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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Plant defensin MtDef4–derived antifungal peptide with multiple modes of action and potential as a bio–inspired fungicide

Chemical fungicides have been instrumental in protecting crops from fungal diseases. However, increasing fungal resistance to many of the single-site chemical fungicides calls for the development of new antifungal agents with novel modes of action (MoA). The sequence-divergent cysteine-rich antifungal defensins with multisite MoA are promising starting templates for design of novel peptide-based fungicides. Here, we experimentally tested such a set of 17-amino-acid peptides containing the γ-core motif of the antifungal plant defensin MtDef4. These designed peptides exhibited antifungal properties different from those of MtDef4. Focused analysis of a lead peptide, GMA4CG_V6, showed that it was a random coil in solution with little or no secondary structure elements. Additionally, it exhibited potent cation-tolerant antifungal activity against the plant fungal pathogen Botrytis cinerea, the causal agent of grey mould disease in fruits and vegetables. Its multisite MoA involved localization predominantly to the plasma membrane, permeabilization of the plasma membrane, rapid internalization into the vacuole and cytoplasm, and affinity for the bioactive phosphoinositides phosphatidylinositol 3-phosphate (PI3P), PI4P, and PI5P. The sequence motif RRRW was identified as a major determinant of the antifungal activity of this peptide. While topical spray application of GMA4CG_V6 on Nicotiana benthamiana and tomato plants provided preventive and curative suppression of grey mould disease symptoms, the peptide was not internalized into plant cells. Our findings open the possibility that truncated and modified defensin-derived peptides containing the γ-core sequence could serve as promising candidates for further development of bio-inspired fungicides.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Broadband cross polarization for ultra-wideline magic-angle spinning NMR

Over the past decade, there has been a sustained interest in using frequency-swept (FS) pulses for the efficient acquisition of wideline and ultra-wideline (UW) NMR powder patterns. Such experiments are typically conducted under static conditions, employing both direct- and indirect-excitation methods (i.e., WCPMG and BRAIN-CP/WCPMG, respectively). Recently, Koppe et al. demonstrated that the WCPMG pulse sequence can be used to efficiently acquire wideline and UW NMR spectra with spinning sideband (SSB) manifolds under magic-angle spinning (MAS) conditions, capitalizing on the increased signal-to-noise ratios (SNR) afforded by MAS. To date, there have been only a few instances of broadband cross-polarization (CP) experiments using FS pulses under MAS conditions and no applications to systems exhibiting wideline and/or ultra-wideline powder patterns, despite the clear advantages these experiments could offer. Herein, we demonstrate that FS pulses selectively applied to a single sideband of the S spin can be used for efficient 1 H-S polarization transfer to S = 1/2 nuclides with large anisotropic chemical shift interactions at slow to moderate MAS rates. The Hartmann–Hahn matching conditions in BRAIN-CP/WCPMG-MAS experiments bear similarity to those of standard CP sequences, yet operate over UW frequency ranges and only require low-amplitude RF pulses on the S channel. Crucial to the success of the BRAIN-CP/WCPMG-MAS experiment is careful calibration of the RF amplitude, transmitter offset, and effective frequency sweep of the FS pulse applied to the S spins at a given MAS rate. Thus, by means of numerical simulations and experimental testing, we provide recommendations for the parameterization and setup of BRAIN-CP/WCPMG-MAS experiments for their most efficient use. Results showcasing the capability of the BRAIN-CP/WCPMG-MAS pulse sequence are presented, including applications to 119 Sn, 195 Pt, and 103 Rh NMR.

