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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

ESS-DIVE Reporting Format for Amplicon Abundance Table

While standardized sequencing data is available in public repositories and efforts such as MIxS for common sample collection and processing metadata are well established, the lack of common bioinformatic processing metadata has hindered the ability to do large-scale metaanalyses and the potential for data re-use by non-experts such as ecosystem, watershed, or earth system modelers. To address this need for Department of Energy researchers, we have developed an amplicon reporting format which captures both sample preparation and bioinformatic processing metadata and stores processed amplicon data as a paired abundance table and sequencing file to maximize the potential for re-use of these data. To aid in the adoption of accessible and reproducible analysis workflows, this reporting format was developed in concert with amplicon functionality within the Department of Energy’s Systems Biology Knowledgebase (KBase) to ensure common data and metadata requirements and facilitate seamless transfer between these platforms.This dataset contains support documentation for the amplicon reporting format (README.md and instructions.md), templates for both bioinformatic and sequencing metadata (amplicon_bioinformatic_metadata_template_2021_10_03.csv and amplicon_sequencing_metadata_template_2021_10_03.csv), a crosswalk indicating how this reporting format relates to the current MIxS format (ESSDIVE-MIxS_crosswalk.csv), a list of available instrument terms (amplicon_seq_instrument_terms_2021_10_03.csv), a map between QIIME2 parameter settings and metadata fields (amplicon_qiime2_plugin_metadata_map.csv), a data dictionary (amplicon_CSV_dd.csv), and file-level metadata (amplicon_FLMD.csv).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

A general theory of avian migratory connectivity

Birds exhibit a remarkable array of seasonal migrations. Despite much research describing migratory behaviour, the underlying forces driving how a species’ breeding and wintering populations redistribute each year, that is, migratory connectivity, remain largely unknown. Here, we test the hypothesis that birds migrate in a way that minimises energy expenditure while considering intraspecific competition for energy acquisition, by developing a modelling framework that simulates an optimal redistribution of individuals between breeding and wintering areas. Using 25 species across the Americas, we find that the model accurately predicts empirical migration patterns, and thus offers a general explanation for migratory connectivity based on first ecological and energetic principles. Our model provides a strong basis for exploring additional processes underlying the ecology and evolution of migration, but also a framework for predicting how migration impacts local adaptation across seasons and how environmental change may affect population dynamics in migratory species.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

New Approach Methodology for Assessing Inhalation Risks of a Contact Respiratory Cytotoxicant: Computational Fluid Dynamics-Based Aerosol Dosimetry Modeling for Cross-Species and In Vitro Comparisons

Regulatory agencies are considering alternative approaches to assessing inhalation toxicity that utilizes in vitro studies with human cells and in silico modeling in lieu of additional animal studies. In support of this goal, computational fluid-particle dynamics models were developed to estimate site-specific deposition of inhaled aerosols containing the fungicide, chlorothalonil, in the rat and human for comparisons to prior rat inhalation studies and new human in vitro studies. Under bioassay conditions, the deposition was predicted to be greatest at the front of the rat nose followed by the anterior transitional epithelium and larynx corresponding to regions most sensitive to local contact irritation and cytotoxicity. For humans, simulations of aerosol deposition covering potential occupational or residential exposures (1–50 µm diameter) were conducted using nasal and oral breathing. Aerosols in the 1–5 µm range readily penetrated the deep region of the human lung following both oral and nasal breathing. Under actual use conditions (aerosol formulations >10 µm), the majority of deposited doses were in the upper conducting airways. Beyond the nose or mouth, the greatest deposition in the pharynx, larynx, trachea, and bronchi was predicted for aerosols in the 10–20 µm size range. Only small amounts of aerosols >20 µm penetrated past the pharyngeal region. Using the ICRP clearance model, local retained tissue dose metrics including maximal concentrations and areas under the curve were calculated for each airway region following repeated occupational exposures. These results are directly comparable with benchmark doses from in vitro toxicity studies in human cells leading to estimated human equivalent concentrations that reduce the reliance on animals for risk assessments.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2023

