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134 records · Page 8

The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species

Abstract Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research. The Monarch App is an integrated platform combining data about genes, phenotypes, and diseases across species. Monarch's APIs enable access to carefully curated datasets and advanced analysis tools that support the understanding and diagnosis of disease for diverse applications such as variant prioritization, deep phenotyping, and patient profile-matching. We have migrated our system into a scalable, cloud-based infrastructure; simplified Monarch's data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features. Furthermore, we advanced Monarch's analytic tools by developing a customized plugin for OpenAI’s ChatGPT to increase the reliability of its responses about phenotypic data, allowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be found at monarchinitiative.org and its corresponding code repository at github.com/monarch-initiative/monarch-app.

60 APPLIED LIFE SCIENCES↗

Connecting Nitrogen Transformations Mediated by the Rhizosphere Microbiome to Perennial Cropping System Productivity in Marginal Lands

The demand for energy from biofuel production is increasing, prompting concerns about the environmental impact and long-term sustainability of bioenergy cropping systems. These cropping systems will make up much of our future landscapes, and threaten to take the place of food cropping systems. Many life cycle analyses of bioenergy sustainability focus on carbon accrual and budgets, since they want to maximize carbon accrual while producing alternative fuel. Less attention has been given to nitrogen (N) dynamics in these systems. N is the most commonly limiting nutrient for plants, but applying nitrogen fertilizer- as we do for most cropping systems – is harmful to the environment, energetically costly, and produces greenhouse gases. In other words, adding nitrogen by fertilizer bioenergy systems could add to the very problems (climate change) it is trying to address. This is especially true for the areas that are proposed for bioenergy systems: marginal lands. These more degraded lands do not complete with food crops, but do have limited nitrogen. If we are to use these marginal lands for bioenergy, we need to understand the mechanisms regulating nutrient acquisition, and identify ways that bioenergy crops can get nitrogen in sustainable ways. Nutrient acquisition in the soil is performed by microbes in the root zone, or rhizosphere. Microbes can either mineralize nitrogen in the soil (from organic forms) or fix nitrogen from the air, in a process called nitrogen fixation. The goal of our project was thus to understand how the rhizosphere microbiome provides nutrients to bioenergy crops on marginal lands. We focus especially on the process of nitrogen fixation, since it has potential to get “fertilizer for free” that has much less environmental harm. We investigated this goal using sites from the DOE Great Lakes Bioenergy Research Center (GLBRC) in the upper Midwest, and associated lab and ‘omics methods. We group our findings into three major areas. First, we showed that nitrogen fixation, the conversion of N2 gas from the air to ammonium that is usable by plants, is performed in bioenergy soils, and benefits switchgrass crops. While more well-studied in leguminous plants, free-living nitrogen fixation can occur in some systems, and represents a potential opportunity to gain ‘free’ sustainable nitrogen source. We identified the nitrogen fixing bacteria that were most active in providing switchgrass with N, and showed that the drivers of nitrogen fixation occurred at a microscale; it is not well-predicted by bulk variables like soil moisture or plant phenology. Second, we showed that nitrogen fixation is not suppressed by long-term fertilizer. We expected that plentiful nitrogen would reduce the symbiotic relationship between nitrogen fixers and plants, and ‘downregulate’ fixation. We did not find evidence for this, either after long-term fertilizer in the field, or short-term fertilizer in the greenhouse. Finally, we identified the root exudates, carbon compounds that are emitted from the root, that best stimulate nitrogen fixation. We found that carbohydrates were better at stimulating fixation than organic acids. We expected these exudates to be emitted from the plant in periods of high N demand, but we found they are emitted when N is plentiful. This suggests that the stimulation of N fixation by plants is a passive process. Overall, we show that nitrogen fixation has potential to support bioenergy cropping system, and future management could develop ways to maximize it. However, this may not be best achieved via the plant – we found very little evidence of a ‘transactional’ system by which plants are controlling when and where nitrogen fixation is stimulated. It will be better to understand how management practices like planting and fertilizer application affect the microscale soil dynamics, which will determine nitrogen fixation rates.

