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At least 1,243 records · Page 69

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Abstract For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical ‘Rosetta Stone’ to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org and KBase.

59 BASIC BIOLOGICAL SCIENCES↗

In Vivo Assay Reveals Microbial OleA Thiolases Initiating Hydrocarbon and β-Lactone Biosynthesis

Microbially produced β-lactones are found in antibiotic, antitumor, and antiobesity drugs. Long-chain olefinic membrane hydrocarbons have potential utility as fuels and specialty chemicals. The metabolic pathway to both end products share bacterial enzymes denoted as OleA, OleC, and OleD that transform acyl-CoA cellular intermediates into β-lactones. Bacteria producing membrane hydrocarbons via the Ole pathway additionally express a β-lactone decarboxylase, OleB. Both β-lactone and olefin biosynthesis pathways are initiated by OleA enzymes that define the overall structure of the final product. There is currently very limited information on OleA enzymes apart from the single representative from Xanthomonas campestris . In this study, bioinformatic analysis identified hundreds of new, putative OleA proteins, 74 proteins were screened via a rapid whole-cell method, leading to the identification of 25 stably expressed OleA proteins representing seven bacteria phyla.

59 BASIC BIOLOGICAL SCIENCES↗

Anaerobic Biohydrogenation of Isoprene by Acetobacterium wieringae Strain Y

Isoprene is a ubiquitously distributed, biogenic, and climate-active organic compound. Microbial isoprene degradation in oxic environments is fairly well understood; however, studies exploring anaerobic isoprene metabolism remain scarce, with no isolates for study available. Here, we obtained an acetogenic isolate, designated Acetobacterium wieringae strain Y, which hydrogenated isoprene to a mixture of methyl-1-butenes at an overall rate of 288.8 ± 20.9 μM day -1 with concomitant acetate production at a rate of 478.4 ± 5.6 μM day -1 . Physiological characterization demonstrated that isoprene was not utilized in a respiratory process; rather, isoprene promoted acetogenesis kinetically. Bioinformatic analysis and proteomics experiments revealed the expression of candidate ene-reductases responsible for isoprene biohydrogenation. Notably, the addition of isoprene to strain Y cultures stimulated the expression of proteins associated with the Wood-Ljungdahl pathway, indicating unresolved impacts of isoprene on carbon cycling and microbial ecology in anoxic environments (e.g., promoting CO 2 plus H 2 reductive acetogenesis while inhibiting methanogenesis). Our new findings advance understanding of microbial transformation of isoprene under anoxic conditions and suggest that anoxic environments are isoprene sinks.

59 BASIC BIOLOGICAL SCIENCES↗

Battery500 Consortium: Development of High Capacity Cathodes and Robust Solid Electrolytes

As the world have witnessed the tremendous development in portable electronic devices as well as electric vehicles, the current generation lithium-ion battery is unlikely to satisfy the bourgeon of market and the demand of the customers. A next generation battery, with cell energy density higher than 500 Wh kg -1 , needs to be developed to meet the growth of the industry. With its high theoretical capacity (3,860 mAh g -1 , or 2,061 mAh cm -3 ) and low electrochemical potential (–3.04 V versus the standard hydrogen electrode), lithium metal has been regarded as the ideal candidate for the next generation battery anode. In fact, Lithium metal anode is irreplaceable for Lithium-Sulfur chemistry. However, the continuous formation of inactive Li, which eventually leads the loss of reversible capacity of the cell, has prevented lithium metal to be used as anode in commercial rechargeable cells. The ultimate goal of the project is to propose a pathway to enable Li metal battery for stable cycling at 99.9% of Coulombic efficiency with energy density higher than 500 Wh kg -1 . A variety of advanced characterization tools, electrolyte systems, 3D current collectors and failure analysis methodologies have been developed throughout the project during the past 5 years. The UCSD effort is carried out by the groups of Ping Liu and Shirley Meng.

