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At least 199 records · Page 11

Genome-wide Association Study Identifies Candidate Loci with Major Contributions to the Genetic Control of Pod Morphological Traits in Snap Bean

Snap beans are cultivars of common bean (Phaseolus vulgaris) that are cultivated for their fleshy immature pods that exhibit a wide diversity of pod shapes and sizes. The genetic basis of the snap bean pod shape is complex and involves the interaction of multiple genes. This study used a snap bean diversity panel composed of heirloom and improved cultivars used in North America and genome-wide association studies (GWAS) to investigate the genetic basis of pod morphological characteristics, including length, width, height, width/height ratio, and coefficients of variation (CVs). The GWAS detected multiple genomic regions associated with each pod trait, with a total of 20 quantitative trait loci (QTLs) for pod length, 9 for pod width, 14 for pod height, and 10 for pod width/height ratio. Regarding theCVof each pod trait, genome-wide association analyses detected six QTL for lengthCVs, five for widthCVs, 15 for heightCVs, and six for width/height ratioCVs. Thirteen regions in seven chromosomes were associated with two or more pod traits. Eighteen QTLs for pod traits in this study colocated with previously reported QTLs for pod and seed traits. The QTL intervals encompass gene models with homologues in other species that are involved in the control of developmental processes. These results capture the complex nature of the genetic control of snap bean pod traits and confirm the significance of genomic regions harboring overlapping QTLs identified in this and other studies. The phenotypic expression of pod traits in snap bean appears to be under the control of a few genomic regions with a strong effect with additional contributions of multiple small-effect regions. Validation of the function of the candidate genes identified in associated regions will contribute to our understanding of legume pod development.

Agriculture↗

Identifying the quantum properties of hadronic resonances using machine learning

With the great promise of deep learning, discoveries of new particles at the Large Hadron Collider (LHC) may be imminent. Following the discovery of a new Beyond the Standard model particle in an all-hadronic channel, deep learning can also be used to identify its quantum numbers. Convolutional neural networks (CNNs) using jet-images can significantly improve upon existing techniques to identify the quantum chromodynamic (QCD) (‘color’) as well as the spin of a two-prong resonance using its substructure. Additionally, jet-images are useful in determining what information in the jet radiation pattern is useful for classification, which could inspire future taggers. These techniques improve the categorization of new particles and are an important addition to the growing jet substructure toolkit, for searches and measurements at the LHC now and in the future.

Filipek, Jakub↗

Identify the influence of microstructure on mesoscale creep and fatigue damage

This report describes the development of a microstructural model that can quantify the uncertainty in the observed rupture life of Grade 91 steel. The model is microstructural, meaning it relates microstructural characteristics of the material to the resulting material response. As such, one of the uses of this model is to identify the key microstructural parameters controlling the development of damage in Grade 91 operating at elevated temperatures. The report describes two veins of work: improvements to the crystal plasticity model required to run the uncertainty quantification analysis and the results of that UQ analysis. For creep, the model identifies the grain boundary diffusivity as the critical parameter controlling the rupture life of the material. The report demonstrates that a reasonable microstructural distribution of grain boundary diffusivity can account for the observed macroscale variation in rupture life at fixed temperature and load.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Identifying Limitations of ASME Section III Division 5 For Advanced SMR Designs

This report provides an overview of the ASME Boiler & Pressure Vessel Section III, Division 5 rules for the design and construction of high temperature nuclear reactor components. The overview focuses on the application of the rules to the design of Small Modular Reactors (SMRs). The discussion covers the general ASME Code rules for base metal design and construction, the rules for designing weldments, and provides an overview of environmental degradation mechanisms affecting reactor structural materials. The analysis includes historical context on the development of the ASME design approach and a description of what actions could be taken to mitigate the gaps identified in the report. The report concludes with a summary of the key gaps identified in the rules, as they apply to SMR, and a list of recommendations on how those gaps might be addressed.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Feasibility of Realizing a Universal Identifier Based on Fiber Bragg Grating Technology

