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At least 127 records · Page 7

Quantum-enhanced detection of viral cDNA via luminescence resonance energy transfer using upconversion and gold nanoparticles

Abstract The COVID-19 pandemic has profoundly impacted global economies and healthcare systems, revealing critical vulnerabilities in both. In response, our study introduces a sensitive and highly specific detection method for cDNA, leveraging Luminescence Resonance Energy Transfer (LRET) between upconversion nanoparticles (UCNPs) and gold nanoparticles (AuNPs), and achieves a detection limit of 242 fM for SARS-CoV-2 cDNA. This innovative sensing platform utilizes UCNPs conjugated with one primer and AuNPs with another, targeting the 5′ and 3′ ends of the SARS-CoV-2 cDNA, respectively, enabling precise differentiation of mismatched cDNA sequences and significantly improving detection specificity. Through rigorous experimental analysis, we established a quenching efficiency range from 10.4 % to 73.6 %, with an optimal midpoint of 42 %, thereby demonstrating the superior sensitivity of our method. Our work uses SARS-CoV-2 cDNA as a model system to demonstrate the potential of our LRET-based detection method. This proof-of-concept study highlights the adaptability of our platform for future diagnostic applications. Instrumental validation confirms the synthesis and formation of AuNPs, addressing the need for experimental verification of the preparation of nanomaterial. Our comparative analysis with existing SARS-CoV-2 detection methods revealed that our approach provides a low detection limit and high specificity for target cDNA sequences, underscoring its potential for targeted COVID-19 diagnostics. This study demonstrates the superior sensitivity and adaptability of using UCNPs and AuNPs for cDNA detection, offering significant advances in rapid, accessible diagnostic technologies. Our method, characterized by its low detection limit and high precision, represents a critical step forward in developing next-generation biosensors for managing current and future viral outbreaks. By adjusting primer sequences, this platform can be tailored to detect other pathogens, contributing to the enhancement of global healthcare responsiveness and infectious disease control.

Esmaeili, Shahriar [Institute for Quantum Science ↗

Biomass yields, reproductive fertility, compositional analysis, and genetic diversity of newly developed triploid giant miscanthus hybrids

Abstract Miscanthus × giganteus (giant miscanthus), first found as a naturally occurring hybrid, has shown promise as a bioenergy/biomass crop throughout much of the temperate world. This allotriploid (2 n = 3 x = 57) hybrid resulted from a cross between tetraploid Miscanthus sacchariflorus (2 n = 4 x = 76) and diploid Miscanthus sinensis (2 n = 2 x = 38) and is particularly desirable due to its low fertility that minimizes reseeding and potential invasiveness. However, there is limited genetic diversity in commonly grown cultivars of triploid M. × giganteus and breeding and development efforts to improve and domesticate this crop have been minimal. Here, we report on newly developed M. × giganteus hybrids compared with the industry standard M. × giganteus '1993‐1780'. Dry biomass yields of new hybrids ranged from 19.5 to 32.4 Mg/ha/year for the fourth growing season, compared with 21.0 Mg/ha/year for M. × giganteus '1993‐1780'. Plant reproductive fertility remained low for all accessions with overall fertility [(seed set × seed germination)/100] ranging from 0.3% to 4.5% for new hybrids compared to 0.4% for M. × giganteus '1993‐1780'. Culm density and height varied among accessions and were positively correlated with increased biomass. Based on compositional analyses, theoretical ethanol yields ranged from 9, 740 to 16,278 L/ha/year for new hybrids compared to 10,406 L/ha/year for M. × giganteus '1993‐1780'. Relative feed value indices were low overall and ranged between 66.0 and 72.8 for new hybrids compared to M. × giganteus '1993‐1780' with 71.3. The genetic diversity of new hybrids, compared with existing cultivars, was characterized using whole genome sequences. Based on pair‐wise distances, cluster analysis clearly showed increased diversity of new hybrids compared with earlier selections. These results document new triploid hybrids of M. × giganteus with enhanced biomass and theoretical ethanol yields in combination with broader genetic diversity and lowreproductive fertility.

