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At least 613 records · Page 34

Mapping invasive alien species in grassland ecosystems using airborne imaging spectroscopy and remotely observable vegetation functional traits

Lespedeza cuneata (sericea lespedeza; hereafter “sericea”) is an invasive species brought to the U.S. from East Asia in the 1890s to be used as forage. However, it has now become a growing ecological and economic threat in grasslands of several states in the U.S. southern Great Plains including Oklahoma, Kansas, Missouri, and Nebraska. Here, we demonstrate the capability of airborne imaging spectroscopy to map sericea in a large natural grassland within the Tallgrass Prairie Preserve, the largest protected tallgrass prairie in the world, located in northeastern Oklahoma. Through this research, we investigated which remotely observable vegetation functional traits (referring to biochemical, physiological, and structural traits) contribute to distinguishing sericea from cooccurring native species and whether we can detect sericea remotely through quantifying these functional traits using imaging spectroscopic data (also known as hyperspectral data). To achieve these objectives, full-range airborne hyperspectral data with spatial resolution of 1 m were collected from the study area in August 2020. In addition, a total of 12 vegetation functional traits were measured through field sampling for model development. We first identified functional traits that contributed to separating sericea from other species, and then used them in a classification model to detect sericea in our study site. We found total carotenoids (sum of neoxanthin, violaxanthin, antheraxanthin, zeaxanthin, and lutein), chlorophyll a + b (sum of chlorophyll a and chlorophyll b), total nitrogen, canopy height, potassium, and magnesium as the main functional traits contributing to the detection of sericea; an overall classification accuracy of approximately 94% was reported. However, the proposed approach overestimated sericea cover in species-rich plant communities. Overall, our findings demonstrated an essential role for airborne remote sensing in 1) direct mapping of invasive plants and 2) quantifying functional traits associated with success strategies of invasive species. Eventually, experiments like ours can aid in developing large-scale and science-driven management practices to both identify the current extent, and to control the spread of invasive species in grasslands and similar short-stature environments. This will not only improve management practices but will have major societal and economic benefits.

Hamed Gholizadeh↗

Climate Change Impacts on the Built Environment in the United States and Implications for Sustainability

As an integral part of the National Climate Assessment (NCA), technical assessment reports for 13 regions in the U.S. that describe the scientific rationale to support climate change impacts within the purview of these regions, and provide adaptation or mitigation measures in response to these impacts. These technical assessments focus on climate change impacts on sectors that are important environmental, biophysical, and social and economic aspects of sustainability within the U.S.: Climate change science, Ecosystems and biodiversity, Water resources, Human health, Energy supply and use, Water/energy/land use, Transportation, Urban/infrastructure/vulnerability, Agriculture, Impacts of climate change on tribal/indigenous and native lands and resources, Forestry, Land use/land cover change, Rural communities development, and Impacts on biogeochemical cycles, with implications for ecosystems and biodiversity. There is a critical and timely need for the development of mitigation and adaptation strategies in response to climate change by the policy and decision making communities, to insure resiliency and sustainability of the built environment in the future.

Quattrochi, Dale A.↗

An Efficient Storage-Driven Machine Learning Model for Performance in the Era of Multimodal Scientific Data

Scientific workflows are increasingly relying on machine learning (ML), simulation, and hybrid techniques to predict, understand, and optimize the behavior of complex experiments. High-performance computing has greatly improved researchers’ ability to acquire diverse data modalities in these workflows. Recent studies suggest that the performance of machine learning models can be improved by integrating data from various sources. Unfortunately, these workloads pose unprecedent pressure on the network storage to meet the demands associated with accessing these multimodal data. To mitigate the impact of intensive IO, we propose a solution that utilizes a multi-tier High-Performance Computing (HPC) distributed storage and data processing framework, placing computation where the data resides for better performance. By adopting this project, the scientific community will gain new opportunities to explore multimodal storage-driven possibilities, integrating multiple scientific data sources with advanced streaming frameworks. Additionally, our framework effectively utilizes computing resources and bridges the gaps identified by HPC experts. Our proposed approach tackles scalability and persistence challenges by leveraging native persistency, which has posed difficulties in traditional approaches. Furthermore, we seek to enhance fault-tolerance and load-balance of computations by leveraging real-time streaming in diverse scientific computing environments, thereby propelling advanced scientific computing research into the next generation.