Over the past year we have collected data on different fiber Bragg gratings (FBG) with the end goal of understanding their suitability for use in a new type of unique identifier (UID) that could be used in both tags and seals for high-value, high-risk assets. The ideal UID will have a complex signature that allows items to be uniquely identified by that signature. Tamper indication must be an integral part of the tag/seal process with measurable changes to the device signature indicative of any attempt to tamper with the monitored item. Further, the signature must be so difficult to reproduce that even state-actors with significant resources at their disposal will be discouraged from attempting it. Finally, readout verification of the product must be simple and secure, while providing red-light/green-light results in real time. To evaluate how well an FBG-based UID could meet these goals, we collected data on a large number of FBG samples from different vendors. Measurements included the response of the devices to uniform tension, tension when wrapped on a mandrel, and the response to changes in temperature and humidity, as well as the effect of simple potting in expanding and nonexpanding potting materials. We tested FBG samples written into single-mode fibers that were coated with the two commonly used materials, polyimide and acrylate and gratings that were both uniform and those with an apodized response (i.e., the intensity of the grating was varied to minimize sidelobes). The result of the work to date did not find any significant issues with the design concept for a UID based on this technology. Specific findings include a baseline design comprising five FBGs with distinct spectral returns analyzed using a difference-correlation approach. To realize this device, careful attention must be given to the impact of environmental factors on the UID response, limiting the properties of the potting compounds and FBG coating materials that can be used.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Causal Evaluations for Identifying Differences between Observations and Earth System Models

We use a nascent data-driven causal discovery method to find and compare causal relationships in observed data and climate model output. We consider ten different features in the Arctic climate collected from public databases on observational and Energy Exascale Earth System Model (E3SM) data. In identifying and analyzing the resulting causal networks, we make meaningful comparisons between observed and climate model interdependencies. This work demonstrates our ability to apply the PCMCI causal discovery algorithm to Arctic climate data, that there are noticeable similarities between observed and simulated Arctic climate dynamics, and that further work is needed to identify specific areas for improvement to better align models with natural observations.

54 ENVIRONMENTAL SCIENCES↗

Coal-dependent Communities in Transition: Identifying Best Practices to Ensure Equitable Outcomes

The U.S. coal industry is experiencing a sharp increase in the numbers of retired and/or decommissioned coal-fired power plants across the U.S. In the years between 2010-2019, around 102 gigawatts (GW) of coal-fired generating capacity has been announced to be decommissioned, representing more than 546 coal-fired power plant units, and an additional 17 GW is planned to be decommissioned by 2025. This change in the energy production landscape presents an impact on the social, environmental, and economic prospects of coal-dependent communities. This report examined the role of communities in the coal power plant decommissioning process and provided community-identified best practices to ensure an equitable process. The experiences of four coal-dependent communities—Wise County, VA, Muskegon, MI, Anderson County, TN, and Becker, MN—are presented as case studies to understand the impacts of the decommissioning process, and associated best practices, from the communities’ perspective. The report results highlight the need to recognize that the decommissioning decision-making process must be community-based to be equitable. Each community’s input is key to the transition away from coal power because there is no one-size-fits-all development plan. In other words, each community’s trajectory through the decommissioning process—from the retirement decision-making stage to the final site redevelopment phase—is unique because each community has distinct needs and wants from the energy transition. What is best for one community may not be suited for another. Ultimately, the framework for site development and community revitalization post-decommissioning cannot be universal because each community’s profile—from a social, cultural, and economic perspective—is different. Community impacts of power plant decommissioning are not limited to job and revenue losses. Communities are likely to be impacted culturally, socially, environmentally, and have long-term health-based impacts that should be acknowledged and addressed in post-retirement plans. Commonly identified decommissioning best practices include: Early and continued engagement throughout, with a number of mediums for communication and feedback (e.g., in-person sessions, virtual meetings, written comment opportunities); Early planning of post-decommissioning projects to replace lost jobs, revenue, and economic activity; Recognition (and mitigation, if possible) of social impacts on the community due to plant closure; Transparency throughout the process, with trusted information being provided about the decommissioning process and timeline; potential impacts on the workforce, economy, and environment; and the feasibility of alternative site uses; Identification of funding sources, technical experts, and/or strategic partnerships to support decommissioning and the affected communities upfront; and, Acknowledgment of communities as stakeholders who have a role in the conversation and right to determine their futures. Three key areas for assisting coal-dependent communities affected by the energy transition: Technical assistance: assessment of site feasibility for alternative uses or to repower with new technologies; Cross-partnership engagement and collaboration: facilitate knowledge-sharing of “lessons learned” about the decommissioning process between communities and provide guidance for decision-making processes; and, Financial assistance: access to grant and/or loan programs to assist with redevelopment survey, bolster community economic security through job creation, and cover environmental clean-up costs. Technical assistance, cross-partnership engagement, and financial aid can be mobilized to help communities throughout various stages of the decommissioning process, including the retirement decision, the site reclamation phase, and eventual revitalization of the site and surrounding community.

