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DOE OSTI2016

An Evaluation of Subsurface Microbial Activity Conditional to Subsurface Temperature, Porosity, and Permeability at North American Carbon Sequestration Sites

Several nations, including the United States, recognize global climate change as a force transforming the global ecosphere. Carbon dioxide (CO 2 ) is a greenhouse gas that contributes to the evolving climate. Reduction of atmospheric CO 2 levels is a goal for many nations and carbon sequestration which traps CO 2 in the Earth’s subsurface is one method to reduce atmospheric CO 2 levels. Among the variables that must be considered in developing this technology to a national scale is microbial activity. Microbial activity or biomass can change rock permeability, alter artificial seals around boreholes, and play a key role in biogeochemistry and accordingly may determine how CO 2 is sequestered underground. Certain physical parameters of a reservoir found in literature (e.g., temperature, porosity, and permeability) may indicate whether a reservoir can host microbial communities. In order to estimate which subsurface formations may host microbes, this report examines the subsurface temperature, porosity, and permeability of underground rock formations that have high potential to be targeted for CO 2 sequestration. Of the 268 North American wellbore locations from the National Carbon Sequestration Database (NATCARB; National Energy and Technology Laboratory, 2015) and 35 sites from Nelson and Kibler (2003), 96 sequestration sites contain temperature data. Of these 96 sites, 36 sites have temperatures that would be favorable for microbial survival, 48 sites have mixed conditions for supporting microbial populations, and 11 sites would appear to be unfavorable to support microbial populations. Future studies of microbe viability would benefit from a larger database with more formation parameters (e.g. mineralogy, structure, and groundwater chemistry), which would help to increase understanding of where CO 2 sequestration could be most efficiently implemented.

25 ENERGY STORAGE↗

DOE OSTI2014

Radiation Therapy Infrastructure and Human Resources in Low- and Middle-Income Countries: Present Status and Projections for 2020

Purpose: Radiation therapy, a key component of cancer management, is required in more than half of new cancer patients, particularly in low- and middle-income countries (LMICs). The projected rise in cancer incidence over the next decades in LMICs will result in an increasing demand for radiation therapy services. Considering the present cancer incidence and that projected for 2020 (as listed in GLOBOCAN), we evaluated the current and anticipated needs for radiation therapy infrastructure and staffing by 2020 for each of the LMICs. Methods and Materials: Based on World Bank classification, 139 countries fall in the category of LMICs. Details of teletherapy, radiation oncologists, medical physicists, and radiation therapy technologists were available for 84 LMICs from the International Atomic Energy Agency–Directory of Radiotherapy Centres (IAEA-DIRAC) database. Present requirements and those for 2020 were estimated according to recommendations from the IAEA and European Society for Radiotherapy and Oncology (ESTRO-QUARTS). Results: Only 4 of the 139 LMICs have the requisite number of teletherapy units, and 55 (39.5%) have no radiation therapy facilities at present. Patient access to radiation therapy in the remaining 80 LMICs ranges from 2.3% to 98.8% (median: 36.7%). By 2020, these 84 LMICs would additionally need 9169 teletherapy units, 12,149 radiation oncologists, 9915 medical physicists, and 29,140 radiation therapy technologists. Moreover, de novo radiation therapy facilities would have to be considered for those with no services. Conclusions: Twelve pragmatic steps are proposed for consideration at national and international levels to narrow the gap in radiation therapy access. Multipronged and coordinated action from all national and international stakeholders is required to develop realistic strategies to curb this impending global crisis.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2023

In silico analyses of diversity and dissemination of antimicrobial resistance genes and mobile genetics elements, for plasmids of enteric pathogens