Kimball, James J. [Florida State University, Talla↗
DOE OSTI2025

Axenisation of oleaginous microalgal cultures via anoxic photosensitisation

Growing interest in sustainable food and biofuel research has necessitated high quality axenic oleaginous microalgal strains. Unfortunately, most strains available in culture banks contain commensal microbes such as bacteria and the default decontamination method involves antibiotic treatment which has begun to exacerbate the emergence of antibiotic resistance. To overcome this problem, anoxic photosensitisation was investigated as an alternate approach. Four oleaginous microalgal species (Tetradesmus obliquus, Desmodesmus armatus, Chlorella vulgaris and Nannochloropsis limnetica) were incubated in varying concentrations of Rose Bengal (0 μM, 1 μM, 3 μM or 9 μM) either in normal (oxic) or anoxic conditions, for 72 h under light (8.85 ± 0.4 W/m 2 ) in a specially designed heterotrophic growth complex (HGC) medium, followed by 72 h in standard Bold's Basal Medium (BBM). Commonly used antibiotics-based protocol was used as the control method. Post treatment, cell numbers and percentage populations were counted with Flow Cytometry, and viability was tested using standard plating methods using BBM and LB. Additionally, the contaminating microbes in the cultures were profiled using 16Ss rRNA sequencing. Anoxic conditions were able to significantly decrease bacterial content, albeit with an equally detrimental effect on the microalgal population. Although the responses differed between the microalgae, anoxic incubation along with Rose Bengal at 3 μM was able to completely decontaminate N. limnetica and C. vulgaris, while D. armatus and T. obliquus could be decontaminated with an additional streak-plating step. None of the cultures could be decontaminated using antibiotics treatment. These results suggest that axenisation of microalgal cultures was largely due to anoxy, that was synergistically enhanced by Rose Bengal at a concentration of ≥3 μM.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Data-driven models of nonautonomous systems

Nonautonomous dynamical systems are characterized by time-dependent inputs, which complicates the discovery of predictive models describing the spatiotemporal evolution of the state variables of quantities of interest from their temporal snapshots. When dynamic mode decomposition (DMD) is used to infer a linear model, this difficulty manifests itself in the need to approximate the time-dependent Koopman operators. Our approach is to approximate the original nonautonomous system with a modified system derived via a local parameterization of the time-dependent inputs. The modified system comprises a sequence of local parametric systems, which are subsequently approximated by a parametric surrogate model using the DRIPS (dimension reduction and interpolation in parameter space) framework. The offline step of DRIPS relies on DMD to build a linear surrogate model, endowed with reduced-order bases for the observables mapped from training data. The online step interpolates on suitable manifolds to construct a sequence of iterative parametric surrogate models; the target/test parameter points on these manifolds are specified by a local parameterization of the test time-dependent inputs. Here, we use numerical experimentation to demonstrate the robustness of our method and compare its performance with that of deep neural networks.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

A data-driven approach to sampling matrix selection for compressive sensing

Sampling is a fundamental aspect of any implementation of compressive sensing. Typically, the choice of sampling method is guided by the reconstruction basis. However, this approach can be problematic with respect to certain hardware constraints and is not responsive to domain-specific context. We propose a method for defining an order for a sampling basis that is optimal with respect to capturing variance in data, thus allowing for meaningful sensing at any desired level of compression. We focus on the Walsh-Hadamard sampling basis for its relevance to hardware constraints, but our approach applies to any sampling basis of interest. We illustrate the effectiveness of our method on the Physical Sciences Inc. Fabry-Perot interferometer sensor multispectral dataset, the Johns Hopkins Applied Physics Lab FTIR-based longwave infrared sensor hyperspectral dataset, and a Colorado State University Swiss Ranger depth image dataset. The spectral datasets consist of simulant experiments, including releases of chemicals such as GAA and SF6. We combine our sampling and reconstruction with the adaptive coherence estimator (ACE) and bulk coherence for chemical detection and we incorporate an algorithmic threshold for ACE values to determine the presence or absence of a chemical. We compare results across sampling methods in this context. We have successful chemical detection at a compression rate of 90%. For all three datasets, we compare our sampling approach to standard orderings of sampling basis such as random, sequency, and an analog of sequency that we term `frequency.' In one instance, the peak signal to noise ratio was improved by over 30% across a test set of depth images.

compressive sensing, hyperspectral imaging, Walsh-↗
DOE OSTI2023

Prescribed fire selects for a pyrophilous soil sub‐community in a northern California mixed conifer forest

Abstract Prescribed fire is a critical strategy for mitigating the effects of catastrophic wildfires. While the above‐ground response to fire has been well‐documented, fewer studies have addressed the effect of prescribed fire on soil microorganisms. To understand how soil microbial communities respond to prescribed fire, we sampled four plots at a high temporal resolution (two burned, two controls), for 17 months, in a mixed conifer forest in northern California, USA. Using amplicon sequencing, we found that prescribed fire significantly altered both fungal and bacterial community structure. We found that most differentially abundant fungal taxa had a positive fold‐change, while differentially abundant bacterial taxa generally had a negative fold‐change. We tested the null hypothesis that these communities assembled due to neutral processes (i.e., drift and/or dispersal), finding that >90% of taxa fit this neutral prediction. However, a dynamic sub‐community composed of burn‐associated indicator taxa that were positively differentially abundant was enriched for non‐neutral amplicon sequence variants, suggesting assembly via deterministic processes. In synthesizing these results, we identified 15 pyrophilous taxa with a significant and positive response to prescribed burns. Together, these results lay the foundation for building a process‐driven understanding of microbial community assembly in the context of the classical disturbance regime of fire.

