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At least 847 records · Page 47

Genetic modification of the shikimate pathway to reduce lignin content in switchgrass ( Panicum virgatum L.) significantly impacts plant microbiomes

Switchgrass (Panicum virgatum L.) is considered a sustainable biofuel feedstock, given its fast-impact growth, low input requirements, and high biomass yields. Improvements in bioenergy conversion efficiency of switchgrass could be made by reducing its lignin content. Engineered switchgrass that expresses a bacterial 3-dehydroshikimate dehydratase (QsuB) has reduced lignin content and improved biomass saccharification due to the rerouting of the shikimate pathway towards the simple aromatic protocatechuate at the expense of lignin biosynthesis. However, the impacts of this QsuB trait on switchgrass microbiome structure and function remain unclear. To address this, wild-type and QsuB-engineered switchgrass were grown in switchgrass field soils, and samples were collected from inflorescences, leaves, roots, rhizospheres, and bulk soils for microbiome analysis. We investigated how QsuB expression influenced switchgrass-associated fungal and bacterial communities using high-throughput Illumina MiSeq amplicon sequencing of ITS and 16S rDNA. Compared to wild-type, QsuB-engineered switchgrass hosted different microbial communities in roots, rhizosphere, and leaves. Specifically, QsuB-engineered plants had a lower relative abundance of arbuscular mycorrhizal fungi (AMF). Additionally, QsuB-engineered plants had fewer Actinobacteriota in root and rhizosphere samples. These findings may indicate that changes in the plant metabolism impact both AMF and Actinobacteriota similarly or potential interactions between AMF and the bacterial community. This study enhances understanding of plant-microbiome interactions by providing baseline microbial data for developing beneficial bioengineering strategies and by assessing nontarget impacts of engineered plant traits on the plant microbiome.

09 BIOMASS FUELS↗

Bichromatic Wave Selection for Validation of the Difference-Frequency Transfer Function for the OC6 Validation Campaign: Preprint

The focus of the Offshore Code Comparison Collaboration, Continuation, with Correlation and unCertainity (OC6) project, which operates under the International Energy Agency (IEA) Wind Task 30, is to refine the accuracy of engineering tools used to design offshore wind turbines. In support of this work, a new validation campaign is being developed that seeks to better understand the nonlinear wave loading that excites floating wind systems at their low-frequency, rigid-body modes in surge and pitch. The validation data will be used in a three-way validation between simplified engineering tools and higher-fidelity tools, such as computational fluid dynamics (CFD). Irregular wave spectrums, which are traditionally used to examine the nonlinear wave interaction with offshore structures, are too computationally expensive to be simulated in CFD tools, and so bichromatic wave cases will be used instead. This paper reviews the process used to choose the bichromatic wave pairs to be used in the campaign to validate the second-order difference-frequency quadratic and potential loads at the surge and pitch natural frequencies of a floating semisubmersible.

17 WIND ENERGY↗

National Hydropower Fish Passage Database User's Guide and Methodology

Fish passage facilities are used to mitigate the impacts of hydropower dams on migratory fish in rivers, but information on the location, types, and characteristics of this infrastructure is incomplete at a national scale. Researchers at Oak Ridge National Laboratory partnered with federal agency and industry stakeholders to create the first national-scale database of fish passage infrastructure at U.S. hydropower developments. This database contains information of great value to a broad range of stakeholders; it includes fish passage facility engineering characteristics, targeted fish species, operational schedules, and costs. This data resource addresses a large gap in knowledge of the deployment of fish passage technology and is freely available to members of the hydropower community, including federal and state regulators and resource agencies, non-governmental organizations, industry, and other user groups to support project planning and regulatory (re)licensing activities. This database supports the U.S. Department of Energy Water Power Technologies Office objective to develop decision support tools and data resources that improve environmental performance and ensure hydropower’s long-term value to the American public.

13 HYDRO ENERGY↗

Reimagining Codesign for Advanced Scientific Computing: Report for the ASCR Workshop on Reimagining Codesign

In March 2021, the U.S. Department of Energy’s Advanced Scientific Computing Research program convened the Workshop on Reimagining Codesign. The workshop, also known as ReCoDe, was organized around discussions on eight topic areas: (1) codesign for traditional high-performance computing workloads; (2) codesign of memory/storage systems; (3) codesign of machine learning, neuromorphic, quantum, and other non-von Neumann accelerators; (4) codesign for edge computing and processing at experimental instruments; (5) codesign for security and privacy; (6) hardware design tools and open-source hardware for high-productivity codesign; (7) tools, software stack, and programming languages for high-productivity codesign; and (8) quantitative tools and data collection for modeling and simulation for codesign. The panels identified four Priority Research Directions from these deliberations: (1) breakthrough computing capabilities with targeted heterogeneity and rapid design; (2) software and applications that embrace radical architecture diversity; (3) engineered security and integrity, from transistors to applications; and (4) design with data-rich processes.