The antimicrobial resistance (AMR) mobilome plays a key role in the dissemination of resistance genes encoded by mobile genetics elements (MGEs) including plasmids, transposons (Tns), and insertion sequences (ISs). These MGEs contribute to the dissemination of multidrug resistance (MDR) in enteric bacterial pathogens which have been considered as a global public health risk. To further understand the diversity and distribution of AMR genes and MGEs across different plasmid types, we utilized multiple sequence-based computational approaches to evaluate AMR-associated plasmid genetics. A collection of 1,309 complete plasmid sequences from Gammaproteobacterial species, including 100 plasmids from each of the following 14 incompatibility (Inc) types: A/C, BO, FIA, FIB, FIC, FIIA, HI1, HI2, I1, K, M, N, P except W, where only 9 sequences were available, was extracted from the National Center for Biotechnology Information (NCBI) GenBank database using BLAST tools. The extracted FASTA files were analyzed using the AMRFinderPlus web-based tools to detect antimicrobial, disinfectant, biocide, and heavy metal resistance genes and ISFinder to identify IS/Tn MGEs within the plasmid sequences. In silico prediction based on plasmid replicon types showed that the resistance genes were diverse among plasmids, yet multiple genes were widely distributed across the plasmids from enteric bacterial species. These findings provide insights into the diversity of resistance genes and that MGEs mediate potential transmission of these genes across multiple plasmid replicon types. This notion was supported by the observation that many IS/Tn MGEs and resistance genes known to be associated with them were common across multiple different plasmid types. Our results provide critical insights about how the diverse population of resistance genes that are carried by the different plasmid types can allow for the dissemination of AMR across enteric bacteria. The results also highlight the value of computational-based approaches and in silico analyses for the assessment of AMR and MGEs, which are important elements of molecular epidemiology and public health outcomes.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2016

Variation in Global Chemical Composition of PM2.5: Emerging Results from SPARTAN

The Surface PARTiculate mAtter Network (SPARTAN) is a long-term project that includes characterization of chemical and physical attributes of aerosols from filter samples collected worldwide. This paper discusses the ongoing efforts of SPARTAN to define and quantify major ions and trace metals found in fine particulate matter (PM (sub 2.5). Our methods infer the spatial and temporal variability of PM (sub 2.5) in a cost-effective manner. Gravimetrically weighed filters represent multi-day averages of PM (sub 2.5), with a collocated nephelometer sampling air continuously. SPARTAN instruments are paired with AErosol RObotic NETwork (AERONET) sun photometers to better understand the relationship between ground-level PM (sub 2.5) and columnar aerosol optical depth (AOD). We have examined the chemical composition of PM (sub 2.5) at 12 globally dispersed, densely populated urban locations and a site at Mammoth Cave (US) National Park used as a background comparison. So far, each SPARTAN location has been active between the years 2013 and 2016 over periods of 2-26 months, with an average period of 12 months per site. These sites have collectively gathered over 10 years of quality aerosol data. The major PM (sub 2.5) constituents across all sites (relative contribution plus or minus Standard Deviation) are ammoniated sulfate (20 percent plus or minus 11 percent), crustal material (13.4 percent plus or minus 9.9 percent), equivalent black carbon (11.9 percent plus or minus 8.4 percent), ammonium nitrate (4.7 percent plus or minus 3.0 percent), sea salt (2.3 percent plus or minus 1.6 percent), trace element oxides (1.0 percent plus or minus 1.1 percent), water (7.2 percent plus or minus 3.3 percent) at 35 percent relative humidity, and residual matter (40 percent plus or minus 24 percent). Analysis of filter samples reveals that several PM (sub 2.5) chemical components varied by more than an order of magnitude between sites. Ammoniated sulfate ranges from 1.1 microns per cubic meter (Buenos Aires, Argentina) to 17 microns per cubic meter (Kanpur, India in the dry season). Ammonium nitrate ranged from 0.2 microns per cubic meter (Mammoth Cave, in summer) to 6.8 microns per cubic meter (Kanpur, dry season). Equivalent black carbon ranged from 0.7 microns per cubic meter (Mammoth Cave) to over 8 microns per cubic meter (Dhaka, Bangladesh and Kanpur, India). Comparison of SPARTAN vs. coincident measurements from the Interagency Monitoring of Protected Visual Environments (IMPROVE) network at Mammoth Cave yielded a high degree of consistency for daily PM (sub 2.5) (r squared equals 0.76, slope equals 1.12), daily sulfate (r squared equals 0.86, slope equals 1.03), and mean fractions of all major PM (sub 2.5) components (within 6 percent). Major ions generally agree well with previous studies at the same urban locations (e.g. sulfate fractions agree within 4 percent for 8 out of 11 collocation comparisons). Enhanced anthropogenic dust fractions in large urban areas (e.g. Singapore, Kanpur, Hanoi, and Dhaka) are apparent from high Zn to Al ratios. The expected water contribution to aerosols is calculated via the hygroscopicity parameter kappa (sub v (volume)) for each filter. Mean aggregate values ranged from 0.15 (Ilorin) to 0.28 (Rehovot). The all-site parameter mean is 0.20 plus or minus 0.04. Chemical composition and water retention in each filter measurement allows inference of hourly PM (sub 2.5) at 35 percent relative humidity by merging with nephelometer measurements. These hourly PM (sub 2.5) estimates compare favourably with a beta attenuation monitor (MetOne) at the nearby US embassy in Beijing, with a coefficient of variation r squared equals 0.67 (number equals 3167), compared to r squared equals 0.62 when v (volume) was not considered. SPARTAN continues to provide an open-access database of PM (sub 2.5) compositional filter information and hourly mass collected from a global federation of instruments.