01 COAL, LIGNITE, AND PEAT↗

Natural Language Processing for Text Based Event Extraction: Identifying Events of Interest Related to Worldwide State-Sponsored Civil Nuclear Power

Beginning in FY20, SRNL was funded by the National Nuclear Security Administration’s Office of Defense Nuclear Non-Proliferation Research and Development to develop a prototype natural language processing/natural language understating machine learning-based modeling and analysis pipeline to extract and forecast events of interest from massive open data sources. The working hypothesis within the approach is that contextual shifts in key words and phrases act as indicators of events of interest over time. Therefore, by identifying points in time where contextual shifts occur, events of interest can be extracted along with explicit and implicit connections of entities and activities. The development of the preliminary prototype pipeline proved successful, meriting further testing of the pipeline on more broad topical domains and in a worldwide data environment. Therefore, SRNL, in collaboration with the Sanghani Center for Artificial Intelligence and Data Analytics at Virginia Tech, have continued development with a test case of identifying events of interest related to worldwide state-sponsored civil nuclear power in open data sources. In the first year of this follow-on effort, the team has curated domain-specific data corpuses using an automated scheme and applied the modeling and analysis pipeline. This robust, focused, and efficient approach consists of an ensemble of analyses applied to time dependent word embedding models that are trained on the data corpuses. In this report, the team has demonstrated the capability of the existing pipeline (as development has continued in parallel) by exploring several specific case-studies centered around Rosatom’s international activities regarding the planning, construction, operation, and/or shutdown of nuclear reactors. A basic timeline events has been generated by manually cataloging known “milestone” events that have occurred at reactors in Turkey, Finland, Hungary, and Egypt and compared with the output of the modeling pipeline. In this approach, the team has characterized the lead time using the prototype pipeline, as well as the ability to capture relevant information, which proved 100% successful. A deep dive example of the Akkuyu reactor (Turkey) is presented that shows the breadth of information that can be captured using the approach. In this case study, events were extracted pertaining to the planning/construction of Akkuyu including protests from the population, information campaigns in response to the protests, forged regulatory documents and lawsuits, budgetary/shareholder information, geopolitical tensions, and the various construction milestones. This has demonstrated the pipeline’s utility as a research aid or real-time event extraction tool, where summary-level information and detailed text extractions from millions of articles or Tweets across long time periods can be generated with significantly less effort than current techniques.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Development and Validation of Algorithms That Analyze Communicating Thermostat Data to Identify Enclosure Retrofit Opportunities

This report, Development and Validation of Algorithms That Analyze Communicating Thermostat Data to Identify Enclosure Retrofit Opportunities , explores ways to automatically identify residential homes with enclosure retrofit opportunities; estimate prospective savings; and perform evaluation, measurement, and verification using interval data from communicating thermostats.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Identifying Hydropower Operational Flexibilities in Presence of Streamflow and Net-load Uncertainty (Final Technical report)