Impacts of Fungal Disease on Algal Biofuel Systems: Using Life Cycle Assessment to Compare Control Strategies

While climate change has incentivized attention on sustainable fuel sources, algae has positioned itself as a both promising and problematic biofuel feedstock. Diseases such as fungal pathogens cause costly algal feedstock crashes, but the life cycle assessments (LCAs) used to analyze the viability of algal feedstocks for biofuel have yet to consider the impact of disease on life cycle metrics. Here, we incorporate a disease model into a well-documented LCA for algal biorefineries to compare two sustainability metrics, energy return on investment (EROI) and global warming potential (GWP). We begin by showing that failure to consider disease leads to overly optimistic LCA metric outputs. Then, we compare two leading control strategies of disease chemical and biological. Our analyses show that biological engineering of a multispecies consortium of algae has a greater positive impact on LCA metrics than chemical control of the fungal pathogen using a fungicide. We expand how and when bi-cultures might advantageously exhibit the “dilution effect” whereby differentially susceptible species exhibit compensatory dynamics that stabilize feedstock production. Furthermore, our results emphasize the impact of disease and suggest that multispecies consortia of algae can be biologically engineered to reduce greenhouse gas emissions and improve the economic viability of biofuel.

09 BIOMASS FUELS↗
DOE OSTI2025

In-situ probing of the Fischer-Tropsch reaction on Co single crystal surfaces up to 1 bar

The surface chemistry of the Fischer-Tropsch catalytic reaction over Co has still several unknows. Here, we report an in-situ X-ray photoelectron spectroscopy study of Co$(0001)$ and Co$(10\bar{1}4)$, and in-situ high energy surface X-ray diffraction of Co$(0001)$ during the Fischer-Tropsch reaction at 0.15 bar - 1 bar and 406 K - 548 K in a H 2 /CO gas mixture. We find that these Co surfaces remain metallic under all conditions and that the coverage of chemisorbed species ranges from 0.4–1.7 monolayers depending on pressure and temperature. The adsorbates include CO on-top, C/-C x H y and various longer hydrocarbon molecules, indicating a rate-limiting direct CO dissociation pathway and that only hydrocarbon species participate in the chain growth. The accumulation of hydrocarbon species points to the termination step being rate-limiting also. Furthermore, we demonstrate that the intermediate surface species are highly dynamic, appearing and disappearing with time delays after rapid changes in the reactants’ composition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus Cenococcum Geophilum Reveals Massive TE Expansion and RIP Defense Mechanism

Transposable elements (TEs) play crucial roles in genome evolution and ecological adaptation in fungi, yet their dynamics in ectomycorrhizal species remain poorly understood. Cenococcum geophilum, the most widespread ectomycorrhizal fungus in boreal and temperate forests with its large, repeat-rich genome, represents an ideal system to investigate TE-mediated adaptation to the physical environment and symbiotic lifestyle. However, previous studies have been limited by fragmented genome assemblies that prevented the resolution of repeat-rich regions. We assembled a telomere-to-telomere reference genome of C. geophilum strain 1.58 using PacBio HiFi and Hi-C datasets, resulting in a 178.54 Mbp genome with seven contiguous chromosomes. We identified 14,145 genes and over 78% of the genome consists of transposable elements (TEs). Of these, 94% are affected by repeat-induced point mutations (RIP), a genome defense mechanism that acts during the sexual reproduction phase, indicating cryptic or ancient sexual reproduction in this putatively asexual fungus. Long terminal repeat retrotransposons, LINEs, and DNA transposons dominate, with three TE families (Ty3, Ty1, and Tad1) contributing over 60% of the genome size, indicating recent transposition bursts. Screening of 15 additional C. geophilum strains revealed recent and lineage-specific TE expansions, implying that several TEs escaped the RIP machinery and retained potential activity. Supporting TE activity in the context of symbiosis, we found 56 TEs differentially transcribed between ectomycorrhizal and free-living mycelium tissues. An even higher number (n = 66) of TEs were differentially expressed between stress resistance morphology (i.e. sclerotia) and free-living mycelium. This supports that TEs are differentially regulated as a response to symbiotic and stress-related conditions. Our results demonstrate that the C. geophilum genome expansion was driven by a few lineage-specific TE families in recent history, with high RIP activity attesting to sexual reproduction. We also provide insights how TEs could respond to lifestyle transitions and traits associated with desiccation resistance.

