of immersive visualization technology, such as improved data comprehension, enhanced communication, and increased engagement in complex scenarios. We present the dynamic realm of virtual and augmented truth (VR/AR) technology in the context of a immersive laboratory system. We spotlight rising trends inside the integration of VR/AR tools for visualization. We also present our experience in dealing with the hardware and software additives in an immersive VR/AR labs, dropping light on the demanding situations and successes encountered throughout everyday operations. Furthermore, it offers practical knowledge and guidance based on years of experience in the field, which can help you overcome challenges and achieve success in your project.

99 GENERAL AND MISCELLANEOUS↗

Data for Intron-Mediated Enhancement of DIACYLGLYCEROL ACYLTRANSFERASE1 Expression in Energycane Promotes a Step Change for Lipid Accumulation in Vegetative Tissues

Metabolic engineering for hyperaccumulation of lipids in vegetative tissues is a novel strategy for enhancing energy density and biofuel production from biomass crops. Energycane is a prime feedstock for this approach due to its high biomass production and resilience under marginal conditions. DIACYLGLYCEROL ACYLTRANSFERASE ( DGAT ) catalyzes the last and only committed step in the biosynthesis of triacylglycerol (TAG) and can be a rate-limiting enzyme for the production of TAG. In this study, we explored the effect of intron-mediated enhancement (IME) on the expression of DGAT1 and resulting accumulation of TAG and total fatty acid (TFA) in leaf and stem tissues of energycane. To maximize lipid accumulation these evaluations were carried out by co-expressing the lipogenic transcription factor WRINKLED1 ( WRI1 ) and the TAG protect factor oleosin ( OLE1 ). Including an intron in the codon-optimized TmDGAT1 elevated the accumulation of its transcript in leaves by seven times on average based on 5 transgenic lines for each construct. Plants with WRI1 (W), DGAT1 with intron (Di), and OLE1 (O) expression (WDiO) accumulated TAG up to a 3.85% of leaf dry weight (DW), a 192-fold increase compared to non-modified energycane (WT) and a 3.8-fold increase compared to the highest accumulation under the intron-less gene combination (WDO). This corresponded to TFA accumulation of up to 8.4% of leaf dry weight, a 2.8-fold or 6.1-fold increase compared to WDO or WT, respectively. Co-expression of WDiO resulted in stem accumulations of TAG up to 1.14% of DW or TFA up to 2.08% of DW that exceeded WT by 57-fold or 12-fold and WDO more than twofold, respectively. Constitutive expression of these lipogenic “push pull and protect” factors correlated with biomass reduction. Intron-mediated enhancement (IME) of the expression of DGAT resulted in a step change in lipid accumulation of energycane and confirmed that under our experimental conditions it is rate limiting for lipid accumulation. IME should be applied to other lipogenic factors and metabolic engineering strategies. The findings from this study may be valuable in developing a high biomass feedstock for commercial production of lipids and advanced biofuels.

Feedstock Production↗

Natural Language Processing-Enhanced Nuclear Industry Operating Experience Data Analysis: Aggregation and Interpretation of Multi-Report Analysis Results

Industry-wide operating experience is a critical source of raw data for reliability and risk model parameter estimations for nuclear power plants. A large portion of operating experience data are failure events stored as reports that contain unstructured data, such as narratives. In current practice, a failure report is usually reviewed and manually coded by analysts. The coding is based on extracting several event characteristics such as system name, component type, sub-part type, failure mode, and failure cause. Event narratives are mostly used to help understand events and extract their characteristics. In this line of research, we aim to maximize the usage of event narratives by leveraging natural language processing (NLP) methods to automatically convert an event narrative to a causal graph. This research has promise to improve physical understanding of failure initiation and propagation and to facilitate use of non-failure data (e.g., near-misses and degradations) to complement the limited data pool of failures. In our previous work, we developed an NLP tool and applied it to analyze a number of licensee event reports submitted by U.S. nuclear power plants to the Nuclear Regulatory Commission. In this paper, we will report our recent research progress in aggregating the results of multiple reports, developing network model(s), and drawing statistical insights.

99 GENERAL AND MISCELLANEOUS↗

Machine learning and LHC event generation

First-principle simulations are at the heart of the high-energy physics research program. They link the vast data output of multi-purpose detectors with fundamental theory predictions and interpretation. This review illustrates a wide range of applications of modern machine learning to event generation and simulation-based inference, including conceptional developments driven by the specific requirements of particle physics. New ideas and tools developed at the interface of particle physics and machine learning will improve the speed and precision of forward simulations, handle the complexity of collision data, and enhance inference as an inverse simulation problem.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