59 BASIC BIOLOGICAL SCIENCES↗

FEED Study of Carbon Capture Inc. DAC and CarbonCure Utilization Using United States Steel's Gary Works Waste Plant

Direct Air Capture (DAC) has been proposed as a means of reducing atmospheric concentrations of CO2. While DAC has been evaluated through lab-scale, bench-scale, and small-scale pilot units, large-scale deployment has not been achieved. Feasibility studies are one tool to understand the potential design, operation, performance, and impact of commercial-scale DAC. This paper presents the results of a feasibility study for a passive DAC system deployed at >100,000 tpy scale in three different regions across the U.S. and awarded to Carbon Collect by the U.S. Department of Energy National Energy Technology Laboratory (DOE NETL). The MechanicalTree™technology has been designed and engineered by Carbon Collect based on the concept initially developed at Arizona State University Center for Negative Carbon Emissions. It uses a tower of stacked, sorbentcontaining disks supported by a lifting mechanism, exposed to the air to capture CO2 during the adsorption phase. The disks are then lowered into a regeneration chamber for vacuum and steam regeneration to produce CO2 product during the desorption step. The modular tree design allows large installations with repeatable, mass-manufactured units connected to common utilities such as steam supply, vacuum, and CO2 processing for compression and geologic storage. The passive DAC system eliminates the equipment and energy of forced air fans by using natural air circulation to contact the sorbent with the CO2 in the air. Because of this, the performance is dependent on the wind speed in addition to the temperature and relative humidity. Performance and flow rate fluctuations were incorporated into equipment and facility design with considerations for turndown to 10% of maximum rated flow to allow operation in all seasons. The feasibility study was undertaken to evaluate the technology in different regions and climates. Three locations were selected for this study representing different climates: Alabama (hot and humid), California (hot and arid), and Wyoming (continental). For each region, the adsorption/desorption cycle was optimized including tuning the heat integration and cycle timings. The performance of individual trees was then scaled to the full facility with the same design of more than 20,000 trees common between all regions. The installations had expected average CO2 capture rates of between 330,000 and 485,000 tonnes of CO2 per year depending on the climate. The initial engineering design for the facility at each location was performed with cost and performance estimates for the trees, carbon purification and compression, and the balance of plant. To supply thermal and electrical energy for the facility, carbon-free or low-carbon power must be considered. Options for low-carbon, continuous thermal and electrical energy were considered. The best-performing option from those considered was identified to be an electrically-heated molten salt energy storage system, powered by an on-site photovoltaic field. During molten salt thermal discharge, steam is produced from heat exchange with the molten salt and used to generate power in a steam turbine as well as steam for regenerating the DAC carbon trees. The thermal and electrical supply and analysis is presented in the context of low-carbon power for carbon removal. Modelling and economics of transportation and geologic storage of the CO2 is considered and presented for each location. The results of the feasibility study are incorporated into the presented techno-economic and life-cycle assessments. This work is intended to provide an understanding of the performance, cost, and impact of capturing CO2 at the commercial scale and the impact of climate and regional siting on the considered passive DAC system.

42 ENGINEERING↗

Controlled environment agriculture: An opportunity to strengthen interagency research collaboration in the US government

Challenges facing food production and agricultural systems are increasingly interconnected with economic, security, health, and equity issues, among others. Threats such as extreme weather, economic volatility, and shrinking water resources and arable land, influence our ability to maintain a safe and resilient food supply. One promising solution to these threats is controlled environment agriculture (CEA). In many cases, CEA can drastically reduce the amount of water and land used in crop production while increasing productivity. Operations may be established in nearly any environment and harvests can take place year-round, supporting food system resiliency and sustainability. CEA sits at the nexus of a number of disciplines and industries, making it well suited for transdisciplinary and multi-institutional research coordination. Herein, authors from multiple US government agencies present CEA as a case study in improving cross-agency research collaboration. The federal government houses a range of scientific expertise and research capabilities, positioning scientists to lead national and global efforts in transdisciplinary, interagency approaches to complex challenges. Navigating cross-agency collaboration can be a challenge, especially coordinating across different scientific disciplines, geographic locations, and funding mechanisms. To enhance multiagency efforts, collaborators could prioritize (i) organizing personnel and resources, (ii) enhancing existing multiagency collaborations, and (iii) focusing on further opportunities for coordination. Adopting these approaches could enable federal researchers to reinforce and advance academic and industry efforts to address current CEA challenges while solidifying the United States as a leader in this arena.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