25 ENERGY STORAGE↗

Techno-Economic Analysis of Large-Scale Hydrogen Production from Solid Oxide Electrolysis Cell Systems

The objective of this study is to establish a detailed techno-economic analysis to assess the effectiveness of incremental technology improvements needed for solid oxide electrolysis cell (SOEC) technology to achieve the U.S. DOE’s Hydrogen Shot goal of hydrogen production at less than $1 per kilogram. The pathway considers incremental technology improvements to key system parameters, with system performance and cost assessed for each pathway step. Briefly, the steps include cell voltage degradation rate improvements, operational current density increases, operating temperature reduction, improved steam utilization, increased system capacity factor, and reduced cell/stack capital costs. Each step is assessed at both atmospheric and pressurized (8 bar) operating conditions. To supplement assessment at each of these discrete stepwise improvements, sensitivity studies are conducted to understand the relative impact of each parameter and identify avenues for additional cost reductions. System efficiency and levelized costs of hydrogen (LCOH) for each case are presented. For the end-of-pathway case, which includes all the incremental research and development improvements, the cost of hydrogen produced is reduced by 50 percent from the state-of-the-art case.

08 HYDROGEN↗

Properties, Physiological Functions and Involvement of Basidiomycetous Alcohol Oxidase in Wood Degradation

Extensive research efforts have been devoted to describing yeast alcohol oxidase (AO) and its promoter region, which is vastly applied in studies of heterologous gene expression. However, little is known about basidiomycetous AO and its physiological role in wood degradation. This review describes several alcohol oxidases from both white and brown rot fungi, highlighting their physicochemical and kinetic properties. Moreover, the review presents a detailed analysis of available AO-encoding gene promoter regions in basidiomycetous fungi with a discussion of the manipulations of culture conditions in relation to the modification of alcohol oxidase gene expression and changes in enzyme production. The analysis of reactions catalyzed by lignin-modifying enzymes (LME) and certain lignin auxiliary enzymes (LDA) elucidated the possible involvement of alcohol oxidase in the degradation of derivatives of this polymer. Combined data on lignin degradation pathways suggest that basidiomycetous AO is important in secondary reactions during lignin decomposition by wood degrading fungi. With numerous alcoholic substrates, the enzyme is probably engaged in a variety of catalytic reactions leading to the detoxification of compounds produced in lignin degradation processes and their utilization as a carbon source by fungal mycelium.

59 BASIC BIOLOGICAL SCIENCES↗

Sustainable Aviation

New technologies are changing the future of aviation, providing actionable pathways for lowering greenhouse gas emissions in a sector that is among the most difficult to decarbonize. The National Renewable Energy Laboratory (NREL) is developing public and private partnerships to accelerate this evolution with critical research, analysis, modeling, and validation expertise in energy carriers, aircraft components, and airport infrastructure. Our solutions will not only permanently lower the carbon intensity of flight, but fundamentally improve the carbon intensity, mobility, and resiliency of the entire aviation ecosystem.

ADVANCED PROPULSION SYSTEMS↗

Characterization of the Aerosol Source Term in Dry Storage Canisters

As long-term dry storage of used nuclear fuel at independent spent fuel storage installations (ISFSI) trends toward the de facto back end of the US fuel cycle, it becomes appropriate to investigate potential degradation and dispersion scenarios for suitable risk mitigation purposes. Pitting and subsequent stress corrosion cracking of the canister wall is currently viewed as a potential scenario leading to a through-wall pathway for contamination to be transferred from within the storage container to the surrounding environment. While stress corrosion cracking measurements are currently underway to further characterize this scenario, a parallel effort endeavors to perform a consequence analysis of conditions in which through wall cracks are indeed formed. This effort consists of engineering scale modeling using the GOTHIC and MELCOR software packages along with experimental depletion and penetration tests.

spent fuel storage, aerosol deposition, Stress Cor↗

CO 2 methanation reaction pathways over unpromoted and NaNO 3 -promoted Ru/Al 2 O 3 catalysts