97 MATHEMATICS AND COMPUTING↗

A Simple Data-Centric Methodology for Producible Geothermal Well Determinations: Preprint

The Bureau of Land Management (BLM) has traditionally lacked a standardized methodology for determining if a newly drilled geothermal well is "producible," a designation essential for deciding whether a lease should be "held by production." This is a straightforward problem to solve in oil and gas: Demonstrate that a well is economically viable, meaning it produces sufficient oil or gas to exceed direct operating costs and lease-related expenses, such as rentals or minimum royalties. In geothermal, the problem is more complex: Geothermal wells are tightly coupled with the downstream infrastructure - specifically, the power plant, which is often not designed until well after a lease is deemed as "held by production." Although this designation is critical for advancing geothermal power plant development on BLM-managed lands, current geothermal well assessments often rely on ad hoc approaches that can be complex, operator-biased, and heavy in assumptions related to economic viability. To address this, we have developed two complementary methodologies: a minimum power requirement-based approach and a productivity index (PI)-based approach. These methods leverage key flow test data - pressure, temperature, flow rate, and specific enthalpy - to provide reliable and standardized producible well determinations. The minimum power requirement-based approach evaluates wells against specific power output thresholds informed by reservoir experts and the associated temperature requirements. The PI-based approach assesses well productivity using widely accepted reservoir engineering metrics, proposing a threshold of 2.5 kg/s/bar. Both methods are data-driven and grounded in empirical production data from operational geothermal wells, avoiding uncertain economic assumptions while maintaining decision-making accuracy. Wells falling below key performance thresholds (i.e., PI, specific power) are deemed non-producible. These methodologies aim to streamline BLM's decision-making process, reduce nontechnical barriers to geothermal energy adoption, and enable regulatory expansion into states lacking geothermal expertise. Preliminary results indicate clear trends and thresholds in production data that provide actionable insights for evaluating well producibility. Validation using well completion report (WCR) data is ongoing, with promising results demonstrating the potential for these standardized methodologies to impact geothermal development significantly.

15 GEOTHERMAL ENERGY↗

Radiation-hard miniature optical engine with high bandwidth

Future silicon trackers will be operated in an intense radiation environment and require large volumes of data to be transmitted off detector. In addition, the optical modules must be of low mass in order to limit multiple scattering and nuclear interactions that would degrade the overall performance of the detector. Here, we present a miniature optical engine that satisfies these constraints. The optical engine consists of an ASIC driving a VCSEL (Vertical Cavity Surface Emitting Laser) array in an optical package. Two ASICs are designed to operate a 12-channel VCSEL array at 1.28 or 5.12 Gb/s per channel, which yields a total data rate of up to 60 Gb/s. The core transistors are fabricated in a 65 nm CMOS process which enhance the radiation-hardness. Each channel contains equalizer (CTLE) and clock-data recovery circuits (CDR) so that the ASIC can restore the highly distorted electrical signal after propagating through several meters of cables of small diameter. The equalizer, CDR, and VCSEL driver are configured via a digital I 2 C chip interface with triple redundant memory to mitigate single event upset (SEU) effects. The bias and modulation currents are controlled by a digital-to-analog converter (DAC). We present the design of the circuit together with the results of the simulations and preliminary measurements.

47 OTHER INSTRUMENTATION↗

Deciphering the R Ψ m correlator in search for the chiral magnetic effect in relativistic heavy ion collisions

The chiral magnetic effect (CME) is extensively studied in heavy-ion collisions at the BNL Relativistic Heavy Ion Collider (RHIC) and the Large Hadron Collider (LHC). An azimuthal correlator called R Ψ m was proposed to measure the CME. By observing the same R Ψ 2 and R Ψ 3 (convex) distributions from A Multi-Phase Transport (ampt) model, by contrasting data and model as well as large and small systems and by event shape engineering (ESE), a recent preprint (arXiv:2006.04251v1) from STAR suggests that the R Ψ m observable is sensitive to the CME signal and relatively insensitive to backgrounds, and their Au + Au data are inconsistent with known background contributions. Our ampt results contradict those from a recent preprint by STAR. Our toy model simulations demonstrate that R Ψ 2 is sensitive to both the CME signal and physics backgrounds. Toy model simulations of isobar collisions show similar centrality dependence and magnitudes for the relative R Ψ 2 strengths as well as the relative Δ γ strengths. We conclude that R Ψ 2 and the inclusive Δ γ are essentially the same.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets

Abstract Background Mass spectrometry-based proteomics can identify and quantify thousands of proteins from individual microbial species, but a significant percentage of these proteins are unannotated and hence classified as proteins of unknown function (PUFs). Due to the difficulty in extracting meaningful metabolic information, PUFs are often overlooked or discarded during data analysis, even though they might be critically important in functional activities, in particular for metabolic engineering research. Results We optimized and employed a pipeline integrating various “guilt-by-association” (GBA) metrics, including differential expression and co-expression analyses of high-throughput mass spectrometry proteome data and phylogenetic coevolution analysis, and sequence homology-based approaches to determine putative functions for PUFs in Clostridium thermocellum . Our various analyses provided putative functional information for over 95% of the PUFs detected by mass spectrometry in a wild-type and/or an engineered strain of C. thermocellum . In particular, we validated a predicted acyltransferase PUF (WP_003519433.1) with functional activity towards 2-phenylethyl alcohol, consistent with our GBA and sequence homology-based predictions. Conclusions This work demonstrates the value of leveraging sequence homology-based annotations with empirical evidence based on the concept of GBA to broadly predict putative functions for PUFs, opening avenues to further interrogation via targeted experiments.

09 BIOMASS FUELS↗

The Design and Implementation of a Secure Datastore Based on Ethereum Smart Contract

In this paper, we present a secure datastore based on an Ethereum smart contract. Our research is guided by three research questions. First, we will explore to what extend a smart-contract-based datastore should resemble a traditional database system. Second, we will investigate how to store the data in a smart-contract-based datastore for maximum flexibility while minimizing the gas consumption. Third, we seek answers regarding whether or not a smart-contract-based datastore should incorporate complex processing such as data encryption and data analytic algorithms. The proposed smart-contract-based datastore aims to strike a good balance between several constraints: (1) smart contracts are publicly visible, which may create a confidentiality concern for the data stored in the datastore; (2) unlike traditional database systems, the Ethereum smart contract programming language (i.e., Solidity) offers very limited data structures for data management; (3) all operations that mutate the blockchain state would incur financial costs and the developers for smart contracts must make sure sufficient gas is provisioned for every smart contract call, and ideally, the gas consumption should be minimized. Our investigation shows that although it is essential for a smart-contract-based datastore to offer some basic data query functionality, it is impractical to offer query flexibility that resembles that of a traditional database system. Furthermore, we propose that data should be structured as tag-value pairs, where the tag serves as a non-unique key that describes the nature of the value. We also conclude that complex processing should not be allowed in the smart contract due to the financial burden and security concerns. The tag-based secure datastore designed this way also defines its applicative perimeter, i.e., only applications that align with our strategy would find the proposed datastore a good fit. Those that would rather incur higher financial cost for more data query flexibility and/or less user burden on data pre- and post-processing would find the proposed database too restrictive.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Data for Development of Vegetative Oil Sorghum: From Lab-to-Field

Biomass crops engineered to accumulate energy-dense triacylglycerols (TAG or ‘vegetable oils’) in their vegetative tissues have emerged as potential feedstocks to meet the growing demand for renewable diesel and sustainable aviation fuel (SAF). Unlike oil palm and oilseed crops, the current commercial sources of TAG, vegetative tissues, such as leaves and stems, only transiently accumulate TAG. In this report, we used grain (Texas430 or TX430) and sugar-accumulating ‘sweet’ (Ramada) genotypes of sorghum, a high-yielding, environmentally resilient biomass crop, to accumulate TAG in leaves and stems. We initially tested several gene combinations for a ‘push-pull-protect’ strategy. The top TAG-yielding constructs contained five oil transgenes for a sorghum WRINKLED1 transcription factor (‘push’), a Cuphea viscosissima diacylglycerol acyltransferase (DGAT; ‘pull’), a modified sesame oleosin (‘protect’) and two combinations of specialized Cuphea lysophosphatidic acid acyltransferases and medium-chain acyl-acyl carrier protein thioesterases. Though intended to generate oils with medium-chain fatty acids, engineered lines accumulated oleic acid-rich oil to amounts of up to 2.5% DW in leaves and 2.0% DW in stems in the greenhouse, 36-fold and 49-fold increases relative to wild-type (WT) plants, respectively. Under field conditions, the top-performing event accumulated TAG to amount to 5.5% DW in leaves and 3.5% DW in stems, 78-fold and 58-fold increases, respectively, relative to WT TX430. Transcriptomic and fluxomic analyses revealed potential bottlenecks for increased TAG accumulation. Overall, our studies highlight the utility of a lab-to-field pipeline coupled with systems biology studies to deliver high vegetative oil sorghum for SAF and renewable diesel production.