ARM Aerial Facility (AAF) Merged Value-Added Product Report for Historical G-1 Field Campaigns

For 30 years, the U.S. Department of Energy (DOE) Office of Science supported an instrumented Grumman Gulfstream-1 (G-1) aircraft for atmospheric field campaigns. Data from the final decade of G-1 operations were archived by the Atmospheric Radiation Measurement (ARM) user facility Data Center (ADC) and made publicly available at no cost to all registered users. To ensure a consistent data format and to improve the accessibility of the ARM airborne data, an integrated data set was recently developed covering the final six years of G-1 operations (2013 to 2018). The integrated data set includes data collected from 236 flights (766.4 hours). Four of the seven field campaigns were based in the U.S. One campaign collected data from the wildfires in the U.S. Pacific Northwest and agricultural burns in the lower Mississippi River valley as part of the Biomass Burning Observation Project (BBOP) in 2013. In 2015, the ARM Cloud Aerosol Precipitation Experiment provided data on atmospheric rivers and associated aerosol-cloud interactions that produce heavy precipitation on the U.S. west coast during the early spring. Research data from Airborne Carbon Measurements-V (ACME-V), collected during the summer of 2015, gave scientists insight into trends and variability of trace gases in the atmosphere over the North Slope of Alaska to improve arctic climate models. In the early summer and autumn of 2016, the Holistic Interactions of Shallow Clouds, Aerosols, and Land-Ecosystems (HI-SCALE) campaign provided an extensive data set geared toward coupled processes that affect the life cycle of shallow clouds through the interaction among aerosol, cloud, land surface, and ecosystems. In 2014 (March and October), the airborne sampling moved outside of the U.S. to the city of Manaus in central Amazonia, Brazil, where residential and industrial emissions were extensively characterized by flights of the G-1. The GoAmazon2014/15 aircraft campaign data are being integrated with aquatic and terrestrial ecosystem measurements to quantify anthropogenic perturbations to a usually pristine tropical environment. Another international airborne mission was carried out in the Eastern North Atlantic region. The Aerosol and Cloud Experiments in the Eastern North Atlantic (ACE-ENA) campaign saw the G-1 aircraft fly from Terceira Island in the Azores during the summer of 2017 and the winter of 2018. The campaign studied both seasons to measure key aerosol and cloud processes under various meteorological and cloud conditions with different aerosol sources. Then the G-1 deployed to the Sierras de Córdoba range in central Argentina from October to November 2018 for the Cloud, Aerosol, and Complex Terrain Interactions (CACTI) campaign to study orographic convective cloud interactions with their surrounding environment. These comprehensive datastreams provide much-needed insight into spatiotemporal variability of thermodynamic quantities, aerosol and cloud states, and properties for addressing essential science questions in Earth system process studies.

54 ENVIRONMENTAL SCIENCES↗

ARM Aerial Facility (AAF) Merged Value-Added Product Report for Historical G-1 Field Campaigns