Cenococcum geophilum↗
DOE OSTI2024

Body size and early marine conditions drive changes in Chinook salmon productivity across northern latitude ecosystems

Disentangling the influences of climate change from other stressors affecting the population dynamics of aquatic species is particularly pressing for northern latitude ecosystems, where climate‐driven warming is occurring faster than the global average. Chinook salmon (Oncorhynchus tshawytscha) in the Yukon‐Kuskokwim (YK) region occupy the northern extent of their species' range and are experiencing prolonged declines in abundance resulting in fisheries closures and impacts to the well‐being of Indigenous people and local communities. These declines have been associated with physical (e.g., temperature, streamflow) and biological (e.g., body size, competition) conditions, but uncertainty remains about the relative influence of these drivers on productivity across populations and how salmon–environment relationships vary across watersheds. To fill these knowledge gaps, we estimated the effects of marine and freshwater environmental indicators, body size, and indices of competition, on the productivity (adult returns‐per‐spawner) of 26 Chinook salmon populations in the YK region using a Bayesian hierarchical stock‐recruitment model. Across most populations, productivity declined with smaller spawner body size and sea surface temperatures that were colder in the winter and warmer in the summer during the first year at sea. Decreased productivity was also associated with above average fall maximum daily streamflow, increased sea ice cover prior to juvenile outmigration, and abundance of marine competitors, but the strength of these effects varied among populations. Maximum daily stream temperature during spawning migration had a nonlinear relationship with productivity, with reduced productivity in years when temperatures exceeded thresholds in main stem rivers. These results demonstrate for the first time that well‐documented declines in body size of YK Chinook salmon were associated with declining population productivity, while taking climate into account.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1976

The impact of stratospheric variability on measurement programs for minor constituents

The scales of temporal and spatial variations in stratospheric minor species concentrations and dynamical quantities are briefly reviewed. Despite the fact that the stratosphere is often considered to be a very quiescent region of the atmosphere, it exhibits transient and generally unpredictable episodes of intense activity. The resultant necessity for some degree of coordination between different observers in their choice of locations and times for measurements of minor constituents is emphasized. A specific suggestion is provided for one or more short 'International Stratospheric Periods' whose duration would depend upon the time of year. During these short periods, as many observers as possible would perform an integrated series of observations designed to optimize the usefulness of their data to atmospheric scientists.

Prinn, R. G.↗
NASA NTRS1999

Reflexive Neurodynamics

Behavioral dynamics of living species is characterized by additional non-Newtonian properties which are not included in the laws of Newtonian or statistical mechanics.

Neurodynamics attractors↗
NASA NTRS2017

Climatic History of the Northeastern United States During the Past 3000 Years

Many ecosystem processes that influence Earth system feedbacks - vegetation growth, water and nutrient cycling, disturbance regimes - are strongly influenced by multidecadal- to millennial-scale climate variations that cannot be directly observed. Paleoclimate records provide information about these variations, forming the basis of our understanding and modeling of them. Fossil pollen records are abundant in the NE US, but cannot simultaneously provide information about paleoclimate and past vegetation in a modeling context because this leads to circular logic. If pollen data are used to constrain past vegetation changes, then the remaining paleoclimate archives in the northeastern US (NE US) are quite limited. Nonetheless, a growing number of diverse reconstructions have been developed but have not yet been examined together. Here we conduct a systematic review, assessment, and comparison of paleotemperature and paleohydrological proxies from the NE US for the last 3000 years. Regional temperature reconstructions (primarily summer) show a long-term cooling trend (1000BCE - 1700CE) consistent with hemispheric-scale reconstructions, while hydroclimate data show gradually wetter conditions through the present day. Multiple proxies suggest that a prolonged, widespread drought occurred between 550 and 750CE. Dry conditions are also evident during the Medieval Climate Anomaly, which was warmer and drier than the Little Ice Age and drier than today. There is some evidence for an acceleration of the longer-term wetting trend in the NE US during the past century; coupled with an abrupt shift from decreasing to increasing temperatures in the past century, these changes could have wide-ranging implications for species distributions, ecosystem dynamics, and extreme weather events. More work is needed to gather paleoclimate data in the NE US to make inter-proxy comparisons and to improve estimates of uncertainty in reconstructions.

