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At least 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Soil Water Potentials (1990-2018) from a calibrated ELM-FATES, and rooting depth analyses scripts, PA-BCI, Panama

This dataset has ELM-FATES simulation outputs and scripts that accompany and reproduce the manuscript, Chitra-Tarak et al. (2021) Hydraulically-vulnerable trees survive on deep-water access during droughts in a tropical forest. New Phytologist. https: //doi.org/10.1111/nph.17464”. This dataset is organized into four parts: (1) source code for the model, Energy Exascale Earth System Land Model-Functionally Assembled Advanced Terrestrial simulator (ELM-FATES) (2) R scripts associated with ELM-FATES simulations: to prepare files for parameter ensemble simulation runs, calibrate the model with observed hydrological fluxes observed at BCI, re-run the model with tuned parameters and obtain long-term soil matric potentials by depth (3) ELM-FATES hydrological simulation outputs at PA-BCI, Panama (1990-2018, daily), and (4) R scripts for inverse rooting depth modeling and post-processing: prepare datasets and inversely model tree rooting depths at BCI, test hypotheses about the relationship of rooting depths with plant hydraulic traits and drought-induced mortality, and reproduce the manuscript itself. n.b. 1. Data needed to run R scripts in (2) and (4) and thus to reproduce the manuscript are sourced from various public datasets. Refer to the data availability section of the accompanying manuscript. 2. This dataset version (prepared on May 12, 2021) matches the revised and published version of the accompanying manuscript (published May 16, 2021) replacing a previous version. In the publication, this dataset is cited as follows: Chitra-Tarak R, Xu C, Aguilar S, Anderson-Teixeira K, Chambers J, Detto M, Faybishenko B, Fisher R, Knox R, Koven C et al. 2020. Soil water potentials (1990–2018) from a calibrated ELM-FATES, and rooting depth analyses scripts, PA-BCI, Panama. 2.0. NGEE Tropics Data Collection. doi: 10.15486/ngt/1696806

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Model-ready benchmarks for NPP, ANPP, litter fluxes, and recruitment into the 1 cm dbh size class

The intended use of this dataset is to serve as an observational benchmark to evaluate model predictions of NPP, ANPP, litter fluxes, and recruitment at Barro Colorado Island, Panama. This dataset contains four CSV files and one text file. “Benchmarks-NPP-ANPP-R-L.csv” provides estimates of annual ecosystem-level reproductive litter flux (R), leaf litter flux (L), aboveground net primary productivity (ANPP), and net primary productivity (NPP) for 61 field plots throughout tropical, temperate, and boreal forest biomes. An additional 499 plots (n = 550) include estimates of just R, L, and R/L. Each row reports a distinct set of estimates for one sampling interval at one plot. “Metadata-Benchmarks-NPP-ANPP-R-L.csv” contains field descriptions for all data fields in “Benchmarks-NPP-ANPP-R-L.csv”. “References-Benchmarks-NPP-ANPP-R-L.txt” contains full references to the original studies used to produce the observations at each plot included in the data. “Benchmarks-Recruitment.csv” provides estimates of species-level recruitment rates into the 1 cm dbh size class at four CTFS-ForestGeo sites using methods that account for unobserved mortality of new recruits between census intervals (Kohyama et al., 2018). “Metadata-Benchmarks-Recruitment.csv” contains field descriptions for all data fields in “Benchmarks-Recruitment.csv”.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Files and scripts to support manuscript Shuman et al 2023 FATES-SPITFIRE ecosystem assembly across tropics