In the existing operations, hydropower contributions to future system flexibility are generally modeled while maintaining traditional operating rules and constraints in supporting grid operation, such as the balancing of variable renewable energy production. Moreover, operation of large scale hydropower systems on major rivers has been investigated for decades, utilizing various systems engineering approaches, with the evolving electric grid, as the result of renewable resources integration, compounded by the changing climate (variability of river flows, intensification of hydrologic cycle resulting in more frequent extreme events) affecting water availability, the need for more advanced stochastic modeling and effective uncertainty analysis approaches have become necessary. The research results supported by this funding and presented in this report provide a new look at hydropower operational flexibility enforced by the changes identified above. Understanding how hydropower operates in response to the underlying uncertainties with respect to the system constraints is crucial in identifying its operational flexibility potentials. In this project, the flexibility of the operating hydropower facility is described by capturing uncertainties in both water and power system and formulating the operations as a multistage stochastic optimization problem. The proposed approach supports short- to seasonal-term operations and planning decision horizons.

13 HYDRO ENERGY↗

Identifying and Explaining Anomalous Activity in Surveillance Video with Compression Algorithms

The primary purpose of this document is to outline the progress made on the LDRD titled “Identifying and Explaining Anomalous Activity in Surveillance Video with Compression Algorithms” in FY22 and FY23. In this LDRD, we explored the usage of compression-based analytics to identify anomalous activity in video. We developed a novel algorithm, Spatio-Temporal N-Gram PPM (STNG PPM) that accounts for spatially and temporally aware anomalies in video. We extracted features using motions vectors from video as well as operating on the raw features. STNG PPM is comparable to many deep learning approaches but does not require specialized hardware (GPUs) to run efficiently. We also examine the evaluation metrics and propose novel measures addressing faults in the current evaluation measures.

97 MATHEMATICS AND COMPUTING↗

Towards a Workforce Roadmap for Distributed Wind: Phase 1 - Identifying Needs and Barriers

Despite recent policy, research efforts, and resources available for utility-scale and offshore wind workforce development, the distributed wind (DW) industry has yet to make similar advances to address its workforce challenges. This report initiates the phased development of a DW workforce roadmap to provide a foundation for roadmap development. Phase 1, contained in this report, uses desk-based research on clean energy workforce approaches and a DW interested-party survey to discuss needs and barriers hindering the workforce from expanding. Findings are summarized into goals and solutions for Phase 2 of roadmap development, which identifies actors responsible for implementing solutions identified in Phase 1. Phase 1 results suggest that the sector's small size and limited growth motivate the short-term need for skilled workers or candidates with well-rounded and multifaceted abilities. Long-term expansion plans must diversify positions while capitalizing on existing utility-scale wind and offshore workforce efforts, as well as other renewable sector best practices where possible. The findings in this report can advance workforce development in the DW sector by aligning interested industry parties around common goals to address challenges. Training providers, installers, operators, manufacturers, federal agencies, national laboratories, academic partners, and labor unions can utilize the findings to help promote sustainable growth of the DW sector.

17 WIND ENERGY↗

Identifying a novel pathway for extracellular electron uptake in Methanosarcina barkeri using shotgun