Microbiology↗
DOE OSTI2024

CovTransformer: A transformer model for SARS-CoV-2 lineage frequency forecasting

With hundreds of SARS-CoV-2 lineages circulating in the global population, there is an ongoing need for predicting and forecasting lineage frequencies and thus identifying rapidly expanding lineages. Accurate prediction would allow for more focused experimental efforts to understand pathogenicity of future dominating lineages and characterize the extent of their immune escape. Here, we first show that the inherent noise and biases in lineage frequency data make a commonly-used regression-based approach unreliable. To address this weakness, we constructed a machine learning model for SARS-CoV-2 lineage frequency forecasting, called CovTransformer, based on the transformer architecture. We designed our model to navigate challenges such as a limited amount of data with high levels of noise and bias. We first trained and tested the model using data from the UK and the USA, and then tested the generalization ability of the model to many other countries and US states. Remarkably, the trained model makes accurate predictions two months into the future with high levels of accuracy both globally (in 31 countries with high levels of sequencing effort) and at the US-state level. Our model performed substantially better than a widely used forecasting tool, the multinomial regression model implemented in Nextstrain, demonstrating its utility in SARS-CoV-2 monitoring. Assuming a newly emerged lineage is identified and assigned, our test using retrospective data shows that our model is able to identify the dominating lineages 7 weeks in advance on average before they became dominant. Overall, our work demonstrates that transformer models represent a promising approach for SARS-CoV-2 forecasting and pandemic monitoring.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

SCALE depletion capabilities for molten salt reactors and other liquid-fueled systems

Nuclear reactor systems that use fuel dissolved in a liquid have the potential for enhanced safety characteristics, improved fuel-cycle outcomes, and more efficient isotope-production configurations. In these reactor systems, the fueled liquid may simultaneously undergo irradiation, physical and chemical removal processes, and fueling. The modeling and simulation of this transmutation and decay with material additions and removals is an ongoing research area. An accurate simulation tool is critical to the reactor and fuel-cycle design, reactor deployment, and source-term characterization for these advanced reactor systems. The work described herein involved implementing, testing, and applying the capability to perform reactor physics simulations within the Oak Ridge National Laboratory-developed SCALE suite for nuclear systems analyses and design, leveraging much of its pedigree in quality-assurance and reactor-analysis capabilities. The functionalities to simulate irradiation with material feeds and removals had been added in ORIGEN, and the TRITON reactor physics sequence was extended to calculate the total removed material and track external nonirradiated mixtures to estimate separate processing or waste streams. Results from these capabilities align with analytical expectations obtained from ORIGEN for simplified test cases and with expectations for a molten salt reactor application. This implementation, available with the SCALE 6.3 release, provides for a more efficient and accurate material accountability methodology, allowing for the characterization, design, and analysis of the complete isotopic material inventory of advanced liquid-fueled systems for a variety of applications.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

Evaluating the mutagenicity of N-nitrosodimethylamine in 2D and 3D HepaRG cell cultures using error-corrected next generation sequencing

Human liver-derived metabolically competent HepaRG cells have been successfully employed in both two-dimensional (2D) and 3D spheroid formats for performing the comet assay and micronucleus (MN) assay. In the present study, we have investigated expanding the genotoxicity endpoints evaluated in HepaRG cells by detecting mutagenesis using two error-corrected next generation sequencing (ecNGS) technologies, Duplex Sequencing (DS) and High-Fidelity (HiFi) Sequencing. Both HepaRG 2D cells and 3D spheroids were exposed for 72 h to N-nitrosodimethylamine (NDMA), followed by an additional incubation for the fixation of induced mutations. NDMA-induced DNA damage, chromosomal damage, and mutagenesis were determined using the comet assay, MN assay, and ecNGS, respectively. The 72-h treatment with NDMA resulted in concentration-dependent increases in cytotoxicity, DNA damage, MN formation, and mutation frequency in both 2D and 3D cultures, with greater responses observed in the 3D spheroids compared to 2D cells. The mutational spectrum analysis showed that NDMA induced predominantly A:T → G:C transitions, along with a lower frequency of G:C → A:T transitions, and exhibited a different trinucleotide signature relative to the negative control. These results demonstrate that the HepaRG 2D cells and 3D spheroid models can be used for mutagenesis assessment using both DS and HiFi Sequencing, with the caveat that severe cytotoxic concentrations should be avoided when conducting DS. With further validation, the HepaRG 2D/3D system may become a powerful human-based metabolically competent platform for genotoxicity testing.