For 30 years, the U.S. Department of Energy (DOE) Office of Science supported an instrumented Grumman Gulfstream-1 (G-1) aircraft for atmospheric field campaigns. Data from the final decade of G-1 operations were archived by the Atmospheric Radiation Measurement (ARM) user facility Data Center (ADC) and made publicly available at no cost to all registered users. To ensure a consistent data format and to improve the accessibility of the ARM airborne data, an integrated data set was recently developed covering the final six years of G-1 operations (2013 to 2018). The integrated data set includes data collected from 236 flights (766.4 hours). Four of the seven field campaigns were based in the U.S. One campaign collected data from the wildfires in the U.S. Pacific Northwest and agricultural burns in the lower Mississippi River valley as part of the Biomass Burning Observation Project (BBOP) in 2013. In 2015, the ARM Cloud Aerosol Precipitation Experiment provided data on atmospheric rivers and associated aerosol-cloud interactions that produce heavy precipitation on the U.S. west coast during the early spring. Research data from Airborne Carbon Measurements-V (ACME-V), collected during the summer of 2015, gave scientists insight into trends and variability of trace gases in the atmosphere over the North Slope of Alaska to improve arctic climate models. In the early summer and autumn of 2016, the Holistic Interactions of Shallow Clouds, Aerosols, and Land-Ecosystems (HI-SCALE) campaign provided an extensive data set geared toward coupled processes that affect the life cycle of shallow clouds through the interaction among aerosol, cloud, land surface, and ecosystems. In 2014 (March and October), the airborne sampling moved outside of the U.S. to the city of Manaus in central Amazonia, Brazil, where residential and industrial emissions were extensively characterized by flights of the G-1. The GoAmazon2014/15 aircraft campaign data are being integrated with aquatic and terrestrial ecosystem measurements to quantify anthropogenic perturbations to a usually pristine tropical environment. Another international airborne mission was carried out in the Eastern North Atlantic region. The Aerosol and Cloud Experiments in the Eastern North Atlantic (ACE-ENA) campaign saw the G-1 aircraft fly from Terceira Island in the Azores during the summer of 2017 and the winter of 2018. The campaign studied both seasons to measure key aerosol and cloud processes under various meteorological and cloud conditions with different aerosol sources. Then the G-1 deployed to the Sierras de Córdoba range in central Argentina from October to November 2018 for the Cloud, Aerosol, and Complex Terrain Interactions (CACTI) campaign to study orographic convective cloud interactions with their surrounding environment. These comprehensive datastreams provide much-needed insight into spatiotemporal variability of thermodynamic quantities, aerosol and cloud states, and properties for addressing essential science questions in Earth system process studies.

54 ENVIRONMENTAL SCIENCES↗

Subtask 1.3 – Integrated Carbon Capture and Storage for North Dakota Ethanol Production