The overarching goal of this project was to identify the genetic and/or enzymatic basis for extracellular electron uptake in Methanosarcina barkeri—an organism we previously characterized to be capable of this process using poised potential electrodes and a range of electrochemical techniques. In our first aim, we will utilized proteomic techniques that labels extracellular proteins with free amine groups with biotin and perform a selective purification of these proteins from the rest of the proteome. These were identified using mass spectrometry, providing us insight into the identity of the cell surface proteins, including redox active proteins present during extracellular electron uptake. We will also used an isobaric tagging technique (iTRAQ labeling) of proteomes from different experiment conditions to look at differential proteins expression and better understand the total pathway involved in extracellular electron uptake coupled to methanogenesis. In our final aim, we will investigated the electrochemical nature of electron uptake in co-cultures, compared to our pure culture data sets. We predict the process of electron uptake from electrodes replicates what goes on in nature when these organisms for co-cultures with electrogenic microbes such as Geobacter, and to test this hypothesis we have begun to probe co-cultures electrochemically during direct interspecies electron transfer. Our final aim took much longer than expected due to challenges replicating co-cultures between Geobacter metallireducens and Methanosarcina barkeri. We found the major problem with this work was the inability of the M. barkeri strain we used (and we tried strains from three different labs) to successfully grow on acetate in the absence of hydrogen. As such, we began to use the strain Methanosarcina acetivorans—another close relative that specializes on acetate growth. We are currently in the process of comparing electrochemical observations of this microorganism between pure and co-culture experiments.

59 BASIC BIOLOGICAL SCIENCES↗

Identifying the speciation of salt-based actinides in the presence of contaminants [Slides]

Molten salt reactors (MSR) present advantages over light water reactors, such as higher safety and energy efficiency, convenient waste processing, and the ability to use more abundant thorium instead of uranium as the fuel source. However, due to the high temperatures associated with these reactors the reactor container corrosion product can have a high influence on the molten salt system, and they are considered as a part of the fuel salt system. It is essential to have a comprehensive understanding of the chemical reactions that are occurring in the molten salt in the presence of contaminants such as nickel, manganese, chromium chlorides and oxides. Because they can change the local structure of these salts and the local structures of these salts govern the thermophysical properties of the molten salts, which would determine the safety and operational parameters of the reactor. This study is focused on identifying f-element materials speciation resulting from reaction with corrosion/degradation products in a molten salt environment to understand the flow of MSR. In this work, f-element chlorides are mixed with alkali and alkali earth metals and corrosion products such as transition metal chlorides are introduced systematically, inside a glovebox. Then these are heated to around 700 ? and slowly cooled to room temperature. Afterwards, these are analyzed using different characterization techniques such as powder X-ray diffraction, UV-vis and Raman spectroscopy and solid-state NMR. The initial work was conducted with lanthanide chlorides as a surrogate for actinides and the acquired data strongly indicates that in the presence of corrosion products new phase formation/ change in coordination environments occurs. This work has been presented at multiple conference presentations. The proposed work would allow to extend this work to actinides (depleted uranium and thorium) and this would assist to identify the speciation of actinide chloride in the presence of corrosion products. Also, this work would open an opportunity to compare the coordination behavior of lanthanides with the actinides.

37 - INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL C↗

Data Mining of Groundwater to Identify MAGs with Methane, Propane and Toluene Monooxygenases

Whole genome sequencing datasets, involving more than 600 groundwater samples, from nine countries, were analyzed to identify metagenome assembled genomes (MAGs) containing full operons for propane monooxygenase, soluble methane monooxygease, toluene monooxygenase and particulate ammonia/methane monooxygenase. The enzymes encoded by these genes are a focus of interest because of their ability to degrade common groundwater contaminants. Due to the large amount of data, sequence analyses involved more than 80 individual KBase narratives. The approach followed the KBase tutorial called "Metagenome-Assembled Genome Extraction from a Compost Microbiome Enrichment" The generated MAGs were exported from each individual narrative into separate summary KBase narratives for each monooxygenase. Three KBase narratives were generated for particulate ammonia/methane monooxygenase, due to the large number of MAGs identified.