Touchell, Darren H.↗

Mechanism-guided engineering of a minimal biological particle for genome editing

The widespread application of genome editing to treat and cure disease requires the delivery of genome editors into the nucleus of target cells. Enveloped delivery vehicles (EDVs) are engineered virally derived particles capable of packaging and delivering CRISPR-Cas9 ribonucleoproteins (RNPs). However, the presence of lentiviral genome encapsulation and replication proteins in EDVs has obscured the underlying delivery mechanism and precluded particle optimization. Here, we show that Cas9 RNP nuclear delivery is independent of the native lentiviral capsid structure. Instead, EDV-mediated genome editing activity corresponds directly to the number of nuclear localization sequences on the Cas9 enzyme. EDV structural analysis using cryo-electron tomography and small molecule inhibitors guided the removal of ~80% of viral residues, creating a minimal EDV (miniEDV) that retains full RNP delivery capability. MiniEDVs are 25% smaller yet package equivalent amounts of Cas9 RNPs relative to the original EDVs and demonstrated increased editing in cell lines and therapeutically relevant primary human T cells. These results show that virally derived particles can be streamlined to create efficacious genome editing delivery vehicles with simpler production and manufacturing.

59 BASIC BIOLOGICAL SCIENCES↗

Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection

Abstract Background Breast cancer (BC) is the most commonly diagnosed cancer and the leading cause of cancer death among women globally. Despite advances, there is considerable variation in clinical outcomes for patients with non-luminal A tumors, classified as difficult-to-treat breast cancers (DTBC). This study aims to delineate the proteogenomic landscape of DTBC tumors compared to luminal A (LumA) tumors. Methods We retrospectively collected a total of 117 untreated primary breast tumor specimens, focusing on DTBC subtypes. Breast tumors were processed by laser microdissection (LMD) to enrich tumor cells. DNA, RNA, and protein were simultaneously extracted from each tumor preparation, followed by whole genome sequencing, paired-end RNA sequencing, global proteomics and phosphoproteomics. Differential feature analysis, pathway analysis and survival analysis were performed to better understand DTBC and investigate biomarkers. Results We observed distinct variations in gene mutations, structural variations, and chromosomal alterations between DTBC and LumA breast tumors. DTBC tumors predominantly had more mutations inTP53,PLXNB3, Zinc finger genes, and fewer mutations inSDC2,CDH1,PIK3CA,SVIL, andPTEN. Notably, Cytoband 1q21, which contains numerous cell proliferation-related genes, was significantly amplified in the DTBC tumors. LMD successfully minimized stromal components and increased RNA–protein concordance, as evidenced by stromal score comparisons and proteomic analysis. Distinct DTBC and LumA-enriched clusters were observed by proteomic and phosphoproteomic clustering analysis, some with survival differences. Phosphoproteomics identified two distinct phosphoproteomic profiles for high relapse-risk and low relapse-risk basal-like tumors, involving several genes known to be associated with breast cancer oncogenesis and progression, includingKIAA1522,DCK,FOXO3,MYO9B,ARID1A,EPRS,ZC3HAV1, andRBM14. Lastly, an integrated pathway analysis of multi-omics data highlighted a robust enrichment of proliferation pathways in DTBC tumors. Conclusions This study provides an integrated proteogenomic characterization of DTBC vs LumA with tumor cells enriched through laser microdissection. We identified many common features of DTBC tumors and the phosphopeptides that could serve as potential biomarkers for high/low relapse-risk basal-like BC and possibly guide treatment selections.

Oncology↗

Microreactor Core Transportation Cask Model Description for Criticality Safety Validation Basis Assessment (Rev. 1)