The dataset includes the parameter and domain files, relevant output files, and scripts to generate simulations and perform analysis with Jupyter notebooks that support the manuscript Shuman, JK et al 2023 “Dynamic ecosystem assembly and escaping the “fire-trap” in the tropics: Insights from FATES_15.0.0”. We have adapted the fire-behavior and effects module, SPITFIRE, for use with the Functionally Assembled Terrestrial Ecosystem Simulator (FATES), a size-structured vegetation demographic model. We test how climate, fire regime and fire-tolerance plant traits interact to determine the biogeography of tropical forests and grasslands. We assign different fire-tolerance strategies based on crown, leaf and bark characteristics, which are key observed fire-tolerance traits across woody plants. For these simulations, three types of vegetation compete for resources: a fire-vulnerable tree with thin bark, a vulnerable deep crown and fire-intolerant foliage; a fire-tolerant tree with thick bark, a thin crown and fire-tolerant foliage; and a fire-promoting C4 grass. We explore the model sensitivity to a critical parameter governing fuel moisture, and show that drier fuels promote increased burning, an expansion of area for grass and fire-tolerant trees and a reduction of area for fire-vulnerable trees. This conversion to lower biomass or grass areas with increased fuel drying results in increased fire burned area and its effects, which could fee back to local climate variables. Simulated size-based fire mortality for trees less than 20 cm in diameter and those with fire-vulnerable traits is higher than that for larger and/or fire-tolerant trees, in agreement with observations. Fire-disturbed forests demonstrate reasonable productivity and capture observed patterns of aboveground biomass in areas dominated by natural vegetation for the recent historical period, but have a large bias in less disturbed areas. Though the model predicts a greater extent of burned fraction than observed in areas with grass dominance, the resulting biogeography of fire-tolerant, thick-bark trees and fire-vulnerable, thin-bark trees corresponds to observations across the tropics. In areas with more than 2500 mm of precipitation, simulated fire frequency and burned area are low, with fire intensities below 150 kW m-1, consistent with observed understory fire behavior across the Amazon. Areas drier than this demonstrate fire intensities consistent with those measured in savannas and grasslands, with high values up to 4000 kW m-1. The results support a positive grass-fire feedback across the region, and suggest that forests which have existed without frequent burning may be vulnerable at higher fire intensities, which is of greater concern under intensifying climate and land use pressures. The ability of FATES to capture the connection between fire disturbance and plant fire-tolerance strategies in determining biogeography provides a useful tool for assessing the vulnerability and resilience of these critical carbon storage areas under changing conditions across the tropics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Differentiating Vaccine-Related Fowl Cholera from Naturally Occurring Disease

Vaccine-related fowl cholera must be considered when flock mortality increases after use of a live Pasteurella multocida vaccine product. All registered live vaccines serotype as Heddleston 3,4; however, in some regions this is also the most common serotype of outbreak isolates in broiler breeders and turkeys. Therefore, serotyping may not be useful for diagnosing vaccine-related fowl cholera. This project sought to apply a vaccine-specific test to differentiate vaccine-related disease from naturally occurring outbreaks. Results indicate that vaccine strains were commonly isolated from broiler breeders exhibiting signs of fowl cholera post vaccination, but some of these isolates exhibited only serotype 4 antigenicity. The isolates’ lipopolysaccharides, the target antigen for serotyping, contained compositional changes that may explain the varying serotype results and virulence of the commercial preparations. Furthermore, these results suggest that vaccine-related disease may be common in broiler breeders, and live commercial vaccine preparations need to be assessed for serotype and titer prior to use in order to reduce vaccine-related fowl cholera.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Survival and Age at Maturity in Head-Started Wood Turtles ( Glyptemys insculpta ) with Implications for Population Recovery

A small relict population of Glyptemys insculpta (Wood Turtle) was discovered on a protected area in New Jersey in 2006. Marking and radio-tracking of the old founder individuals helped to determine movement patterns and habitat use. Monitoring of nesting females revealed that nesting habitat and nest success was limited due to invasive plants, human landscape alteration, and Procyon lotor (Raccoon) depredation. We initiated habitat restoration including creation of protected nesting areas, mowing in winter, invasive plant removal, and adjacent landowner education. Here, we direct-released hatchlings from protected nests from 2006 to 2015, yet only a few were detected in subsequent years. Between 2011 and 2023, some or all of each hatchling cohort were head-started indoors at a high school for 9 months. We have continuously radio-tracked all head-starts from the 2011 cohort and portions of the 2012–2014 cohorts. Head-started turtles found their own food, established home ranges, and hibernated communally with founder adults. Subsidized Raccoons, mowers, automobiles, and flooding events—all human-instigated—were the causes of mortality. The first males and first females from the 2011 head-start cohort reached maturity in 2017 and 2019, respectively, at ages 6–8, younger than expected by 4–5 years. Successful reproduction by head-starts was confirmed by viable hatchlings produced in 2019, 2020, and 2023. Head-starting can pull a relict population out of the nose-dive to extirpation when used in conjunction with habitat-restoration practices, but it must be conducted with persistence and continuity over at least the number of years it takes for the earliest cohorts to reach maturity and begin producing offspring of their own.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