3D spheroids↗
DOE OSTI2024

Graph-learning approach to combine multiresolution seismic velocity models

SUMMARY The resolution of velocity models obtained by tomography varies due to multiple factors and variables, such as the inversion approach, ray coverage, data quality, etc. Combining velocity models with different resolutions can enable more accurate ground motion simulations. Toward this goal, we present a novel methodology to fuse multiresolution seismic velocity maps with probabilistic graphical models (PGMs). The PGMs provide segmentation results, corresponding to various velocity intervals, in seismic velocity models with different resolutions. Further, by considering physical information (such as ray path density), we introduce physics-informed probabilistic graphical models (PIPGMs). These models provide data-driven relations between subdomains with low (LR) and high (HR) resolutions. Transferring (segmented) distribution information from the HR regions enhances the details in the LR regions by solving a maximum likelihood problem with prior knowledge from HR models. When updating areas bordering HR and LR regions, a patch-scanning policy is adopted to consider local patterns and avoid sharp boundaries. To evaluate the efficacy of the proposed PGM fusion method, we tested the fusion approach on both a synthetic checkerboard model and a fault zone structure imaged from the 2019 Ridgecrest, CA, earthquake sequence. The Ridgecrest fault zone image consists of a shallow (top 1 km) high-resolution shear-wave velocity model obtained from ambient noise tomography, which is embedded into the coarser Statewide California Earthquake Center Community Velocity Model version S4.26-M01. The model efficacy is underscored by the deviation between observed and calculated traveltimes along the boundaries between HR and LR regions, 38 per cent less than obtained by conventional Gaussian interpolation. The proposed PGM fusion method can merge any gridded multiresolution velocity model, a valuable tool for computational seismology and ground motion estimation.

Geochemistry & Geophysics↗
DOE OSTI2024

Multiplex detection and identification of viral, bacterial, and protozoan pathogens in human blood and plasma using an expanded high-density resequencing microarray platform

Introduction: Nucleic acid tests for blood donor screening have improved the safety of the blood supply; however, increasing numbers of emerging pathogen tests are burdensome. Multiplex testing platforms are a potential solution. Methods: The Blood Borne Pathogen Resequencing Microarray Expanded (BBP-RMAv.2) can perform multiplex detection and identification of 80 viruses, bacteria and parasites. This study evaluated pathogen detection in human blood or plasma. Samples spiked with selected pathogens, each with one of 6 viruses, 2 bacteria and 5 protozoans were tested on this platform. The nucleic acids were extracted, amplified using multiplexed sets of primers, and hybridized to a microarray. The reported sequences were aligned to a database to identify the pathogen. To directly compare the microarray to an emerging molecular approach, the amplified nucleic acids were also submitted to nanopore next generation sequencing (NGS). Results: The BBP-RMAv.2 detected viral pathogens at a concentration as low as 100 copies/ml and a range of concentrations from 1,000 to 100,000 copies/ml for all the spiked pathogens. Coded specimens were identified correctly demonstrating the effectiveness of the platform. The nanopore sequencing correctly identified most samples and the results of the two platforms were compared. Discussion: These results indicated that the BBP-RMAv.2 could be employed for multiplex detection with potential for use in blood safety or disease diagnosis. The NGS was nearly as effective at identifying pathogens in blood and performed better than BBP-RMAv.2 at identifying pathogen-negative samples.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Special Considerations for the Removal and Disposal of Micro-Reactor Experiments