Biofuels↗

Data for Reshaping the 2-Pyrone Synthase Active Site for Chemoselective Biosynthesis of Polyketides

Engineering enzymes with novel reactivity and applying them in metabolic pathways to produce valuable products are quite challenging due to the intrinsic complexity of metabolic networks and the need for high in vivo catalytic efficiency. Triacetic acid lactone (TAL), naturally generated by 2-pyrone synthase (2PS), is a platform molecule that can be produced via microbial fermentation and further converted into value-added products. However, these conversions require extra synthetic steps under harsh conditions. We herein report a biocatalytic system for direct generation of TAL derivatives under mild conditions with controlled chemoselectivity by rationally engineering the 2PS active site and then rewiring the biocatalytic pathway in the metabolic network of E. coli to produce high-value products, such as kavalactone precursors, with yields up to 17 mg/L culture. Computer modeling indicates sterics and hydrogen-bond interactions play key roles in tuning the selectivity, efficiency, and yield.

Conversion↗

Detect and correct bias in multi-site neuroimaging datasets

The desire to train complex machine learning algorithms and to increase the statistical power in association studies drives neuroimaging research to use ever-larger datasets. The most obvious way to increase sample size is by pooling scans from independent studies. However, simple pooling is often ill-advised as selection, measurement, and confounding biases may creep in and yield spurious correlations. In this work, we combine 35,320 magnetic resonance images of the brain from 17 studies to examine bias in neuroimaging. In the first experiment, Name That Dataset, we provide empirical evidence for the presence of bias by showing that scans can be correctly assigned to their respective dataset with 71.5% accuracy. Given such evidence, we take a closer look at confounding bias, which is often viewed as the main shortcoming in observational studies. In practice, we neither know all potential confounders nor do we have data on them. Hence, we model confounders as unknown, latent variables. Kolmogorov complexity is then used to decide whether the confounded or the causal model provides the simplest factorization of the graphical model. Finally, we present methods for dataset harmonization and study their ability to remove bias in imaging features. In particular, we propose an extension of the recently introduced ComBat algorithm to control for global variation across image features, inspired by adjusting for unknown population stratification in genetics. Overall, our results demonstrate that harmonization can reduce dataset-specific information in image features. Further, confounding bias can be reduced and even turned into a causal relationship. However, harmonization also requires caution as it can easily remove relevant subject-specific information. Code is available at https://github.com/ai-med/Dataset-Bias.

42 ENGINEERING↗

Development of a Solar Heat and Power Co-Generation System. Final Report, CRADA No. TC02152.0

Final Report, CRADA No. TC02152.0. Date Technical Work Ended: October 28, 2013. This was a collaborative effort between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and Tassajara Technologies, Inc. (TTI), to develop, fabricate and demonstrate a Solar Heat and Power Co-generation System. The technical objectives of this CRADA were to engineer, design and build a prototype Solar Thermal Process Heat and Power Demonstration System that would be suitable for use at the Arc of Hilo food processing facility. This would be accomplished in two phases. The first phase would entail the building of a prototype at Tassajara facilities. Base design parameters, including the subsystem interactions that would produce reliable performance at the lowest cost per watt of energy generated with the desired balance of power and heat to meet the requirements of the designated food processing applications from Arc of Hilo, would be provided by LLNL. The data and design development would be integrated into the second phase engine prototype and solar thermal system that would be built and delivered, with interface requirements to the Miko Building. This project was originally designated as an eight (8) month project. However, it was ultimately extended by an additional thirty-five (35) months, for total project duration of forty-three (43) months.

14 SOLAR ENERGY↗

Development of a Solar Heat and Power Co-Generation System. Final CRADA Report

Final Report CRADA No. TC02152.0 Date Technical Work Ended: October 28, 2013. This was a collaborative effort between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and Tassajara Technologies, Inc. (TTI), to develop, fabricate and demonstrate a Solar Heat and Power Co-generation System. The technical objectives of this CRADA were to engineer, design and build a prototype Solar Thermal Process Heat and Power Demonstration System that would be suitable for use at the Arc of Hilo food processing facility. This would be accomplished in two phases. The first phase would entail the building of a prototype at Tassajara facilities. Base design parameters, including the subsystem interactions that would produce reliable performance at the lowest cost per watt of energy generated with the desired balance of power and heat to meet the requirements of the designated food processing applications from Arc of Hilo, would be provided by LLNL. The data and design development would be integrated into the second phase engine prototype and solar thermal system that would be built and delivered, with interface requirements to the Miko Building.