AmeriFlux FLUXNET-1F US-GLE GLEES

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-GLE GLEES. This is the FLUXNET version of the carbon flux data for the site US-GLE GLEES produced by applying the standard ONEFlux (1F) software. Site Description - The Glacier Lakes Ecosystem Experiments Site (GLEES) site is located on land owned by the U.S. government and managed by US Forest Service as part of the Medicine Bow National Forest. Many of the trees in the immediate vicinity of the site are older than 400 years, inter-dispersed among trees much younger in age. This widespread age distribution is most likely a derivation of one of two scenarios: 1) A widespread stand replacement about 400 years ago followed by a slow replacement; 2) Intermittent random disturbances over the past 400 years (Bradford et al. 2008). A decade long spruce beetle outbreak that peaked in 2008 resulted in the mortality of 85% of the forested basal area. There are a few private land holdings in the area, with scattered uncorked mining claims. Following the establishment of the National Forest, mining was banned and grazing was closed in the early 1990's in the upper portion of the GLEES site. Recreation in the winter, when snow can remain in patches into the summer months, snow mobiling and cross country skiing are popular. During the limited summer, hiking, camping and fishing are common activities. The site is accessible by vehicle only during the summer on Forest Road FDR 317, and in the winter, the tower is only reachable via snowmobile.

Frank, John↗
DOE OSTI2022

AmeriFlux FLUXNET-1F US-UMd UMBS Disturbance

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-UMd UMBS Disturbance. This is the FLUXNET version of the carbon flux data for the site US-UMd UMBS Disturbance produced by applying the standard ONEFlux (1F) software. Site Description - The UMBS Disturbance site is an artificial disturbance site that has recently been created as part of the Forest Accelerate Succession ExperimenT (FASET). In Spring 2008, every aspen and birch tree (>6,700, ~35% canopy LAI), the dominant early successional trees, were girdled over 39 ha of the FASET treatment plot to stimulate a disturbance that will move the forest into a later successional stage, dominated by maples, oaks, and white pine. This treatment caused aspen and birch mortality within 2 - 3 years. As a result of the changed canopy structure, there is a divergence in net ecosystem exchange between the control plot (enhanced carbon uptake) and the treatment plot (reduced carbon uptake).

Classen, Aimee↗
DOE OSTI2023

AmeriFlux FLUXNET-1F US-CPk Chimney Park

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-CPk Chimney Park. This is the FLUXNET version of the carbon flux data for the site US-CPk Chimney Park produced by applying the standard ONEFlux (1F) software. Site Description - High elevation, primarily lodge-pole pine forest with high amounts of Mountain Pine Bark Beetle mortality. Site burned in June/July 2018, characterized by a highly heterogeneous fire behavior that resulted in unburned, understory-only, as well as severely-burned patches within the tower footprint.

Ewers, Brent↗
DOE OSTI2023

AmeriFlux US-EvM Everglades Saltwater intrusion marsh

This is the AmeriFlux version of the carbon flux data for the site US-EvM Everglades Saltwater intrusion marsh. Site Description - This is a site in Southeaster Florida that is experience an ecosystem state shift caused by saltwater flooding. We are seeing sawgrass mortality and mangrove invasion

Starr, Gregory↗
DOE OSTI2025

AmeriFlux FLUXNET-1F US-Slt Silas Little- New Jersey

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-Slt Silas Little- New Jersey. This is the FLUXNET version of the carbon flux data for the site US-Slt Silas Little- New Jersey produced by applying the standard ONEFlux (1F) software. Site Description - Wildfires, prescribed fires, insect defoliation events and windstorms are the common disturbances in the NJ Pinelands. The oak-dominated forest at Silas Little Experimental Forest was most recently defoliated by Gypsy moth (Lymantria dispar L.) in 2006 to 2008, with complete defoliation occuring in 2007. Following this multi-year defoliation event, oak mortality was significant, and resulted in the death of approximately 20 % of the overstory oaks, and a similar reduction in stand biomass. Previous disturbances have included windstorms and earlier Gypsy moth defoliation events in the 1990's. The last major wildfire to occur at and near the Experimental Forest was in 1963. Since then, a number of prescribed fires have been conducted in the vicinity of the Silas Little flux site.