The Energy & Environmental Research Center (EERC), in partnership with Red Trail Energy, LLC (RTE), a North Dakota ethanol producer; the North Dakota Industrial Commission (NDIC) Renewable Energy Program (REP); and the U.S. Department of Energy (DOE), conducted a feasibility and implementation study for a commercial carbon capture and storage (CCS) effort. This subtask provided technical support and developed recommended practices of how small-scale industrial CO2 emitters (<1,000,000 tonnes of CO2 emitted annually) may economically deploy CCS. The 64-million-gallon dry mill RTE ethanol facility, emitting an average 180,000 tonnes of CO2 annually, was the subject of the case study. The positive outcome of this research, which shows technical and economic potential for ethanol–CCS in North Dakota, has resulted in RTE acquiring an approved Permit to Drill on December 2, 2019, for a stratigraphic test well in early 2020, a necessary step toward a North Dakota CO2 Storage Facility Permit (SFP) for the RTE CCS effort. Outcomes include 1) validating the Broom Creek Formation as a regional target for CCS, 2) determining the full carbon life cycle of an industrial fuel production facility with CCS, 3) developing a field implementation plan (FIP) for small-scale CCS, and 4) determining the validity and pathway for using CCS to meet low-carbon fuel (LCF) standards. The technical team included the EERC, RTE, Trimeric Corporation, Schlumberger Carbon Services, and Computer Modelling Group (CMG). Findings from activities conducted November 2016 – May 2020 are summarized as follows. Several key steps have been accomplished toward validating the Broom Creek Formation as a CO2 injection and storage target at the RTE CCS site, including verification of the presence and structure of sandstone layers that may comprise the potential CO2 storage reservoir and the several thousand feet of overlying confining zone. Work included site characterization using existing data, interpretation of seismic data within the study area, and geologic modeling simulation of CO2 injection. Interpreted results estimate 3000 feet of confining zone between the Broom Creek Formation (storage target) and the lowermost underground source of drinking water (e.g., the Fox Hills Formation). The thickness of the Broom Creek injection target varies 230–420 ft within the survey area. Results were used to inform the location of a stratigraphic test well and associated characterization test program. No impediments were identified within the targeted CO2 storage complex that would prevent the project from moving forward. A stratigraphic test well is the next step to validate these results and to acquire remaining data necessary to develop a North Dakota CO2 SFP application. The EERC generated full carbon life cycle estimates for CCS integration with the RTE ethanol facility. Results indicated that an average 40% reduction in CO2 emissions is possible through CCS implementation. Approximately half of the carbon in the overall life cycle for a dry mill ethanol plant is generated through the fermentation process and emitted to the atmosphere; this is the CO2 stream targeted for CCS. The remaining carbon is attributed to corn feedstock farming (diesel, fertilizer), energy for fuel processing (natural gas, electricity), and transportation (diesel) of the fuel product. Life cycle carbon estimates are also affected by the anticipated energy consumption of a potential capture facility, which depend on the type of CO2 product generated. For example, a 30%–40% net CO2 emission reduction is estimated if a liquefied CO2 facility were incorporated compared to a 40%–50% net CO2 reduction if a supercritical “injection-grade” CO2 product is generated; i.e., more energy is required to further refine the CO2 stream, affecting the full carbon life cycle estimates. A CCS FIP was developed and initiated at the RTE CCS site, resulting in the development of several guidance documents: a CO2 Capture Process Design Package, a North Dakota CO2 geologic Storage Permits Template, and a Public Outreach Package for CCS in North Dakota. General FIP components include CO2 capture system, pipeline and well designs; monitoring, verification, and accounting (MVA) plans; geologic characterization and testing programs; and permitting and outreach plans. Vendor bids were also acquired for the CO2 liquefaction facility. Near-surface characterization (groundwater and soil gas sampling) and geologic characterization (seismic survey) were initiated to inform development of a UIC Class VI-compliant MVA plan compliant with a North Dakota CO2 SFP. Designs (well and geologic testing) were completed for a stratigraphic test well compliant with a North Dakota CO2 SFP. In addition, the outreach plan was executed, including community open houses, meetings with city/county/state officials, and development of public materials. Although other entities continued to mature incentive programs in 2019–2020, California and the Internal Revenue Service (IRS) currently provide the most advanced economic opportunities for CCS integrated with fuel production. The California Low-Carbon Fuel Standard (LCFS) adopted a CCS Protocol in January 2019, allowing submittal of a design-based pathway (DBP) application for an approved temporary (not certified) carbon intensity value for a fully engineered facility. An ethanol–CCS DBP application to the California LCFS Program (officially approved February 28, 2020) was developed to show that the RTE CCS effort meets LCFS requirements. The approved DBP provides confidence to advance the project and supports potential investments. Other entities continue to mature incentive programs. The IRS issued guidance in February 2020 that addresses the definition of beginning of construction and revenue procedure on partnerships for the Enhancement of Carbon Dioxide Sequestration Credit (a.k.a. Section 45Q) CCS tax credit program; the IRS anticipates issuing further guidance on issues such as secure geologic storage, utilization qualifications, and recapture of claimed credits. Maturing incentive programs coupled with workable permitting regulations provide confidence to advance CCS projects in North Dakota and support financial investment to proceed with designing, constructing, and implementing CCS projects at small-scale fuel production facilities. The largest hurdles for CCS implementation at small-scale industrial systems are often business/economic-related (i.e., not technical). Market uncertainty already exists for agriculture-based alternative fuels such as corn ethanol, for which production has increased by ~33%, and prices have correspondingly lowered since 2015. Passing the Section 45Q tax credit program improves economic feasibility for CCS but may require external investors for a small business to achieve maximum benefits. Public–private partnerships with NDIC and DOE have resulted in foundational technical and regulatory knowledge, growing stakeholder confidence, and a pathway to implementation that enables similar industrial CCS projects in the region to advance. This subtask was funded through the EERC–DOE Joint Program on Research and Development for Fossil Energy-Related Resources Cooperative Agreement No. DE-FE0024233. Nonfederal funding was provided by NDIC and RTE. The authors would also like to thank CMG, ESRI, IHS, Neuralog, and Schlumberger for allowing the use of their software packages in support of this work.