59 BASIC BIOLOGICAL SCIENCES↗

Gene network centrality analysis identifies key regulators coordinating day-night metabolic transitions in Synechococcus elongatus PCC 7942 despite limited accuracy in predicting direct regulator-gene interactions

Synechococcus elongatus PCC 7942 is a model organism for studying circadian regulation and bioproduction, where precise temporal control of metabolism significantly impacts photosynthetic efficiency and CO 2 -to-bioproduct conversion. Despite extensive research on core clock components, our understanding of the broader regulatory network orchestrating genome-wide metabolic transitions remains incomplete. We address this gap by applying machine learning tools and network analysis to investigate the transcriptional architecture governing circadian-controlled gene expression. While our approach showed moderate accuracy in predicting individual transcription factor-gene interactions - a common challenge with real expression data - network-level topological analysis successfully revealed the organizational principles of circadian regulation. Our analysis identified distinct regulatory modules coordinating day-night metabolic transitions, with photosynthesis and carbon/nitrogen metabolism controlled by day-phase regulators, while nighttime modules orchestrate glycogen mobilization and redox metabolism. Through network centrality analysis, we identified potentially significant but previously understudied transcriptional regulators: HimA as a putative DNA architecture regulator, and TetR and SrrB as potential coordinators of nighttime metabolism, working alongside established global regulators RpaA and RpaB. This work demonstrates how network-level analysis can extract biologically meaningful insights despite limitations in predicting direct regulatory interactions. The regulatory principles uncovered here advance our understanding of how cyanobacteria coordinate complex metabolic transitions and may inform metabolic engineering strategies for enhanced photosynthetic bioproduction from CO 2 .

59 BASIC BIOLOGICAL SCIENCES↗

Novel candidate genes for lignin structure identified through genome-wide association study of naturally varying Populus trichocarpa

Populus is a promising lignocellulosic feedstock for biofuels and bioproducts. However, the cell wall biopolymer lignin is a major barrier in conversion of biomass to biofuels. To investigate the variability and underlying genetic basis of the complex structure of lignin, a population of 409 three-year-old, naturally varying Populus trichocarpa genotypes were characterized by heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR). A subsequent genome-wide association study (GWAS) was conducted using approximately 8.3 million single nucleotide polymorphisms (SNPs), which identified 756 genes that were significantly associated (−log 10 ( p -value)>6) with at least one lignin phenotype. Several promising candidate genes were identified, many of which have not previously been reported to be associated with lignin or cell wall biosynthesis. These results provide a resource for gaining insights into the molecular mechanisms of lignin biosynthesis and new targets for future genetic improvement in poplar.

59 BASIC BIOLOGICAL SCIENCES↗

A Pilot Study of Whole-Blood Transcriptomic Analysis to Identify Genes Associated with Repetitive Low-Level Blast Exposure in Career Breachers

Repetitive low-level blast exposure is one of the major occupational health concerns among US military service members and law enforcement. This study seeks to identify gene expression using microRNA and RNA sequencing in whole-blood samples from experienced breachers and unexposed controls. We performed experimental RNA sequencing using Illumina’s HiSeq 2500 Sequencing System, and microRNA analysis using NanoString Technology nCounter miRNA expression panel in whole-blood total RNA samples from 15 experienced breachers and 14 age-, sex-, and race-matched unexposed controls. We identified 10 significantly dysregulated genes between experienced breachers and unexposed controls, with FDR corrected <0.05: One upregulated gene, LINC00996 (long intergenic non-protein coding RNA 996); and nine downregulated genes, IGLV3-16 (immunoglobulin lambda variable 3-16), CD200 (CD200 molecule), LILRB5 (leukocyte immunoglobulin-like receptor B5), ZNF667-AS1 (ZNF667 antisense RNA 1), LMOD1 (leiomodin 1), CNTNAP2 (contactin-associated protein 2), EVPL (envoplakin), DPF3 (double PHD fingers 3), and IGHV4-34 (immunoglobulin heavy variable 4-34). The dysregulated gene expressions reported here have been associated with chronic inflammation and immune response, suggesting that these pathways may relate to the risk of lasting neurological symptoms following high exposures to blast over a career.

59 BASIC BIOLOGICAL SCIENCES↗