Clark, Kenneth [USDA Forest Service]↗
DOE OSTI2025

AmeriFlux FLUXNET-1F US-EvM Everglades Saltwater intrusion marsh

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-EvM Everglades Saltwater intrusion marsh. This is the FLUXNET version of the carbon flux data for the site US-EvM Everglades Saltwater intrusion marsh produced by applying the standard ONEFlux (1F) software. Site Description - This is a site in Southeaster Florida that is experience an ecosystem state shift caused by saltwater flooding. We are seeing sawgrass mortality and mangrove invasion

Starr, Gregory [University of Alabama]↗
DOE OSTI2026

AmeriFlux FLUXNET-1F US-xSP NEON Soaproot Saddle (SOAP)

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-xSP NEON Soaproot Saddle (SOAP). This is the FLUXNET version of the carbon flux data for the site US-xSP NEON Soaproot Saddle (SOAP) produced by applying the standard ONEFlux (1F) software. Site Description - The Soaproot Saddle is a complex terrain of coarse hills, steep slopes and narrow drainages. With an elevation of 3274 - 4537’ this site encompasses 1438 acres of mixed conifer forests that are experiencing high levels of mortality due to native Pine beetles. At the core of this site stands a 171’ tall flux tower that collects physical and chemical properties of atmosphere and related process. Soaproot Saddle also hosts an array of sensor measurements along with field observations collected by highly trained NEON staff. The automated instrument measurements and some of the terrestrial observational safor this field site are colocted with NEON's aquatic site, Upper Big Creek, which is located just north of Soaproot Saddle's site boundaries.

Network), NEON (National Ecological Observatory [N↗
DOE OSTI2020

Accelerated epigenetic aging as a risk factor for chronic obstructive pulmonary disease and decreased lung function in two prospective cohort studies

Chronic obstructive pulmonary disease (COPD) is a frequent diagnosis in older individuals and contributor to global morbidity and mortality. Given the link between lung disease and aging, we need to understand how molecular indicators of aging relate to lung function and disease. Using data from the population-based KORA (Cooperative Health Research in the Region of Augsburg) surveys, we associated baseline epigenetic (DNA methylation) age acceleration with incident COPD and lung function. Models were adjusted for age, sex, smoking, height, weight, and baseline lung disease as appropriate. Associations were replicated in the Normative Aging Study. Of 770 KORA participants, 131 developed incident COPD over 7 years. Baseline accelerated epigenetic aging was significantly associated with incident COPD. The change in age acceleration (follow-up – baseline) was more strongly associated with COPD than baseline aging alone. The association between the change in age acceleration between baseline and follow-up and incident COPD replicated in the Normative Aging Study. Associations with spirometric lung function parameters were weaker than those with COPD, but a meta-analysis of both cohorts provide suggestive evidence of associations. Accelerated epigenetic aging, both baseline measures and changes over time, may be a risk factor for COPD and reduced lung function.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Exposure to ionizing radiation disrupts normal epigenetic aging in Japanese medaka

Alterations to the epigenome are a hallmark of biological aging and age-dependent patterning of the DNA methylome (“epigenetic aging”) can be modeled to produce epigenetic age predictors. Rates of epigenetic aging vary amongst individuals and correlate to the onset of age-related disease and all-cause mortality. Yet, the origins of epigenetic-to-chronological age discordance are not empirically resolved. Here, we investigate the relationship between aging, DNA methylation, and environmental exposures in Japanese medaka (Oryzias latipes). We find age-associated DNA methylation patterning enriched in genomic regions of low CpG density and that, similar to mammals, most age-related changes occur during early life. We construct an epigenetic clock capable of predicting chronological age with a mean error of 61.1 days (~8.4% of average lifespan). To test the role of environmental factors in driving epigenetic age variation, we exposed medaka to chronic, environmentally relevant doses of ionizing radiation. Because most organisms share an evolutionary history with ionizing radiation, we hypothesized that exposure would reveal fundamental insights into environment-by-epigenetic aging interactions. Radiation exposure disrupted epigenetic aging by accelerating and decelerating normal age-associated patterning and was most pronounced in cytosines that were moderately associated with age. These findings empirically demonstrate the role of DNA methylation in integrating environmental factors into aging trajectories.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

FrESCO: Framework for Exploring Scalable Computational Oncology

The National Cancer Institute (NCI) monitors population level cancer trends as part of its Surveillance, Epidemiology, and End Results (SEER) program. This program consists of state or regional level cancer registries which collect, analyze, and annotate cancer pathology reports. From these annotated pathology reports, each individual registry aggregates cancer phenotype information from electronic health records. This data is then used to create summary statistics about cancer incidence and mortality to facilitate population health monitoring. Extracting phenotypic information from these reports is a labor intensive task, requiring specialized knowledge about the reports and cancer. Automating the information extraction process from cancer pathology reports has the potential to improve data quality by extracting information in a consistent manner across registries. It can also improve patient outcomes by reducing the time from diagnosis, enabling rapid case ascertainment for clinical trials. Here we present FrESCO, a modular deep-learning natural language processing (NLP) library initially designed for extracting pathology information from clinical text documents. This repository is not solely limited to clinical medical text, but may also be used by researchers just getting started with NLP methods and those looking for a robust solution for their classification problems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Modeling efficient and equitable distribution of COVID-19 vaccines