Criticality safety analyses are completed on transportation casks used for microreactor whole core shipment to provide examples of models and analyses to industry, regulators, and nuclear community at large to be used in verification and validation analyses of similar applications. The microreactors considered are based on a Gas-Cooled Microreactor (GCMR) and a Heat-Pipe Microreactor (HPMR), both utilize HALEU fuel in the form of TRISO particles and various other design options considered in industry microreactor designs. Variant design options of GCMR and HPMR were also investigated to provide a wider application range for each technology. Criticality safety analyses for the GCMR and HPMR packages were performed using the CSAS6 sequence of SCALE 6.3.2 with the ENDF/B-VII.1-based continuous energy neutron libraries. Different scenarios were investigated, including normal operation and water flooded conditions to represent nominal and hypothetical accident scenarios. Sensitivity and similarity analyses are also performed using the TSUNAMI sequence of SCALE 6.3.2, and the similarity analysis uses all the experiments from the ICSBEP Handbook with Intermediate and mixed Enriched Uranium (IEU) and Low Enriched Uranium (LEU) systems, together with additional experiments that are sponsored by the DNCSH program. Many experiments were found marginally similar to the GCMR and HPMR models, with similarity index (ck) values greater than 0.8 but less than 0.9. Among all the experiments analyzed, no case has a ck value greater than 0.9, indicating that additional critical experiments might be needed to further validate the criticality safety models for microreactors transport packages.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Microreactor Core Transportation Cask Model Description for Criticality Safety Validation Basis Assessment (Rev. 2)

Criticality safety analyses are completed on transportation casks used for microreactor whole core shipment to provide examples of models and analyses to industry, regulators, and nuclear community at large to be used in verification and validation analyses of similar applications. The microreactors considered are based on a Gas-Cooled Microreactor (GCMR) and a Heat-Pipe Microreactor (HPMR), both utilize HALEU fuel in the form of TRISO particles and various other design options considered in industry microreactor designs. Variant design options of GCMR and HPMR were also investigated to provide a wider application range for each technology. Criticality safety analyses for the GCMR and HPMR packages were performed using the CSAS6 sequence of SCALE 6.3.2 with the ENDF/B-VII.1-based continuous energy neutron libraries. Different scenarios were investigated, including normal operation and water flooded conditions to represent nominal and hypothetical accident scenarios. Sensitivity and similarity analyses are also performed using the TSUNAMI sequence of SCALE 6.3.2, and the similarity analysis uses all the experiments from the ICSBEP Handbook with High Enriched Uranium (HEU), Intermediate and mixed Enriched Uranium (IEU) and Low Enriched Uranium (LEU) systems. Many ICSBEP experiments were found marginally similar, with similarity index (ck) values greater than 0.8, to the GCMR and HPMR cask models, especially in flooded conditions that may be more constraining due to reduced reactivity margins. Some experiments using TRISO fuel particles and graphite moderator, including the recent THETA and Deimos experiments from LANL, together with some IRPhEP experiments, were also used for the similarity analyses. These TRISO-fueled and graphite moderated experiments behaved similarly to the GCMR models, with maximum ck value greater than 0.9, but they are less similar to the HPMR models. This observation indicates that additional critical experiments might be needed to further validate the criticality safety models, especially for heat-pipe based microreactor transport packages and for non-flooded transportation configurations.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Exploring the Potential of ASHRAE Guideline 36 in District Cooling Systems: Preprint

ASHRAE Guideline 36-2021 (G36) provides high-performance control sequences for all-air and hydronic HVAC systems, and it has proven effective at reducing energy use for single building all-air equipment. The most recent version of G36 included control sequences for water-cooled chiller plants, which can be used in district cooling systems (DCSs). Despite not being a traditional application of G36 controls, DCSs could benefit from energy savings that G36 control sequences have demonstrated in single building systems. We therefore investigate the possibility to extend G36 chiller plant control from a single building to district cooling using a real-world district cooling system in Boulder, Colorado as a case study. Four timeframes representing low to peak loads are simulated and analyzed to compare energy use of the district cooling system for three control sequences. Results show that although G36 chiller plant sequences can be applied to DCSs, further analysis and potentially control optimization is needed to ensure energy savings compared to default controls.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Integrative Modeling and Analysis of Fungal Central Carbon Metabolism