14 SOLAR ENERGY↗

A multi-scale cognitive interaction model of instrument operations at the Linac Coherent Light Source

The Linac Coherent Light Source (LCLS) is the world’s first x-ray free electron laser. It is a scientific user facility operated by the SLAC National Accelerator Laboratory, at Stanford, for the U.S. Department of Energy. As beam time at LCLS is extremely valuable and limited, experimental efficiency—getting the most high quality data in the least time—is critical. Our overall project employs cognitive engineering methodologies with the goal of improving experimental efficiency and increasing scientific productivity at LCLS by refining experimental interfaces and workflows, simplifying tasks, reducing errors, and improving operator safety and stress. Here, in this study, we describe a multi-agent, multi-scale computational cognitive interaction model of instrument operations at LCLS. Our model simulates the aspects of human cognition at multiple cognitive and temporal scales, ranging from seconds to hours, and among agents playing multiple roles, including instrument operator, real time data analyst, and experiment manager. The model can roughly predict impacts stemming from proposed changes to operational interfaces and workflows. Example results demonstrate the model’s potential in guiding modifications to improve operational efficiency. We discuss the implications of our effort for cognitive engineering in complex experimental settings and outline future directions for research. The model is open source, and the videos of the supplementary material provide extensive detail.

47 OTHER INSTRUMENTATION↗

Review of Release Behavior of Hydrogen & Natural Gas Blends from Pipelines

Hydrogen can be used to reduce carbon emissions by blending into other gaseous energy carriers, such as natural gas. However, hydrogen blending into natural gas has important implications for safety which need to be evaluated. Hydrogen has different physical properties than natural gas, and these properties affect safety evaluations concerning a leak of the blended gas. The intent of this report is to begin to investigate the safety implications of blending hydrogen into the natural gas infrastructure with respect to a leak event from a pipeline. A literature review was conducted to identify existing data that will better inform future hazard and risk assessments for hydrogen/natural gas blends. Metrics with safety implications such as heat flux and dispersion behavior may be affected by the overall blend ratio of the mixture. Of the literature reviewed, there was no directly observed separation of the hydrogen from the natural gas or methane blend. No literature was identified that experimentally examined unconfined releases such as concentration fields or concentration at specific distances. Computational efforts have predicted concentration fields by modified versions of existing engineering models, but the validation of these models is limited by the unavailability of literature data. There are multiple literature sources that measured flame lengths and heat flux values, which are both relevant metrics to risk and hazard assessments. These data can be more directly compared to the outputs of existing engineering models for validation.

03 NATURAL GAS↗

Classification of Dissolution Events Using Fusion of Effluents Measurements and Classifiers

Classifiers for dissolution events at a radiochemical processing facility are studied using gamma spectra measurements of effluents collected by a high purity germanium detector located at its off-gas stack. Data sets collected at the Oak Ridge National Laboratory’s Radiochemical Engineering Development Center under a Pu dissolution campaign spanning a three months period are utilized. Features corresponding to the activity levels of 15 radionuclides, including isotopes of iodine, krypton, and xenon, that are indicated by the target decay chains, are computed from the spectra at 1 hour intervals. A conceptualization diagram is developed to reflect the steps from the source to measurement to feature computation that depend on fission products indicated by decay chains, chemical processing, and effluents transport to the off-gas stack. A diverse set of eight classifiers based on different design principles are trained using the ground truth data for this campaign, and the outputs of top three classifiers, namely, classification trees, Ensemble of Trees (EOT), and k-nearest neighbor, are combined using EOT classifier-fuser. Our results show that for 5-fold cross validation, features associated with isotopes of xenon provide the lowest classification error among the different elements across the classifiers; the classification error is furthered improved when all 15 isotope features are used by each classifier, and it is again improved by the fusion of three classifiers. Further reduction in classification error is achieved by using a measurement window of 1-2 days which is identified based on half-life time estimates of the isotopes; it is long enough for the stabilization of feature estimates while being short enough not to be affected by the follow on dissolution events. As a net result of feature and classifier fusion, combined with the incorporation of decay chain and isotope half-life information, this approach achieves 98% detection rate while maintaining a false alarm rate under 2% for this data set.

Rao, Nageswara↗