Idaho National Laboratory (INL) is preparing to host several microreactor experiments through 2030 and beyond. Two new test beds currently under development will operate as microreactor or nuclear system experiment user facilities. Test bed experiments will be performed in series, with each nuclear experiment installed, operated, and removed before installation of the subsequent experiment. The necessarily brief transition period between experiments introduces unique equipment removal and radioactive waste disposal challenges. This paper evaluates equipment removal and radioactive waste management topics associated with tight sequencing of nuclear experiments and presents some of the solutions and approaches currently planned to meet these special considerations for one such experiment, the Molten Chloride Reactor Experiment (MCRE), slated for operation at INL’s Laboratory for Operation and Testing in the United States (LOTUS). The MCRE project is a collaboration between Southern Company Services, TerraPower, and INL, among others, to provide integral nuclear data that will advance molten salt fast reactor technology. MCRE will be the first critical fast-spectrum circulating fuel system ever operated and the first experiment operated in the LOTUS test bed. The experiment will nominally operate at zero power with planned low power excursions as part of operational planning for MCRE has been to minimize at-power operations to limit fission product formation while still achieving experimental objectives. After the experiment is complete, MCRE will be allowed to radioactively decay for a short period (nominally 90 days) prior to system defueling, flushing, removal, and disposal of all MCRE equipment, readying the test bed for the next nuclear experiment. Equipment removal and radioactive waste disposal have been integral to MCRE project planning since the Cooperative Research and Development Agreement was formalized in 2021. Due to requirements for future use of the test bed, the MCRE system, of necessity, must be removed in a much shorter time frame than typical for historic reactor decommissioning projects at INL. This results in minimal time for radioactive decay, resulting in not only elevated radiation dose rates but also the presence of short-to-medium-lived isotopes not typically encountered in the reactor decommissioning and radioactive waste management space. Additional unique constraints placed on the project include lack of intrinsic remote-operations capabilities in the test bed, space constraints in the test bed once MCRE has been installed, and contamination minimization requirements to return the test bed to as-found conditions to enable future use. This paper discusses planned solutions to these challenges. Approaches for implementing remote or semi-remote technologies in a non-hot cell environment with limited space availability are discussed. The paper also summarizes the systems engineering approach for concept development and design of equipment removal systems, which are being implemented concurrent with the MCRE design phase, providing feedback to system designers to incorporate features enabling efficient and safe equipment removal approaches. The timing of this paper at a relatively early phase of the project is meant to highlight the importance of early planning for nuclear system decommissioning while reactor design is ongoing to allow design feedback on componentry driven from decommissioning system needs. As new, innovative nuclear reactor technologies enter the nuclear market sector, reactor experiments are crucial for providing new integral nuclear data that establish safe operational margins for technology advancement. Microreactor experiments at INL will require safe, effective, and timely decommissioning approaches, which in turn require nuclear systems designed to expedite decommissioning. In addition to the advancement of nuclear reactor technologies, these nuclear experiments provide an opportunity to demonstrate, deploy, and test new removal and disposal capabilities to support the next generation of nuclear reactor technology.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

Overestimated prediction using polygenic prediction derived from summary statistics

When polygenic risk score (PRS) is derived from summary statistics, independence between discovery and test sets cannot be monitored. We compared two types of PRS studies derived from raw genetic data (denoted as rPRS) and the summary statistics for IGAP (sPRS). Two variables with the high heritability in UK Biobank, hypertension, and height, are used to derive an exemplary scale effect of PRS. sPRS without APOE is derived from International Genomics of Alzheimer’s Project (IGAP), which records ΔAUC and ΔR 2 of 0.051 ± 0.013 and 0.063 ± 0.015 for Alzheimer’s Disease Sequencing Project (ADSP) and 0.060 and 0.086 for Accelerating Medicine Partnership - Alzheimer’s Disease (AMP-AD). On UK Biobank, rPRS performances for hypertension assuming a similar size of discovery and test sets are 0.0036 ± 0.0027 (ΔAUC) and 0.0032 ± 0.0028 (ΔR 2 ). For height, ΔR 2 is 0.029 ± 0.0037. Considering the high heritability of hypertension and height of UK Biobank and sample size of UK Biobank, sPRS results from AD databases are inflated. Independence between discovery and test sets is a well-known basic requirement for PRS studies. However, a lot of PRS studies cannot follow such requirements because of impossible direct comparisons when using summary statistics. Thus, for sPRS, potential duplications should be carefully considered within the same ethnic group.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Acceleration Factors for Combined‐Accelerated Stress Testing of Photovoltaic Modules

Combined‐accelerated stress testing (C‐AST) is developed to establish the durability of photovoltaic (PV) products, including for degradation modes that are not a priori known or examined in standardized tests. C‐AST aims to comprehensively represent the sample, stress factors, and their combinations using levels at the statistical tails of the natural environment. Acceleration factors for relevant climate sequences within the C‐AST cycle with respect to the Florida USA climate are estimated for selected degradation mechanisms. It is found that for degradation of the outer backsheet polymer layer, the acceleration factor of the tropical climate sequence (the longest of the climate sequences) is f ( T , G ) = 17.3 with ultraviolet photodegradation; for polyethylene terephthalate hydrolysis (backsheets), f ( T , RH ) = 426; for electrochemical corrosion (PV cell), f ( I ) = 14.1; and for PbSn solder fatigue f (Δ T , r ( T )) = 17.3. Here, T is the module temperature, G is the broadband spectrum irradiance on the plane of array of the module, RH is the relative humidity on the module surface, I is the leakage current through the module packaging, and r ( T ), the number of temperature reversals. The methods discussed herein are generally applicable for evaluating acceleration factors in other accelerated test methods.