Over a thousand fungal genomes have been sequenced, yet manually curated genome-scale metabolic models (GEMs) are available for only a limited number of species. Moreover, these models have often been developed independently, leading to inconsistencies in namespaces, compartment definitions, and pathway representations that hinder comparative analysis, the systematic reuse of prior curation efforts, and the integration of consolidated metabolic knowledge. Here, we present the Consolidated Fungal Core Metabolism Model (CFCMM), constructed by integrating thirteen published fungal models spanning Ascomycota, Mucoromycota, and both Crabtree-positive and Crabtree-negative yeasts. We harmonized metabolites and reactions into a non-redundant shared ModelSEED ontological space, standardized compartmentalization, and refined gene–protein–reaction (GPR) rules. Using pathway-level visualization and systematic gap detection, we further improved the integrated network through literature-guided curation to correct stoichiometry, stereospecificity, and pathway architecture. Orthologous protein family reconstruction and functional annotation workflows were used to validate and inform GPR associations, with particular emphasis on ambiguous enzyme superfamilies and membrane-associated components. Using the resulting CFCMM, we built high-quality central carbon core models for each fungus and performed flux balance analysis to quantify ATP-yield variation under aerobic and anaerobic conditions, explicitly evaluating scenarios driven by differences in electron transport chain (ETC) composition. Simulations reproduced the expected fermentative yield of approximately 2 mmol ATP per mmol glucose under anaerobic conditions and separated the thirteen fungi into two bioenergetic groups under aerobic respiration based on Complex I status, with predicted yields of approximately 30 versus 22 mmol ATP per mmol glucose. Forcing flux through the alternative oxidase bypass further reduced ATP yields to approximately 12 and 4 mmol ATP per mmol glucose in Complex I-containing and Complex I-lacking fungi, respectively. Collectively, this work provides a manually curated, ModelSEED-consistent, and extensible fungal core metabolic template, deployed in DOE KBase as a resource for automated reconstruction of central carbon core models from any sequenced fungal genome. In addition, the CFCMM provides modular components for developing GEMs with more accurate energy predictions and enables robust comparative analyses of fungal bioenergetics and core metabolic diversity

59 BASIC BIOLOGICAL SCIENCES↗

Bulk segregant and QTL analysis of maltose metabolism in Saccharomyces eubayanus

This study investigates natural variation in maltose utilization among Saccharomyces eubayanus strains isolated from different tree hosts. An F2 population was generated from a cross between strain QC18 (Quercus-associated) and strain CL467.1 (Nothofagus-associated). Bulk segregant analysis (BSA) was performed on the F2 offspring, and QTL mapping was conducted by whole-genome sequencing of two pools of 30 segregants each, representing the lowest and highest growth in high maltose concentrations. For QTL analysis, the parental strains QC18 and CL467.1 were also sequenced.

evolutionary plasticity↗

Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing

Microglia, the innate immune cells of the central nervous system, have been genetically implicated in multiple neurodegenerative diseases. Mapping the genetics of gene expression in human microglia has identified several loci associated with disease-associated genetic variants in microglia-specific regulatory elements. However, identifying genetic effects on splicing is challenging because of the use of short sequencing reads. Here, we present the isoform-centric microglia genomic atlas (isoMiGA), which leverages long-read RNA sequencing to identify 35,879 novel microglia isoforms. We show that these isoforms are involved in stimulation response and brain region specificity. We then quantified the expression of both known and novel isoforms in a multi-ancestry meta-analysis of 555 human microglia short-read RNA sequencing samples from 391 donors, and found associations with genetic risk loci in Alzheimer’s and Parkinson’s disease. We nominate several loci that may act through complex changes in isoform and splice-site usage.

59 BASIC BIOLOGICAL SCIENCES↗

Pseudomonas aeruginosa : One Health approach to deciphering hidden relationships in Northern Portugal

Abstract Aims Antimicrobial resistance in Pseudomonas aeruginosa represents a major global challenge in public and veterinary health, particularly from a One Health perspective. This study aimed to investigate antimicrobial resistance, the presence of virulence genes, and the genetic diversity of P. aeruginosa isolates from diverse sources. Methods and results The study utilized antimicrobial susceptibility testing, genomic analysis for resistance and virulence genes, and multilocus sequence typing to characterize a total of 737 P. aeruginosa isolates that were collected from humans, domestic animals, and aquatic environments in Northern Portugal. Antimicrobial resistance profiles were analyzed, and genomic approaches were employed to detect resistance and virulence genes. The study found a high prevalence of multidrug-resistant isolates, including high-risk clones such as ST244 and ST446, particularly in hospital sources and wastewater treatment plants. Key genes associated with resistance and virulence, including efflux pumps (e.g. MexA and MexB) and secretion systems (T3SS and T6SS), were identified. Conclusions This work highlights the intricate dynamics of multidrug-resistant P. aeruginosa across interconnected ecosystems in Northern Portugal. It underscores the importance of genomic studies in revealing the mechanisms of resistance and virulence, contributing to the broader understanding of resistance dynamics and informing future mitigation strategies.