Marlon, Jennifer R.↗
DOE OSTI2026

Visualizing Millisecond Atomic Dynamics of Nanocrystals in Liquid

Atomic structures of nanomaterials are inherently dynamic and continuously reshaped through interactions with chemical species and external stimuli. Such dynamics are further amplified as the size and dimensionality of nanomaterials decrease. Despite advances in analytical methods, it remains challenging to capture the structural dynamics of nanomaterials in reactive environments with both atomic spatial resolution and commensurate temporal resolution. Here, in this study, we directly visualize atomic-scale dynamics of gold (Au) nanocrystals in reactive liquid environments with millisecond-speed liquid-cell electron microscopy (EM) and deep-learning denoising. We uncover reversible fluctuations in the local crystallinity of Au nanocrystals dependent on the surrounding chemical environment. These transient fluctuations, driven by interactions at nanocrystal–liquid interfaces, critically influence the dissolution kinetics and grain boundary relaxation. By overcoming the spatiotemporal limitations in conventional liquid-cell EM, our findings provide insights into how transient nanoscale structures dictate the stability and reactivity of nanomaterials.

Kang, Sungsu [University of Chicago, IL (United St↗
NASA NTRS1976

Construction of analytically solvable models for interacting species

The basic form of a model representation for systems of n interacting biological species is a set of essentially nonlinear autonomous ordinary differential equations. A generic canonical expression for the rate functions in the equations is reported which permits the analytical general solution to be obtained by elementary computation. It is shown that a general analytical solution is directly obtainable for models where the rate functions are prescribed by the generic canonical expression from the outset. Some illustrative examples are given which demonstrate that the generic canonical expression can be used to construct analytically solvable models for two interacting species with limit-cycle dynamics as well as for a three-species interdependence.

Rosen, G.↗
DOE OSTI2022

Integrating terrestrial scavenging ecology into contemporary wildlife conservation and management

Scavenging plays a vital role in maintaining ecosystem health and contributing to ecological functions; however, research in this sub-discipline of ecology is underutilized in developing and implementing wildlife conservation and management strategies. We provide an examination of the literature and recommend priorities for research where improved understanding of scavenging dynamics can facilitate the development and refinement of applied wildlife conservation and management strategies. Due to the application of scavenging research broadly within ecology, scavenging studies should be implemented for informing management decisions. In particular, a more direct link should be established between scavenging dynamics and applied management programs related to informing pharmaceutical delivery and population control through bait uptake for scavenging species, prevention of unintentional poisoning of nontarget scavenging species, the epidemiological role that scavenging species play in disease dynamics, estimating wildlife mortalities, nutrient transfer facilitated by scavenging activity, and conservation of imperiled facultative scavenging species. This commentary is intended to provide information on the paucity of data in scavenging research and present recommendations for further studies that can inform decisions in wildlife conservation and management. Additionally, we provide a framework for decision making when determining how to apply scavenging ecology research for management practices and policies. Due to the implications that scavenging species have on ecosystem health, and their overall global decline as a result of anthropic activities, it is imperative to advance studies in the field of scavenging ecology that can inform applied conservation and management programs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Soil biogeochemical properties and metrics of tree-mycorrhizal dominance for a 25-Ha forest in South Central Indiana, USA.