Catalytic CO 2 sorbents, materials that adsorb and pre-concentrate CO 2 on the catalyst surface prior to subsequent conversion, are becoming important materials in CO 2 capture and utilization. In this work, a prototypical CO 2 methanation catalyst – Ru/Al 2 O 3 – and a related catalytic sorbent – NaNO 3 /Ru/Al 2 O 3 – are used for CO 2 methanation in flowing hydrogen in a fixed bed reactor at temperatures ranging from 220 to 280 °C. Activation energies for the NaNO 3 /Ru/Al 2 O 3 material are slightly higher than unpromoted Ru/Al 2 O 3 catalysts, and the reaction orders vary more significantly. In situ IR spectroscopy and steady-state isotopic kinetic analysis (SSITKA) using in situ IR/MS spectroscopy show that bicarbonate and linear carbonyl species are the likely reaction intermediates over unpromoted Ru/Al 2 O 3 , while bidentate carbonate, formate and linear carbonyl species are among likely reaction intermediates over NaNO 3 /Ru/Al 2 O 3 . Rate laws consistent with the obtained experimental data are proposed after kinetic modeling of multiple plausible reaction pathways. In conclusion, results suggest that the pathway over the NaNO 3 /Ru/Al 2 O 3 catalyst likely has an additional kinetically relevant irreversible step in the CO 2 methanation reaction pathway.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Enabling the Broader Use of MOOSE for Nuclear Energy and Other Simulation

This Final Scientific and Technical Report summarizes work performed under the Phase IIA SBIR project “Enabling the Broader Use of MOOSE for Nuclear Energy and Other Simulation” (DE-SC0020906) from August 2023 through August 2025. The objective of the Phase IIA effort was to mature and harden capabilities developed during Phase II, with the goal of enabling practical interoperability between Coreform’s isogeometric analysis (IGA) technologies and the Multiphysics Object-Oriented Simulation Environment (MOOSE), while improving robustness, performance, and scalability for complex, nuclear-relevant geometries. Over the course of Phase IIA, the project established and validated an extraction-based interoperability pathway between Coreform tools and MOOSE. A combined mesh and matrix format was defined collaboratively with MOOSE developers and integrated into the solver, enabling standard MOOSE workflows to operate on data exported from Coreform’s IGA and Flex Representation Method (FRM) pipelines. Early demonstrations validated architectural compatibility using linear solid mechanics problems, while later efforts focused on benchmark testing and external use. By the end of the project period, engineers at BWXT were able to independently set up and execute a simulation using the Coreform–MOOSE workflow and provide direct feedback that informed further refinement. In parallel, substantial effort was devoted to improving the robustness of trimmed U-spline construction for complex CAD geometries. A growing test suite of nuclear-relevant models was compiled through collaboration with multiple stakeholders and used to drive extensive bug fixing and reliability improvements. These efforts resulted in improved robustness and performance, including the addition of fallback capabilities that enhance reliability when the underlying commercial CAD kernel fails. Performance-oriented work progressed later in the project, with the development and demonstration of methods to decompose complex geometries into structured subregions and updated data representations to support more efficient solver processing. Additionally, extensive enhancements to threadsafe parallel data structures and trimming operations established a foundation for scalable processing of large assemblies. Collaboration with Sandia National Laboratories on the SGM geometric modeling kernel advanced to a functioning interface test case, positioning the workflow for future kernel integration. Overall, the Phase IIA effort successfully transitioned the project from architectural proof-of-concept to externally exercised, solver-integrated capability, while clarifying remaining technical challenges related to standardization, performance optimization, and kernel integration.

42 ENGINEERING↗

Supply Chain Sustainability Analysis of Renewable Hydrocarbon Fuels via Indirect Liquefaction, Ex Situ Catalytic Fast Pyrolysis, Hydrothermal Liquefaction, Combined Algal Processing, and Biochemical Conversion: Update of the 2020 State-of-Technology Cases