de Sousa, Telma↗

Real-time PCR assays that detect genes for botulinum neurotoxin A–G subtypes

The role of Real-Time PCR assays for surveillance and rapid screening for pathogens is garnering more and more attention because of its versatility and ease of adoption. The goal of this study was to design, test, and evaluate Real-Time TaqMan PCR assays for the detection of botulinum neurotoxin (bont/A-G) genes from currently recognized BoNT subtypes. Assays were computationally designed and then laboratory tested for sensitivity and specificity using DNA preparations containing bont genes from 82 target toxin subtypes, including nine bivalent toxin types; 31 strains representing other clostridial species; and an extensive panel that consisted of DNA from a diverse set of prokaryotic (bacterial) and eukaryotic (fungal, protozoan, plant, and animal) species. In addition to laboratory testing, the assays were computationally evaluated using in silico analysis for their ability to detect bont gene sequences from recently identified toxin subtypes. Seventeen specific assays (two for each of the bont/C, bont/D, bont/E, and bont/G subtypes and three for each of the bont/A, bont/B, and bont/F subtypes) were designed and evaluated for their ability to detect bont genes encoding multiple subtypes from all seven serotypes. These assays could provide an additional tool for the detection of botulinum neurotoxins in clinical, environmental and food samples that can complement other existing methods used in clinical diagnostics, regulatory, public health, and research laboratories.

59 BASIC BIOLOGICAL SCIENCES↗

Enhancement on selenium volatilization for phytoremediation: role of plant and soil microbe interaction

This study aimed at quantifying the potential effects of plant and soil microbial interaction on selenium (Se) volatilization, with the specific objectives of identifying soil bacteria associated with rabbitfoot grass (Polypogon monspeliensis) and demonstrating the enhancement of Se volatilization in the soil-Indian mustard (Brassica juncea) system through inoculation of the soil with the identified best Se-volatilizing bacterial strain. Soil bacteria were isolated from topsoil and rhizosphere soils of rabbitfoot grass, and the bacterial colonies were characterized via PCR-DGGE and DGGE band analysis prior to their identification using 16S rDNA sequencing technique.Bacillus cereusproduced over 500-fold more volatile Se in a culture medium treated with 15 µg Se/mL (equal mixture of SeO 4 2- , SeO 3 2- and selenomethionine) than any of the other eight identified bacterial strains. Inoculation of Indian mustard vegetated soil with the best Se volatilizing bacterial strainB. cereusresulted in a significant (p<0.05) increase in Se volatilization during a 7-day time period, compared to the soil-plant system without inoculation ofB. cereus. Thus, inoculation of the soil withB. cereussubstantially enhanced Se removal via biogenic volatilization in the soil-Indian mustard system. This study evaluated the role ofB. cereusin enhancing Se volatilization in soil-plant systems, and demonstrated the importance of plant and soil microbial interaction for Se phytoremediation.

Plant Sciences↗

Governing in Time: Temporal Capacity and the Feasibility of Energy Transitions

Energy systems function as both technological systems and temporal institutions that shape how societies coordinate, justify, and support collective choices over time. This paper introduces the concept of governance horizons to explain why energy transitions can remain morally supported yet become institutionally weak under increasing pressure. We argue that governability depends on institutions' capacity to synchronize across multiple timeframes - aligning short-term decisions with intermediate coordination and long-term commitments. When this synchronization fails, transitions struggle not because their goals are dismissed, but because governance lacks sufficient time to justify, coordinate, and uphold decisions. Comparative analysis of San Antonio, Texas, and Interior Alaska reveals how energy system pressures generate distinct temporal configurations: San Antonio exhibits governance horizon stretching, where institutions must simultaneously meet near-term reliability demands and long-term transformation goals, while Interior Alaska exhibits horizon compression, where extreme environmental constraints force decision-making into short stabilization cycles. In both contexts, public support for sustainability goals coexists with institutional strain because evaluative judgments are unevenly distributed over time. A temporal configuration analysis is introduced as a diagnostic analytic stance for identifying these patterns. By treating temporal alignment as an explanatory variable rather than a background condition, this approach clarifies how feasibility, sequencing, and legitimacy are shaped by constraints on institutional time. The analysis demonstrates that successful energy transitions depend not only on technological innovation or institutional support, but on governance systems’ ability to sustain credible coordination across multiple time horizons.