This data package contains a dataset used in the papers “Seeing the forest for all the trees: Mycorrhizal-associated nutrient economies are modulated by stem density and the synchrony between overstory and understory communities” and “Mycorrhizal associations of tree species influence soil nitrogen dynamics via effects on soil acid–base chemistry”. Four csv files are included along with a dataset. The dataset features chemical soil properties for a single sampling campaign within the 25 Ha Lilly-Dickey Woods Smithsonian Forest Global Earth Observatory (ForestGEO) plot in South Central Indiana, USA (ldw_dat_raw.csv). Also included are separate files focused on pH (pH_data.csv), carbon and nitrogen (CN_data.csv), and nitrification rates (Nitrification_data.csv). These variables are commonly associated with the tree-mycorrhizal dominance of forest stands. In these data subsets, each soil variable was matched to a 10 meter radius neighborhood wherein metrics of tree-mycorrhizal dominance (basal area, stem count, importance value, etc.) were calculated. Models between these soil variables and dominance metrics were used to investigate how different assessments of mycorrhizal associated nutrient economies (MANE) capture these relationships. This research was performed as a part of the Smithsonian ForestGEO project. This data package can be used to explore spatial variability in soil chemistry within a mature hardwood forest, or it can be combined with the included tree data, other fine-scale spatial information, or other tree inventory data for the site to evaluate how soil chemistry varies with tree community composition or edaphic or topographic properties.

Craig, Matthew [ORNL] (ORCID:0000000288907920)↗
NASA NTRS2005

New Species of Fire Discovered: Fingering Flamelets Form a Dynamic Population

Poets and artists have long used fire as a metaphor for life. At the NASA Glenn Research Center, recent experiments in a subcritical Rayleigh number flow channel demonstrated that this analogy holds up surprisingly well when tools developed to characterize a biological population are applied to a class of fire that occurs in near-extinction, weakly convective environments (such as microgravity) or in vertically confined spaces (such as our apparatus). Under these conditions, the flame breaks into numerous 'flamelets" that form a Turing-type reaction-diffusion fingering pattern as they spread across the fuel. It is standard practice on U.S. spacecraft for the astronaut crew to turn off the ventilation to help extinguish a fire, both to eliminate the fresh oxygen supply and to reduce the distribution of the smoke. When crew members think that the fire is fully extinguished, they reactivate the ventilation system to clear the smoke. However, some flamelets can survive, and our experiments have demonstrated that flamelets quickly grow into a large fire when ventilation increases.

Olson, Sandra L.↗
DOE OSTI2023

Coexistence between similar invaders: The case of two cosmopolitan exotic insects

Biological invasions are usually examined in the context of their impacts on native species. However, few studies have examined the dynamics between invaders when multiple exotic species successfully coexist in a novel environment. Yet, long-term coexistence of now established exotic species has been observed in North American lady beetle communities. Exotic lady beetles Harmonia axyridis and Coccinella septempunctata were introduced for biological control in agricultural systems and have since become dominant species within these communities. In this study, we investigated coexistence via spatial and temporal niche partitioning among H. axyridis and C. septempunctata using a 31-year data set from southwestern Michigan, USA. We found evidence of long-term coexistence through a combination of small-scale environmental, habitat, and seasonal mechanisms. Across years, H. axyridis and C. septempunctata experienced patterns of cyclical dominance likely related to yearly variation in temperature and precipitation. Within years, populations of C. septempunctata peaked early in the growing season at 550 degree days, while H. axyridis populations grew in the season until 1250 degree days and continued to have high activity after this point. C. septempunctata was generally most abundant in herbaceous crops, whereas H. axyridis did not display strong habitat preferences. These findings suggest that within this region H. axyridis has broader habitat and abiotic environmental preferences, whereas C. septempunctata thrives under more specific ecological conditions. These ecological differences have contributed to the continued coexistence of these two invaders. Understanding the mechanisms that allow for the coexistence of dominant exotic species contributes to native biodiversity conservation management of invaded ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Vertebrate and invertebrate competition for carrion in human‐impacted environments depends on abiotic factors