42 ENGINEERING↗

TRACER-Coastal Urban Boundary-Layer Interactions with Convection (TRACER-CUBIC) Field Campaign Report

To better understand the complicated web of processes governing convective cloud life cycle and aerosol-convection interactions, the U.S. Department of Energy (DOE)’s Atmospheric Radiation Measurement (ARM) user facility supported deployment of a variety of advanced atmospheric measurement systems to the greater Houston, Texas, area from 1 October 2021 to 30 September 2022 as part of the Tracking Aerosol Convection Interactions Experiment (TRACER). Houston was selected as a study area because isolated convection and a variety of aerosol conditions are common in this region. This one-year ARM Mobile Facility (AMF) deployment featured a four-month intensive operational period (IOP) during summer 2022 (1 June–30 September). The ARM instrumentation was deployed at three sites along an east-west transect from La Porte, Texas to an ancillary site in a less-polluted rural region southwest of downtown Houston (Figure 1). At the La Porte Site, which is located near the Houston ship channel in an area that experiences significant pollution, the first ARM Mobile Facility (AMF1) was deployed. During the IOP, the ARM tethered balloon system (TBS) operated at the ancillary site. The second-generation C-Band Scanning ARM Precipitation Radar (CSAPR) operated near Pearland, Texas, roughly halfway between the Laporte and ancillary sites. As part of the TRACER- Coastal Urban Boundary-Layer Interactions with Convection (CUBIC) project, three boundary-layer profiling systems) were deployed along a north-south transect spanning from the University of Houston Coastal Center to the Aldine site north of downtown Houston (also blue dot in Figure 1) during the TRACER IOP. These systems included the National Oceanic and Atmospheric Administration (NOAA) National Severe Storms Laboratory CLAMPS2 (C2), which was deployed at the UHCC, the University of Wisconsin SPARC, which was deployed at the ARM CSAPR site near Pearland (orange diamond in middle of map in Figure 1), and the University of Oklahoma CLAMPS1 (C1), which was deployed at Aldine. These three systems have been successfully operated in various field campaigns, providing data sets that collectively offer new insights into atmospheric-boundary-layer (ABL) processes, sea-breeze (SB) circulations, and convection initiation (CI). For the TRACER IOP window, these systems ran continuously between 1 June and 26 September, 2022. Due to commitments to NOAA projects, the Doppler lidar at the UHCC site was not available until 24 June 2022. The CLAMPS and SPARC profiling systems are self-contained platforms that have benefited from several years of development and deployment. Instruments and data processing were maintained remotely, which made the 4-month deployment for the TRACER-CUBIC IOP period possible. The same basic instrument configuration comprises each system: a scanning Doppler wind lidar for flow characterization and passive profiler(s) for characterizing planetary-boundary-layer (PBL) thermodynamic properties. Each platform includes a Halo Streamline Doppler wind lidar, an Atmospheric Emitted Radiance Interferometer (AERI), and a surface meteorology station. CLAMPS1 and CLAMPS2 each also include a microwave radiometer (MWR, Figure 1d). The TRACER-CUBIC hypotheses included (i) Interactions of SB and urban circulations and how they affect the PBL structure in the Houston environment, causing spatially (horizontally and vertically) and temporally highly variable flow patterns, (ii) heat, moisture, and aerosol transport and mixing depend on these flow dynamics, and (iii) an improved understanding of the flow patterns and PBL structure are critical for investigating the processes leading to CI. To test these hypotheses, the project aimed at (i) characterizing SB circulations and their impacts on the diurnal evolution of the structure of the ABL, (ii) studying the evolution of Houston’s complex urban boundary layer, and (iii) identifying effects of urban-induced circulations on pre-convective environments. TRACER-CUBIC observations generally provide good coverage during the summer IOP. Initial screening of the data indicates a good number of cases with bay-breeze (BB) and/or SB signatures, local CI, and interesting boundary-layer features such as strong nocturnal low-level jets (LLJs, Table 1). The numbers listed in rows 3-5 in this table will be further updated as part of ongoing in-depth analyses and systematic identification of local circulations and CI events. More detailed information about the data availability and quality for each instrument is provided in the “readme” files that were submitted to the ARM Data Center along with each archived data sets. These “readme” files also provide instrument descriptions, information about the data collection and processing procedures, data formats, and any additional information relevant for further data analysis.

54 ENVIRONMENTAL SCIENCES↗