This technical report describes the SCSAs for the production of renewable hydrocarbon transportation fuels via a range of conversion technologies in the 2020 SOTs: (1) renewable high octane gasoline (HOG) via indirect liquefaction (IDL) of woody lignocellulosic biomass (note that the IDL pathway in this SCSA represents the syngas conversion design); (2) renewable gasoline (RG) and diesel (RD) blendstocks via ex situ catalytic fast pyrolysis of woody lignocellulosic biomass; (3) RD via hydrothermal liquefaction (HTL) of wet sludge from a wastewater treatment plant; (4) renewable hydrocarbon fuels via biochemical conversion of herbaceous lignocellulosic biomass; (5) renewable diesel via HTL of a blend of algae and woody biomass; and (6) renewable diesel via combined algae processing (CAP). This technical report focuses on the environmental performance of these six biofuel production pathways in their 2020 SOT cases. The results of these renewable hydrocarbon fuel pathways in these SCSA analyses update those for the respective 2019 SOT cases. They also provide an opportunity to examine the impact of technology improvements in both biomass feedstock production and biofuel production that have been achieved in 2020 SOTs on the sustainability performance of these renewable transportation fuels. The SCSA results also reflect updates to Argonne National Laboratory’s Greenhouse gases, Regulated Emissions, and Energy use in Technologies (GREET ® ) model, which was released in October 2020. These GREET updates include the production of natural gas, electricity, and petroleum-based fuels that can influence biofuels’ supply chain greenhouse gas (GHG) (CO 2 , CH 4 , and N 2 O) emissions, water consumption, and air pollutant emissions. GHG emissions, water consumption, and nitrogen oxides (NO x ) emissions are the main sustainability metrics assessed in this analysis. In this analysis, we define water consumption as the amount of water withdrawn from a freshwater source that is not returned (or returnable) to a freshwater source at the same level of quality. Life-cycle fossil energy consumption and net energy balance, which is the life-cycle fossil energy consumption deducted from the renewable biofuel energy produced, are also assessed.

09 BIOMASS FUELS↗

Image-Based Methods to Score Fungal Pathogen Symptom Progression and Severity in Excised Arabidopsis Leaves

Image-based symptom scoring of plant diseases is a powerful tool for associating disease resistance with plant genotypes. Advancements in technology have enabled new imaging and image processing strategies for statistical analysis of time-course experiments. There are several tools available for analyzing symptoms on leaves and fruits of crop plants, but only a few are available for the model plant Arabidopsis thaliana (Arabidopsis). Arabidopsis and the model fungus Botrytis cinerea (Botrytis) comprise a potent model pathosystem for the identification of signaling pathways conferring immunity against this broad host-range necrotrophic fungus. Here, we present two strategies to assess severity and symptom progression of Botrytis infection over time in Arabidopsis leaves. Thus, a pixel classification strategy using color hue values from red-green-blue (RGB) images and a random forest algorithm was used to establish necrotic, chlorotic, and healthy leaf areas. Secondly, using chlorophyll fluorescence (ChlFl) imaging, the maximum quantum yield of photosystem II (Fv/Fm) was determined to define diseased areas and their proportion per total leaf area. Both RGB and ChlFl imaging strategies were employed to track disease progression over time. This has provided a robust and sensitive method for detecting sensitive or resistant genetic backgrounds. A full methodological workflow, from plant culture to data analysis, is described.

59 BASIC BIOLOGICAL SCIENCES↗

Holistic energy analysis method for thermal management architectures of data centers