Abstract Human altered landscapes have caused declines in the diversity of wildlife where behaviorally plastic species (i.e., mesocarnivores and invasive species) tend to monopolize these areas and consume predictable and readily accessible food resources, such as human food waste and carrion. Increased consumption of carrion by vertebrates and invasive invertebrate species can alter population dynamics of native necrophagous insects relying on these resources. We tested the hypothesis that vertebrate scavengers and invasive species reduce blow fly (1) ability to use carrion and (2) reproduction in human‐impacted environments in central Texas, USA, with season, habitat (field and wooded landscapes), and carrion type (species of carrion and coat color) acting synergistically. Vertebrate scavengers in this habitat, of which 75% of the documented species were mesocarnivores and obligate scavengers, consumed 100% of carrion during the winter and 62% during summer despite having low species richness (2–5 species). Of the remaining carcasses available for arthropod activity during summer, the invasive red imported fire ant, Solenopsis invicta (Hymenoptera: Formicidae), monopolized 34%, and blow flies (e.g., Lucilia eximia and Chrysomya rufifacies [Diptera: Calliphoridae]) were only able to colonize 25%. Approximately 90% of carrion that was utilized by blow flies was co‐colonized by fire ants, and subsequent production of adult blow flies experienced up to a ninefold reduction in production compared with carcasses that were not scavenged by vertebrates or fire ants. Our results demonstrate oviposition resources used by blow flies in environments altered by human activity are reduced significantly by vertebrate scavengers and an invasive ant species. Future research should determine whether competitive interactions between vertebrate and invasive ant competitors for access to carrion resources have population‐level impacts to blow flies in human‐mediated ecosystems, or whether blow flies are able to shift to other resources to maintain sustainable populations and continue providing ecosystem services, such as pollination.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

In situ catalyst activation and regeneration enable energy-efficient high-current CO 2 reduction to ethanol-rich C 2+ mixtures

Electrochemical conversion of dissolved CO 2 in bicarbonate electrolytes, i.e., bicarbonate electrolysis, offers distinct advantages over gas diffusion electrode systems by enabling direct utilization of the CO 2 capture electrolyte while bypassing the energy-intensive CO 2 release step. However, bicarbonate electrolysis faces challenges such as CO 2 mass-transfer limitation, local pH-driven CO 2 depletion, and high cathodic potentials. The higher potential often causes catalyst surface reorganization, leading to a gradual loss of active sites and variations in selectivity during CO 2 reduction. Here, we report a directed, in situ activation and regeneration method that allows precatalysts to equilibrate under dynamic (pulsed) electrolysis conditions. We demonstrate in situ activation of a scalable Cu 2 O/Cu mesh that, under short-width (t = 4 s) pulsed electrolysis, provides stable mixed oxidation states of Cu, favoring the formation of an ethanol-rich crude mixture. The pulsed electrolysis waveform, consisting of six distinct segments, is tuned to form Cu + oxides, which are then reduced to generate local alkaline conditions favoring C–C coupling. This synergistic effect results in FEs of 73% for C2+ products and 39% for ethanol at an applied current density of −150 mA cm −2 and a cathodic potential of −1.45 V (vs. RHE). The overall half-cell energy efficiency is ∼30% for C 2+ products. The in situ Raman experiments confirm the role of pCO 2 R in dynamically regenerating Cu+-containing surface species during pulsed operation, thereby steering selectivity towards C 2+ products. A comprehensive multiscale, multiphysics model is developed to investigate the dynamic behavior of copper surface species (Cu, Cu + , and Cu 2+ ) and local microenvironmental conditions during the pCO 2 R. The results reveal that the coexistence of different copper oxidation states, especially the Cu+ intermediate, is critical in steering selectivity towards multicarbon (C 2+ ) products. The dynamic modulation of surface redox states via tailored pulsing strategies favors C–C coupling pathways by inducing localized alkaline conditions and stabilizing reactive intermediates. This work establishes a predictive modeling platform that links pulse waveform design with mechanistic insights into catalyst state evolution and product selectivity. Overall, this study provides valuable insights into the synergistic effect of in situ activation of pre-catalysts and pulsed electrolysis for higher selectivity towards C 2+ products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