Producing and distributing COVID-19 vaccine during the pandemic is a major logistical challenge requiring careful planning and efficient execution. This report presents information on logistical, policy and technical issues relevant to rapidly fielding a COVID-19 vaccination program. For this study we (a) conducted literature review and subject matter expert elicitation to understand current vaccine manufacturing and distribution capabilities and vaccine allocation strategies, (b) designed a baseline vaccine distribution strategy and modeling strategy to provide insight into the potential for targeted distribution of limited initial vaccine supplies, and (c) developed parametric interfaces to enable vaccine distribution scenarios to be analyzed in depth with Sandias Adaptive Recovery Model that will allow us evaluate the additional sub- populations and alternative distribution scenarios from a public health benefit and associated economic disruption Principal issues, challenges, and complexities that complicate COVID-19 vaccine delivery identified in our literature and subject matter expert investigation include these items: The United States has not mounted an urgent nationwide vaccination campaign in recent history. The existing global manufacturing and distribution infrastructure are not able to produce enough vaccine for the population immediately. Vaccines, once available will be scarce resources. Prioritization for vaccine allocation will be built on existing distribution networks. Vaccine distribution may not have a universal impact on disease transmission and morbidity because of scarcity, priority population demographics, and underlying disease transmission rates. Considerations for designing a vaccine distribution strategy are discussed. A baseline distribution strategy is designed and tested using the Adaptive Recovery Model, which couples a deterministic compartmental epidemiological model and a stochastic network model. We show the impact of this vaccine distribution strategy on hospitalizations, mortality, and contact tracing requirements. This model can be used to quantitatively evaluate alternative distribution scenarios, guiding policy decisions as vaccine candidates are narrowed down.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Evaluation of Modular and Scalable Downstream Passage Systems for Silver American Eels

Implementation of effective downstream passage for silver-phase American Eel (Anguilla rostrata) at hydropower dams using methods that are economically feasible has been a challenge for many project owners. Due to the potential for high mortality rates during turbine passage, resource agencies have focused on mandatory prescriptions that prevent entrainment by physically excluding eels (i.e., narrow trash rack bar spacing) or eliminating turbines as a passage route (i.e., unit shutdowns at night when eel movement is greatest). Both of these options can significantly impact the economic viability of a project. Consequently, there is a need for alternative technologies that can provide safe and effective downstream passage for silver eels without having a major impact on the ability of a project to generate power during the eel downstream migration period. This need is of particular concern now because about 300 hydropower projects within the range of American Eel freshwater habitats are scheduled to be relicensed by the Federal Energy Regulatory Commission (FERC) in the next 15 years

13 HYDRO ENERGY↗
DOE OSTI2021

Acoustic and Genetic Approaches for Informing Population Status and Trends of Migratory Tree Bats

Through the systematic collection of acoustic and genetic data over time, a weight of evidence may be built that will support an improved understanding around population stability for migratory tree-roosting bat species. This information can be leveraged to infer the influence stressors have on population stability, and subsequently determine the level of response necessary to sustain healthy populations. Here, we synthesize the existing information related to bat population status and trends, uncertainty regarding existing estimates, current and novel methods for assessing population-level data, and recommendations for near-term and long-term studies to reduce uncertainty surrounding population data. Although this report focuses on wind energy development and bats, the methods used are broadly applicable and are being implemented by other industries, academia, government agencies, and nongovernmental organizations. Through efforts outside of the wind energy industry, it is likely we will gain a better understanding of bat populations, but the pace of data collection and analysis will be expedited by further participation by the wind energy industry. In return, the wind energy industry will benefit by contributing to these efforts either by 1) discovering that the population status of the species of interest is stable or growing, which may prevent the need for listing one or more species; or 2) recognizing the population status of certain species is in decline and implementing relatively moderate measures to reduce wind turbine-related mortality in the near term to stave off more stringent measures, which may be necessary if action is delayed.

17 WIND ENERGY↗