Modern high-performance computing (HPC) data centers (DCs), particularly those supporting energy-intensive artificial intelligence (AI) workloads, face escalating thermal management challenges that degrade performance through thermal throttling and drive up cooling power consumption and operational costs. To address this challenge, many have developed a wide variety of thermal management solutions (single-phase, two-phase, direct, indirect, hybrid, and more) which attempt to cool HPC DCs effectively while attempting to minimize overall system power consumption. However, the analysis of these solutions and methods to effectively compare one with another is lacking. Overall power usage effectiveness (PUE) and total-power usage effectiveness (TUE) provide a metric to quantify power consumption but fail to identify components in the system which require further optimization. To address this, we propose a holistic analytical framework – the waterfall diagram (WFD) – which leverages a waterfall chart methodology, offering a comprehensive visualization of both the thermal management system loop and heat flow pathways from individual server components to the outdoor ambient. Use of the WFD enables graphical estimations of power efficiency and cooling performance across each component of a DC cooling system and complements Sankey-style energy flow visualizations by additionally resolving stage-wise temperature changes and incremental TUE contributions. The framework is used in conjunction with simulation-based approaches, to conduct a detailed pressure drop and flow distribution analysis aimed at identifying the optimal coolant distribution architecture for a single-phase direct-to-chip water-cooled DC, which serves as the baseline for subsequent WFD analysis. Among the evaluated architectures, the 3 U modular coolant distribution architecture is found to demonstrate the best performance, considering minimal pressure drop and uniform flow distribution. In addition, TUE is calculated for each cooling loop component based on its associated pressure drop and corresponding pumping power, which are integrated into the WFD. This correlation between TUE and local temperature offers immediate insight into the power efficiency and thermal performance contributions of individual components, facilitating further development and optimization. Examples of WFD applications are presented under varying thermal loads and ambient conditions, demonstrating reasonable cooling strategies. Notably, the 3 U modular architecture maintains a consistent chip case temperature of 85°C, achieving a TUE of 1.016 at ambient temperature of 47°C, and a TUE of 1.026 at ambient temperature of 52°C. The WFD methodology provides an efficient, holistic, and streamlined framework for DC thermal management architecture assessment and enables design optimization which is important for addressing the thermal-fluidic energy challenges of current and next-generation DCs.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Coupling extracellular glycan composition with metagenomic data in papermill and brewery anaerobic granular sludges

Glycans are crucial for the structure and function of anaerobic granular sludge in wastewater treatment. Yet, there is limited knowledge regarding the microorganisms and biosynthesis pathways responsible for glycan production. In this study, we analysed samples from anaerobic granular sludges treating papermill and brewery wastewater, examining glycans composition and using metagenome-assembled genomes (MAGs) to explore potential biochemical pathways associated with their production. Uronic acids were the predominant constituents of the glycans in extracellular polymeric substances (EPS) produced by the anaerobic granular sludges, comprising up to 60 % of the total polysaccharide content. MAGs affiliated with Anaerolineacae, Methanobacteriaceae and Methanosaetaceae represented the majority of the microbial community (30–50 % of total reads per MAG). Based on the analysis of MAGs, it appears that Anaerolinea sp. and members of the Methanobacteria class are involved in the production of exopolysaccharides within the analysed granular sludges. These findings shed light on the functional roles of microorganisms in glycan production in industrial anaerobic wastewater treatment systems.

59 BASIC BIOLOGICAL SCIENCES↗

Green synthesis of sulfur‐doped g‐C 3 N 4 nanosheets for enhanced removal of oxytetracycline under visible‐light irradiation and reduction of its N ‐nitrosodimethylamine formation potential

Abstract BACKGROUND In this study, sulfur‐doped g‐C 3 N 4 (SCN) nanosheets were synthesized using thiourea as a precursor, and then used to catalyze the degradation of oxytetracycline (OTC) under visible‐light irradiation. OTC was chosen as target contaminant because of it being an important precursor of N ‐nitrosodimethylamine (NDMA). RESULTS The removal of OTC was influenced by its initial concentration, initial pH, SCN dosage and water matrices. OTC (≤10 mg L −1 ) was almost completely removed in 40 min under the conditions of an initial pH of 7.0 and a SCN dose of 1.0 g L −1 , and its degradation was well described by the pseudo‐first‐order kinetics model. Water matrices would also influence the degradation of OTC in the system. Electron paramagnetic resonance analysis and trapping experiments confirmed that the function of the radicals for OTC removal followed the order of • O 2 − > • OH > h + . Eight transformation products were determined during the degradation of OTC, it being removed through four pathways: methyl oxidization, demethylation, decarbonylation and secondary alcohol oxidation. SCN was stable in the system, as the removal efficiency of OTC was not significantly reduced even after three recycles. In addition, 55.5% of NDMA formation potential of OTC was reduced after SCN catalytic oxidation. CONCLUSIONS The results imply that the visible‐light‐driven SCN catalytic oxidation is an effective technology not only for the removal of OTC but also for the reduction of NDMA formation potential. © 2021 Society of Chemical Industry