Snider, Graydon↗

NASA NTRS2020

How emissions uncertainty influences the distribution and radiative impacts of smoke from fires in North America

Fires and the aerosols that they emit impact air quality, health, and climate, but the abundance and properties of carbonaceous aerosol (both black carbon and organic carbon) from biomass burning (BB) remain uncertain and poorly constrained. We aim to explore the uncertainties associated with fire emissions and their air quality and radiative impacts from underlying dry matter consumed and emissions factors. To investigate this, we compare model simulations from a global chemical transport model, GEOS-Chem, driven by a variety of fire emission inventories with surface and airborne observations of black carbon (BC) and organic aerosol (OA) concentrations and satellite-derived aerosol optical depth (AOD). We focus on two fire-detection-based and/or burned-area-based (FD-BA) inventories using burned area and active fire counts, respectively, i.e., the Global Fire Emissions Database version 4 (GFED4s) with small fires and the Fire INventory from NCAR version 1.5 (FINN1.5), and two fire radiative power (FRP)-based approaches, i.e., the Quick Fire Emission Dataset version 2.4 (QFED2.4) and the Global Fire Assimilation System version 1.2 (GFAS1.2). We show that, across the inventories, emissions of BB aerosol (BBA) differ by a factor of 4 to 7 over North America and that dry matter differences, not emissions factors, drive this spread. We find that simulations driven by QFED2.4 generally overestimate BC and, to a lesser extent, OA concentrations observations from two fire-influenced aircraft campaigns in North America (ARCTAS and DC3) and from the Interagency Monitoring of Protected Visual Environments (IMPROVE) network, while simulations driven by FINN1.5 substantially underestimate concentrations. The GFED4s and GFAS1.2-driven simulations provide the best agreement with OA and BC mass concentrations at the surface (IMPROVE), BC observed aloft (DC3 and ARCTAS), and AOD observed by MODIS over North America. We also show that a sensitivity simulation including an enhanced source of secondary organic aerosol (SOA) from fires, based on the NOAA Fire Lab 2016 experiments, produces substantial additional OA; however, the spread in the primary emissions estimates implies that this magnitude of SOA can be neither confirmed nor ruled out when comparing the simulations against the observations explored here. Given the substantial uncertainty in fire emissions, as represented by these four emission inventories, we find a sizeable range in 2012 annual BBA PM2.5 population-weighted exposure over Canada and the contiguous US (0.5 to 1.6 µg/cu. m). We also show that the range in the estimated global direct radiative effect of carbonaceous aerosol from fires (−0.11 to −0.048 W/sq. m) is large and comparable to the direct radiative forcing of OA (−0.09 W/sq. m) estimated in the Fifth Assessment Report (AR5) of the Intergovernmental Panel on Climate Change (IPCC). Our analysis suggests that fire emissions uncertainty challenges our ability to accurately characterize the impact of smoke on air quality and climate.