Comparative case study↗

Prioritizing Uncertainties in Hydrogen Contribution to Risk in Post-Crash Outcomes for Rail

This report presents analysis from Sandia National Laboratories predicting contributions to risk associated with the use of hydrogen technology for rail. Event sequence diagrams are used to describe possible accident scenarios and progressions. Initiating event frequencies and branch event probabilities for each scenario are quantified with uncertainty using distributions fit to Federal Railroad Administration and U.S. Department of Transportation Pipeline and Hazardous Materials Safety Administration data on applicable accidents from 2000 to 2020. Uncertainty is propagated through the event sequence diagram to estimate the frequency and conditional probability of accident end states. The analysis identifies four scenarios with significant contributions to risk from hydrogen that are predicted to occur relatively frequently, which may inform priorities for reducing uncertainty. These scenarios are 1) overpressure events resulting from collisions with hydrogen release due to mechanical damage and delayed ignition, 2) jet fire events resulting from collisions with hydrogen release due to mechanical damage and immediate ignition, 3) jet fires resulting from fire or explosion initiating events involving the hydrogen tank and correct operation of the thermally-activated pressure relief device (TPRD) subsequent to the thermal insult, and 4) pressure burst resulting from fire or explosion initiating events involving the hydrogen tank and failure of the TPRD. Delayed and immediate hydrogen ignition probabilities are identified as being highly uncertain and potential candidates for reducing conservatism in the predicted frequencies for these two scenarios.

08 HYDROGEN↗

Extreme Thermal Stabilization of Carborane–Cyanate Composites via B–N Dative-Bonded Boroxine Barriers

Enhancing the thermal stability of cyanate ester (CE) resins is crucial for high-temperature aerospace applications. This study elucidates the degradation mechanisms of CE composites reinforced with carborane additives, focusing on the formation of boron–nitrogen (B–N) dative bonds and their role in improving thermal resistance. Using thermogravimetric analysis, we examined char formation and evolved gases at multiple degradation stages. Reaction sequences and char products were characterized via Fourier transform infrared spectroscopy (FTIR), solid-state 13C and 11B NMR, and evolved gas analysis using mass spectrometry and FTIR. The solid-state 11B NMR was instrumental in detecting various boron oxidation states and the formation of B–N dative bonds during decomposition. These bonds facilitate cross-linking in the char phase, enhancing material integrity at elevated temperatures. However, in inert environments, the volatility of boron additives like carborane limits their effectiveness. These findings advance the understanding of CE composite degradation mechanisms and offer critical insights for developing high-temperature-resistant materials for aerospace applications.

Fourier transform infrared spectroscopy↗

Tuning Copolymer Microstructure Using Ring-Opening Cross-Metathesis Polymerization

The capability of ring-opening cross-metathesis (RO/CM) polymerization to produce alternating copolymers was studied. By treating commercial polybutadiene (PB) with bulky oxanorbornene monomers and Ru-based olefin metathesis catalysts, alternating copolymers were produced under mild conditions with high sequence fidelities. Here, we found that alternating copolymers could be produced starting from a variety of butadiene sources including PB, cyclooctadiene (COD), or t,t,t-1,5,9-cyclododecatriene (CDT), highlighting for the first time the kinetic pathway independence of this process. Kinetic copolymerization analysis of an oxanorbonene monomer with CDT revealed that much higher monomer conversions were obtained compared with the analogous homopolymerizations and showed evidence of alternating monomer incorporation. Copolymerization of these monomers also enabled good control when targeting different molecular weights. Copolymer thermal analysis revealed a strong correlation between thermal behavior and alternating sequence fidelity, providing a second lever beyond composition to tune thermal behavior. These data demonstrate that a broad variety of polymer microstructures can be accessed via RO/CM polymerization and highlight the potential of CDT in alternating copolymer synthesis.

Foster, Jeffrey C. [Oak Ridge National Laboratory ↗