Dou, Yicheng↗

Efficient Size-Dependent Hot Electron Transfer from Au to TiO 2 Nanoparticles

Harvesting of plasmon-induced hot carriers at the metal/semiconductor interface offers a promising and innovative avenue for solar energy conversion. However, their practical implementation is often hampered by their limited efficiencies. Herein, we have demonstrated a highly efficient plasmonic hot electron transfer with a quantum efficiency (QE) of up to 57 ± 4% from 5.25 nm Au nanoparticles (NPs) to TiO 2 films under 400 nm ultrafast laser excitation. The observed hot electron transfer QEs decrease at larger particle sizes, to 20% for 9.1 nm Au, and show negligible changes with excitation wavelengths at 400, 500, and 600 nm. Analysis of the size and excitation wavelength dependent hot electron transfer QEs suggests they contain contributions of interband absorption, indirect plasmon-induced hot electron transfer (PHET), and direct plasmon-induced interfacial charge transfer transition (PICTT) pathways, and QEs of all three pathways increase at smaller Au size. Our result suggests that reducing plasmon particle sizes is a promising approach for efficient plasmonic hot-carrier extraction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Intrinsically Conductive {pi}‑d Conjugated Layers with Co–N4 Active Sites for Efficient Nitrate Electrocatalysis and Zinc-Nitrate Batteries

Electrochemical synthesis of ammonia from nitrate has been extensively investigated as a potential alternative to the energy-intensive Haber-Bosch process. This approach not only operates under ambient conditions but also simultaneously removes nitrate contaminants while producing ammonia as a value-added product. However, the ongoing quest lies in designing an efficient electrocatalyst that achieves a high ammonia yield rate, high selectivity, and long-term stability. Herein, we report the outstanding performance of a Co–N4 coordinated π-d layered Co3(HITP)2 (HITP = 2,3,6,7,10,11-hexaiminotriphenylene) in nitrate electrocatalysis. The unique combination of abundant Co–N4 active sites and superior electrical conductivity enables significant electrocatalytic activity, delivering a maximum ammonia yield rate of 56.8 mg cm–2 h–1 at −0.8 V vs RHE and a Faradaic efficiency of ∼91% at −0.4 V vs RHE. Mechanistic analysis reveals that alkaline conditions accelerate water dissociation to generate adsorbed hydrogen intermediates (H*), which are utilized by Co–N4 sites to drive the stepwise hydrogenation of nitrate to ammonia while suppressing competing hydrogen evolution reaction (HER) pathways. Furthermore, integration of this catalyst into a zinc-nitrate battery resulted in a maximum power density of 5.3 mW cm–2 and an open-circuit potential of ∼1.45 V. These results highlight the potential of π-d conjugated Co–N4 materials as an efficient catalyst for both environmental remediation and energy conversion.

Namvar, shahrirar↗

Impacts of long-term temperature change and variability on electricity investments

Long-term temperature change and variability are expected to have significant impacts on future electric capacity and investments. This study improves upon past studies by accounting for hourly and monthly dynamics of electricity use, long-term socioeconomic drivers, and interactions of the electric sector with rest of the economy for a comprehensive analysis of temperature change impacts on cooling and heating services and their corresponding impact on electric capacity and investments. Using the United States as an example, here we show that under a scenario consistent with a socioeconomic pathway 2 (SSP2) and representative concentration pathway 8.5 (RCP 8.5), mean temperature changes drive increases in annual electricity demands by 0.5-8% across states in 2100. But more importantly, peak temperature changes drive increases in capital investments by 3-22%. Moreover, temperature-induced capital investments are highly sensitive to both long-term socioeconomic assumptions and spatial heterogeneity of fuel prices and capital stock characteristics, which underscores the importance of a comprehensive approach to inform long-term electric sector planning.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