North America↗

DOE OSTI2023

Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton

ABSTRACT Metagenomics is a powerful method for interpreting the ecological roles and physiological capabilities of mixed microbial communities. Yet, many tools for processing metagenomic data are neither designed to consider eukaryotes nor are they built for an increasing amount of sequence data. EukHeist is an automated pipeline to retrieve eukaryotic and prokaryotic metagenome-assembled genomes (MAGs) from large-scale metagenomic sequence data sets. We developed the EukHeist workflow to specifically process large amounts of both metagenomic and/or metatranscriptomic sequence data in an automated and reproducible fashion. Here, we applied EukHeist to the large-size fraction data (0.8–2,000 µm) from Tara Oceans to recover both eukaryotic and prokaryotic MAGs, which we refer to as TOPAZ (Tara Oceans Particle-Associated MAGs). The TOPAZ MAGs consisted of >900 environmentally relevant eukaryotic MAGs and >4,000 bacterial and archaeal MAGs. The bacterial and archaeal TOPAZ MAGs expand upon the phylogenetic diversity of likely particle- and host-associated taxa. We use these MAGs to demonstrate an approach to infer the putative trophic mode of the recovered eukaryotic MAGs. We also identify ecological cohorts of co-occurring MAGs, which are driven by specific environmental factors and putative host-microbe associations. These data together add to a number of growing resources of environmentally relevant eukaryotic genomic information. Complementary and expanded databases of MAGs, such as those provided through scalable pipelines like EukHeist, stand to advance our understanding of eukaryotic diversity through increased coverage of genomic representatives across the tree of life. IMPORTANCE Single-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers’ efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1998

Locating Biodiversity Data Through The Global Change Master Directory

The Global Change Master Directory (GCMD) presently holds descriptions for almost 7000 data sets held worldwide. The directory's primary purpose is for data discovery. The information provided through the GCMD's Directory Interchange Format (DIF) is the set of information that a researcher would need to determine if a particular data set could be of value. By offering data set descriptions worldwide in many scientific disciplines - including meteorology, oceanography, ecology, geology, hydrology, geophysics, remote sensing, paleoclimate, solar-terrestrial physics, and human dimensions of climate change - the GCMD simplifies the discovery of data sources. Direct linkages to many of the data sets are also provided. In addition, several data set registration tools are offered for populating the directory. To search the directory, one may choose the Guided Search or Free-Text Search. Two experimental interfaces were also made available with the latest software release - one based on a keyword search and another based on a graphical interface. The graphical interface was designed in collaboration with the Human Computer Interaction Laboratory at the University of Maryland. The latest version of the software, Version 6, was released in April, 1998. It features the implementation of a scheme to handle hierarchical data set collections (parent-child relationships); a hierarchical geospatial location search scheme; a Java-based geographic map for conducting geospatial searches; a Related-URL field for project-related data set collections, metadata extensions (such as more detailed inventory information), etc.; a new implementation of the Isite software; a new dataset language field; hyperlinked email addresses, and more. The key to the continued evolution of the GCMD is in the flexibility of the GCMD database, allowing modifications and additions to made relatively easily to maintain currency, thus providing the ability to capitalize on current technology while importing all existing records. Changes are discussed and approved through an online "interoperability" forum. The next major release of the GCMD is scheduled for early 1999 and will include the incorporation of a new matrix-based interface, a rapid valids-based query system; improvement in the operations facility - important for future distributed options; new streamlined code for greater performance and maintainability; improvements in the handling of seven current fields proposed through the interoperability forum (at no expense to the data providers); and the release of DOCmorph, a more robust version of DIFmorph to translate many 'standards' multi-directionally. Issues and actions will also be addressed.