14 SOLAR ENERGY↗
DOE OSTI2021

Learning to Unknot

We introduce natural language processing into the study of knot theory, as made natural by the braid word representation of knots. We study the UNKNOT problem of determining whether or not a given knot is the unknot. After describing an algorithm to randomly generate N-crossing braids and their knot closures and discussing the induced prior on the distribution of knots, we apply binary classification to the UNKNOT decision problem. We find that the Reformer and shared-QK Transformer network architectures outperform fully-connected networks, though all perform at 95% accuracy. Perhaps surprisingly, we find that accuracy increases with the length of the braid word, and that the networks learn a direct correlation between the confidence of their predictions and the degree of the Jones polynomial. Finally, we utilize reinforcement learning (RL) to find sequences of Markov moves and braid relations that simplify knots and can identify unknots by explicitly giving the sequence of unknotting actions. Trust region policy optimization (TRPO) performs consistently well, reducing 80% of the unknots with up to 96 crossings we tested to the empty braid word, and thoroughly outperformed other RL algorithms and random walkers. Studying these actions, we find that braid relations are more useful in simplifying to the unknot than one of the Markov moves.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Combining compositional data sets introduces error in covariance network reconstruction

Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these statistical associations across kingdoms are more difficult to infer than intra-kingdom associations due to the nature of the data involved using standard network inference techniques. We quantify the challenges of cross-kingdom network inference from both theoretical and practical points of view using synthetic and real-world microbiome data. We detail the theoretical issue presented by combining compositional data sets drawn from the same environment, e.g. 16S and ITS sequencing of a single set of samples, and we survey common network inference techniques for their ability to handle this error. We then test these techniques for the accuracy and usefulness of their intra- and inter-kingdom associations by inferring networks from a set of simulated samples for which a ground-truth set of associations is known. We show that while the two methods mitigate the error of cross-kingdom inference, there is little difference between techniques for key practical applications including identification of strong correlations and identification of possible keystone taxa (i.e. hub nodes in the network). Furthermore, we identify a signature of the error caused by transkingdom network inference and demonstrate that it appears in networks constructed using real-world environmental microbiome data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Wire-arc Additive Manufacturing Benchmark

This is the dataset associated with the 2022 SRP Additive Manufacturing Prediction Challenge, originally hosted on Github at https://github.com/SRP-AM/SRP_AM_Prediction_Challenge. The benchmark was designed for validating prediction for the temperature history, residual stress, and distortion of an additively manufactured metal part with relatively simple geometry. A calibration problem with the same as-built geometry is provided with measured quantities of interest; including temperature histories at selective locations, post-build residual stress at selective locations, and overall distortion measurements. The challenge problem is presented with a different build sequence (i.e. thermal history). In this dataset, we include the actual recorded calibration and challenge measurements, as well as benchmark template files for testing predictions without incorporating the challenge data. Supplementary files around the materials and setup are available for transparency and reproducibility.

Bachus, Nicholas [UC Davis, Davis, CA]↗
DOE OSTI2024

Combining compositional data sets introduces error in covariance network reconstruction

Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these statistical associations across kingdoms are more difficult to infer than intra-kingdom associations due to the nature of the data involved using standard network inference techniques. We quantify the challenges of cross-kingdom network inference from both theoretical and practical points of view using synthetic and real-world microbiome data. We detail the theoretical issue presented by combining compositional data sets drawn from the same environment, e.g. 16S and ITS sequencing of a single set of samples, and we survey common network inference techniques for their ability to handle this error. We then test these techniques for the accuracy and usefulness of their intra- and interkingdom associations by inferring networks from a set of simulated samples for which a ground-truth set of associations is known. We show that while the two methods mitigate the error of cross-kingdom inference, there is little difference between techniques for key practical applications including identification of strong correlations and identification of possible keystone taxa (i.e. hub nodes in the network). Furthermore, we identify a signature of the error caused by transkingdom network inference and demonstrate that it appears in networks constructed using real-world environmental microbiome data.

59 BASIC BIOLOGICAL SCIENCES↗