Olsen, Lola M.↗

DOE OSTI2015

Ecological Monitoring and Compliance Program 2014 Report

The Ecological Monitoring and Compliance Program (EMAC), funded through the U.S. Department of Energy, National Nuclear Security Administration Nevada Field Office (NNSA/NFO, formerly Nevada Site Office), monitors the ecosystem of the Nevada National Security Site (NNSS) and ensures compliance with laws and regulations pertaining to NNSS biota. This report summarizes the program’s activities conducted by National Security Technologies, LLC (NSTec), during calendar year 2014. Program activities included (a) biological surveys at proposed activity sites, (b) desert tortoise compliance, (c) ecosystem monitoring, (d) sensitive plant species monitoring, (e) sensitive and protected/regulated animal monitoring, and (f) habitat restoration monitoring. During 2014, all applicable laws, regulations, and permit requirements were met, enabling EMAC to achieve its intended goals and objectives. Sensitive and protected/regulated species of the NNSS include 42 plants, 1 mollusk, 2 reptiles, 236 birds, and 27 mammals. These species are protected, regulated, or considered sensitive according to state or federal regulations and natural resource agencies and organizations. The desert tortoise (Gopherus agassizii) and the western yellow-billed cuckoo (Coccyzus americanus) are the only species on the NNSS protected under the Endangered Species Act, both listed as threatened. However, only one record of the cuckoo has ever been documented on the NNSS, and there is no good habitat for this species on the NNSS. It is considered a rare migrant. Biological surveys for the presence of sensitive and protected/regulated species and important biological resources on which they depend were conducted for 18 projects. A total of 199.18 hectares (ha) was surveyed for these projects. Sensitive and protected/regulated species and important biological resources found during these surveys included a predator burrow, one sidewinder rattlesnake (Crotalus cerastes), two mating speckled rattlesnakes (Crotalus mitchellii), and several species of cacti. NSTec provided to project managers a written summary report of all survey findings and mitigation recommendations, where applicable. Of the 18 projects on the NNSS, 15 occurred within the range of the threatened desert tortoise. Approximately 2.19 ha of desert tortoise habitat were disturbed. No desert tortoises were accidentally injured or killed by project activities, and no tortoises were killed by vehicles. On 13 occasions, tortoises were moved off the road and out of harm’s way. Six tortoises were found and transmitters attached as part of an approved study to assess impacts of vehicles on tortoises on the NNSS. NSTec biologists continued to monitor 37 juvenile desert tortoises as part of a collaborative effort to study survival and temperament of translocated animals. From 1978 until 2013, there has been an average of 11.2 wildland fires per year on the NNSS with an average of about 83.7 ha burned per fire. There were no wildland fires documented on the NNSS during 2014. Results from the wildland fuel surveys showed a very low risk of wildland fire due to reduced fuel loads caused by limited natural precipitation. Limited reptile trapping and reptile roadkill surveys were conducted to better define species distribution on the NNSS. Sixteen reptiles were trapped representing five species. Combined with data from 2013, 183 road kills were detected, representing 11 snake and 8 lizard species. Selected natural water sources were monitored to assess trends in physical and biological parameters, and one new water source was found. Wildlife use at five water troughs and four radiologically contaminated sumps was documented using motion-activated cameras. As part of the statewide effort to disseminate information throughout the botanical community, NSTec prepared a shape file with site-specific data for all 17 sensitive plants on the NNSS and provided it to the Nevada Natural Heritage Program for inclusion in their statewide database. No field surveys were conducted this year for sensitive plants on the NNSS due to poor growing conditions. Surveys of sensitive and protected/regulated animals during 2014 focused on winter raptors, bats, wild horses (Equus caballus), mule deer (Odocoileus hemionus), desert bighorn sheep (Ovis Canadensis nelsoni), and mountain lions (Puma concolor). Two permanent, long-term winter raptor survey routes were established and sampled in January and February. A total of 27 raptors representing 4 species were observed. The wild horse population increased from 30 to 41, with several yearlings recruiting into the population, possibly due to the death of a mountain lion known to prey on horse foals. Mule deer abundance and density measured with standardized deer surveys was similar to 2013 and appears to be stable. Desert bighorn sheep, including rams, ewes, and lambs, were detected using motion-activated cameras at four water sources. There are plans to conduct helicopter surveys to census the population during September 2015 and then capture and radio-collar up to 20 sheep during November 2015. Over 150 sheep scat samples have been collected for genetic analysis to try to determine how sheep on the NNSS are related to surrounding sheep populations. Information is presented about bird mortalities, Migratory Bird Treaty Act compliance, and a summary of nuisance animals and their control on the NNSS. A total of 93 mountain lion images (i.e., photographs or video clips) were taken during 220,379 camera hours at 16 of 32 sites sampled and another 11,946 images of at least 29 species other than mountain lions were taken as well. A mountain lion telemetry study continued in 2014. NNSS7 was tracked from January 1 to November 15 using a global positioning system satellite transmitter. He consumed 21 mule deer, 17 desert bighorn sheep, 1 juvenile bobcat, and 3 coyotes. Mule deer were primarily taken in the summer and fall. No new mountain lions were captured. A minimum of four adult lions (two males, two females), a subadult male, and three kittens were known to inhabit the NNSS during 2014. Two previously revegetated sites on the NNSS and one on the Tonopah Test Range (TTR) were monitored in 2014. The cover cap on the U-3ax/bl disposal unit, revegetated in 2000, and the 92-Acre Site at the Area 5 Radioactive Waste Management Complex, revegetated in 2011, were the restoration sites monitored on the NNSS. The Corrective Action Unit 407 Rollercoaster RADSAFE site, revegetated in 2000, was the restoration site monitored on the TTR. Plant cover and density were recorded at all sites except U-3ax/bl (qualitative monitoring), and reclamation success standards were evaluated, where applicable.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRSDate not supplied

Assessing Stratospheric Aerosols Contamination Due to Space Activities

The life cycle of a spacecraft starts and ends in the atmosphere: it interacts with the atmosphere right after the launch and during the atmospheric reentry when it usually mostly ablates. Both phases induce emissions of gases and solid particles, providing a source of these components in the middle atmosphere. Little is known about the exact nature, composition and effects of these emissions on the atmosphere and climate, but their impact is expected to rise as more and more orbiting satellites are launched. Ever since the years 2000, the number of space rockets launched per year has increased by a factor 3 globally. At the same time, the number of satellites launched in orbit around the Earth per year has been multiplied by about 30. One may wonder whether changes in the anthropogenic material injected in the terrestrial stratosphere can be detected and what its influence may be. In order to study the cosmic dust particles arriving on Earth, the NASA Johnson Space Center (JSC) has been systematically collecting solid dust particles from the Earth’s stratosphere by aircraft equipped with dedicated particle collectors since 1981. So far, 25 catalogs have been published, covering campaigns of collection from 1981 to 2020, with a total of 5071 solid particles that have been preliminary characterized and curated. In this work, we use the preliminary classification of the dust particles. Based on SEM images and X-ray EDS composition the collected dust is separated into four groups: C (Cosmic), TCN (Terrestrial Contaminant Natural), TCA (Terrestrial Contaminant Artificial) and AOS (Aluminum Oxide Sphere). The AOS being mostly generated by solid rocket propellant, they also belong to the TCA class. Our analysis of the data published indicates that from 1980 to 2009 the cosmic dust particles typically represent on average 40% of the collection with TCA and TCN corresponding to about 30% each. In the recent years, the TCA fraction has doubled to about 60% of the collection (2010-2020). This increase in anthropogenic particles is likely due to the overall human space activity and its recent increase. We will present the properties of the solid stratospheric dust particles collected and their evolution with time. Future work will be dedicated to better classify the natural and anthropogenic particles collected and described in the existing databases. We will use numerical modelling to produce quantitative estimates of the injected mass, the lifetime of particles in the middle atmosphere (stratosphere) and the relative abundance of the anthropogenic particles with respect to the stratospheric background particle population.

J Lasue↗

DOE OSTI2025

Dependence of ion-cyclotron range of frequencies instabilities on species mix and fast-ion distribution: II. Time evolution

Dedicated DIII-D experiments studied instabilities below the ion cyclotron frequency f ci and at cyclotron harmonics by injecting thirteen different neutral beam populations into plasmas with different thermal compositions of H and D at five different values of toroidal field. The resulting database of 2529 conditions is described in Part 1: Stability. This paper focuses on the temporal evolution. For some beam geometries, the ion cyclotron emission (ICE) is much stronger at the beginning of injection, suggesting the importance of ‘bump-on-tail’ energy drive. Sawtooth crashes cause the emission to cease for some beam types and emission bands, but the opposite effect occurs for others. When unstable, for virtually all conditions and frequency bands, the emission bursts in a cycle reminiscent of predator-prey oscillations. Evidence for nonlinear interaction between ICE harmonics is observed. Strongly unstable modes typically appear within 1 ms from the start of beam injection and often decay within 0.1 ms when the beam turns off, but both the initial rise and final decay of the mode power exhibit a wide variety of behavior.

electromagnetic ion cyclotron instabilities↗

DOE OSTI2025

Mondo: integrating disease terminology across communities

Precision medicine aims to enhance diagnosis, treatment, and prognosis by integrating multimodal data at the point of care. However, challenges arise due to the vast number of diseases, differing methods of classification, and conflicting terminological coding systems and practices used to represent molecular definitions of disease. This lack of interoperability artificially constrains the potential for diagnosis, clinical decision support, care outcome analysis, as well as data linkage across research domains to support the development or repurposing of therapeutics. There is a clear and pressing need for a unified system for managing disease entities⁠—including identifiers, synonyms, and definitions. To address these issues, we created the Mondo disease ontology—a community-driven, open-source, unified disease classification system that harmonizes diverse terminologies into a consistent, computable framework. Mondo integrates key medical and biomedical terminologies, including Online Mendelian Inheritance in Man (OMIM), Orphanet, Medical Subject Headings (MeSH), National Cancer Institute Thesaurus (NCIt), and more, to provide a comprehensive and accurate representation of disease concepts with fully provenanced and attributed links back to the sources. Mondo can be used as the handle for curation of gene–disease associations utilized in diagnostic applications, research applications such as computational phenotyping, and in clinical coding systems in clinical decision support by pointing the clinician to the numerous knowledge resources linked to the Mondo identifier. Mondo's community-centric approach, stewarded by the Monarch Initiative's expertise in ontologies, ensures that the ontology remains adaptable to the evolving needs of biomedical research and clinical communities, as well as the knowledge providers.

biomedical informatics↗

DOE OSTI2018

Connecting AmeriFlux to the Globe, Extending the Partnership with Global Flux Network FLUXNET

We propose a project that will extend and expand the activities and contributions of AmeriFlux, to the global stage by working with our international partners to continue operating and expand the functioning of global FLUXNET database. One goal is to produce the next-generation FLUXNET dataset. This will be an integrated dataset on carbon, water and energy fluxes, on meteorological conditions and on the structure and function of the ecosystems; we have to potential to construct a new database, double the size of the La Thuile dataset, with over 2000 site-years of trace gas flux measurements, and supporting meteorological and site meta-data from over 400 sites world-wide. The production of the next FLUXNET database is critical to the activities of this ROSE’s solicitation because these data will drive many of the carbon cycle synthesis activities and the model parameterization and validation activities. A second goal is to build the next-generation, data-system that will house, distribute and query data and discover new information by the broader biogeoscience user community. The third goal is to use these data in synthesis activities that improve our understanding on how climate, weather, ecological, physiological and soil factors govern the exchange of carbon, water and energy between vegetation and the atmosphere at multiple time and space scales. The fourth goal is to act as a coordinator of the project to recruit data, to organize a workshop/conference and to build a community of data sharing and interaction across vast cultural spectrum of participating scientists. The rationale for proposing this work is based on the fact that the vast databases that are produced by flux networks cannot perpetuate and evolve without continued support of the intellectual activities of scientists who produce data, expert in databases, and scientists who use data for modeling. The actuality of a flux network takes human intervention to recruit data from different countries and cultures, to build trust to share data in open-access format, to support data users, and to collaborate. Specifically, we will develop an updated data portal that is easy to navigate and conducive for distributing, visualization, evaluation and discovery of the multiple types of flux and environmental data and information. We will foster collaboration and interactions with our national and international partners and the recruitment of data by: 1) continuing the periodic publication of the newsletter, FLUXLETTER; 2) by hosting an international conference; 3) by coordinating and launching multi-investigator data synthesis activities; and 4) by developing tools that coordinate the development of research papers resulting from the dataset. Data products include raw and gap-filled data at their native time steps (30 minute averages), data products that are integrated on daily and annual time scales and value added products like ecosystem respiration and canopy photosynthesis. Uncertainty analysis and quality control metrics will be produced in coordination with AmeriFlux and ICOS. We will also work with colleagues to expand the scope of FLUXNET beyond carbon dioxide and water vapor, and start archiving the growing methane flux databases that are being collected, world-wide. The interpretation of the flux data relies on good meta-data. We will work with data providers to populate and expand the meta-data archives. We will also work with collaborators to incorporate data from remote sensing products such as MODIS and Landsat, from corresponding climate and weather stations. Another goal is to incorporate new data on canopy structure, with recent LIDAR acquisitions, to populate the data archive with automated soil respiration and understory flux measurements, where available and local climate records for corresponding sites. And, we will collaborate with the TRY database, by merging flux data with plant trait information.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Illuminating the pathways to carbon liberation: a systems approach to characterizing the consequential unknowns of carbon transformation and loss from thawing permafrost peatlands (Final Report)

The IsoGenie3 Project delivered new systems-level insights into carbon cycling in thawing permafrost landscapes, with an emphasis on methane and carbon dioxide emissions. From >200 samples from the site collected over a decade, co-analyzed for geochemistry and microbiology, the team recovered ~1,500 assembled microbial genomes and ~1,900 viral population genomes, revealing appreciable genetic novelty - from a new highly abundant bacterial phylum, to novel methane consumers and their activities, to rampant viral novelty. IsoGenie3 linked these organisms to carbon compound transformations (which define the cycling of organic matter in soils, and the loss of the greenhouse gases carbon dioxide and methane), and saw that the microbes at each stage of permafrost thaw had different genetic potential to degrade categories of compounds, expressed that genetic potential differently, and actually transformed carbon compounds into greenhouse gases in different ways. IsoGenie 3 identified that some of the thaw-stage differences were due to plant-microbiome relationships; the plant species across the thaw gradient contributed different carbon compounds into the soil, and hosted distinct microbiota (differing among parts of plants as well as species). Lastly, microbes in the saturated post-thaw conditions appeared likely to contribute to the mobilization and toxification of mercury released during thaw. In parallel with ongoing field sampling and analysis, hypotheses arising from field observations were tested via lab incubation experiments. When communities are taken out of their native habitats, they behave differently, and the team first rigorously quantified the magnitude of this effect on microbiome composition and functional capacity, organic matter composition, and gas production; overall the main system processes were maintained in the lab incubations under the conditions tested. Further, the microbial data could inform geochemical reaction network models of those processes. Then, the team ran experiments with additions of compounds, varying temperature, and “live” vs. “dead” peat (the latter having been gamma irradiated, with a few additional variants to control for methodological artifacts). From these, we (a) determined the importance of plant-derived soluble phenolic compounds in bogs’ extraordinary recalcitrance of organic matter, and carbon gas emissions skewed to carbon dioxide; (b) proposed an abiotic ‘tanning’ mechanism, which could contribute to Sphagnum’s inhibitory effect on anaerobic decomposition through alteration of N availability. IsoGenie3 illuminated longer-term and landscape-scale interactions of permafrost thaw and carbon cycling, advancing knowledge of the drivers of methane dynamics not only across in the permafrost-associated peatland (where hydrology and plant communities dictate microbiomes) but also their interconnected lakes (where sediment carbon quality and resident microbiota are determined by position within lake, and lake features). By leveraging observations of site methane dynamics extending well before this project, the team was able to construct a 44-year portrait of the interplay of permafrost thaw, hydrology, vegetation dynamics, and carbon gas emissions, and the doubling of the fully-thawed fens over this time. From the detailed study of this focal site, IsoGenie3 also aimed to improve model representation of these kinds of sites and processes. To improve predictions of methane transformations, we incorporated acetate and isotope dynamics into the ‘DNDC’ biogeochemistry model. In addition, recovered genomes were grouped into ‘functional groups’, i.e. the genomes that perform a specific function of interest, then used to parameterize maximum growth rate and optimum growth temperature (via signatures in their sequence composition) for the BioCrunch model. The BioCrunch model was then in turn used to test the impact of increasing functional resolution of the microbes, on the carbon gas emissions. Lastly for modeling, the ecosys model was parameterized from the microbial and other data, and used to evaluate drivers of e.g. change in methane emissions. Finally, this project also led to the development of a range of new methods and tools, a new metric of organic matter decomposability, as well as a graph-database solution to multidisciplinary data storage and querying. This project’s ongoing analyses at our focal site also contributed to broader advancements in understanding elements of genetic plasticity and methane metabolism, climate change microbiology and community assembly, global peatland geochemistry and Arctic lakes’ roles in climate feedbacks.

54 ENVIRONMENTAL SCIENCES↗