97 MATHEMATICS AND COMPUTING↗

An Undergraduate Intern Program at PACES

The University of Texas at El Paso (UTEP) established the Pan American Center for Earth and Environmental Studies (PACES) in 1995 to conduct basic and applied research that contributes to NASA's Mission to Planet Earth. Specifically, PACES provides a repository of remote sensing and other information that supports investigations into an improved understanding of geological, ecological and environmental processes occurring in the southwestern United States and Northern Mexico. Approximately 85% of UTEP's students come from El Paso County, a fast growing urban region representative of many large cities in the Southwest that have, or will soon have, a majority of their population composed of groups currently underrepresented in the scientific and technical workforce. UTEP's student population has an ethnic distribution (63% Hispanic, 32% Anglo, 3% African American, 1.5 % Asian American, and less than 1% Native American) that closely matches the demographics of the region it serves. Thus, UTEP has a mission to serve a multicultural population where minority students comprise the majority. Most Hispanic students at UTEP are primarily of Mexican origin. A large number are first or second-generation U.S. citizens. Characteristics that unite Hispanic students, in particular those of Mexican-origin, are a strong sense of family loyalty and a belief that all family members are responsible for contributing to the economic stability and well-being of the family. Most of their families are larger in number than the national average, and a variety of generations live together or share considerable resources. Thus, many young people feel an obligation and a desire to go to work at a young age and to continue working while in college, thereby assisting their parents and other family members. Older siblings understand that they have responsibilities to do household chores, to aid their younger siblings economically, and to assist elderly family members. This "work ethic" within the context of family responsisilities is often viewed as being as important as higher education aspirations by both parents and university students. As a consequence, much effort at UTEP has been placed in recent years upon creating opportunities for students to earn income while working on campus as undergraduate research assistants on research projects related to their majors. Work assignments of this sort serve to promote retention efforts, to introduce students with the possibility of graduate study and to develop students professionally. Also, the involvement of students in group-oriented research projects at UTEP which require frequent oral and written reports has been proven beneficial at promoting communication skills of students. Because an estimated 60% of UTEP's students are first-generation college students, many are often uncertain graduate education.

Starks, Scott A.↗

SCPAssistant v1.20

Critical need to rapidly and quantitatively measure the chemistry of single cells in their natural state, without extensive sample preparation procedures. Developed at ORNL an innovative single cell droplet ejection-liquid vortex capture mass spectrometry (SCDE-LVC-MS) platform for rapid, in situ molecular characterization of single cells in suspension. This platform provides rapid, quantitative, targeted and/or untargeted mass spectrometric analysis of single cells without extensive sample preparation procedures. Enable real-time untargeted mass spectrometry analysis of chemical constituents of single cells in their native environment. Send a TTL signal via a connected AD/DA board to start mass spectrometry (MS) data acquisition - analyze MS data - classification of analyzed samples (e.g. separate single cell types based on their chemistry) - quantitation of analyzed samples (e.g. quantify lipids in single cells). List of features: external instrument control; screen capture; reporting; real-time MS data (single cell) analysis; classification; quantitation. Specific application: real-time mass spectrometry analysis of chemical constituents of single cells in their native environment. The software starts MS acquisition; then monitors a folder where the Cytena Single Cell Printer saves images of ejected single cells; real-time extracts MS spectra from MS files for a) either classification of single cells, or b) quantitation of (a) chemical constituent(s) of single cells.

Kertesz, Vilmos↗

Effects of excess carriers on charged defect concentrations in wide bandgap semiconductors

Unintentional doping and doping limits in semiconductors are typically caused by compensating defects with low formation energies. Since the formation enthalpy of a charged defect depends linearly on the Fermi level, doping limits can be especially pronounced in wide bandgap semiconductors where the Fermi level can vary substantially. Introduction of non-equilibrium carrier concentrations during growth or processing alters the chemical potentials of band carriers and allows populations of charged defects to be modified in ways impossible at thermal equilibrium. We demonstrate that in the presence of excess carriers, the rates of carrier capture and emission involving a defect charge transition level determine the admixture of electron and hole quasi-Fermi levels involved in the formation enthalpy of non-zero charge defect states. To understand the range of possible responses, we investigate the behavior of a single donor-like defect as functions of extrinsic doping and charge transition level energy. We find that that excess carriers will increase the formation enthalpy of compensating defects for most values of the charge transition level in the bandgap. Thus, it may be possible to use non-equilibrium carrier concentrations to overcome limitations on doping imposed by native defects. Cases also exist in which the concentration of defects with the same charge polarity as the majority dopant is either left unchanged or actually increases. This surprising effect arises when emission rates are suppressed relative to the capture rates and is most pronounced in wide bandgap semiconductors. We provide guidelines for carrying out experimental tests of this model.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Impact of Sugarcane Cultivation on C Cycling in Southeastern United States Following Conversion From Grazed Pastures

ABSTRACT The expansion of sugarcane, a tropical high‐yielding feedstock, will likely reshape the Southeastern United States (SE US) bioenergy landscape. However, the sustainability of sugarcane, particularly as it displaces grazed pastures, is highly uncertain. Here, we investigated how pasture conversion to sugarcane in subtropical Florida impacts net ecosystem CO 2 exchange (NEE) and net ecosystem carbon (C) balance (NECB). Measurements were made over three full growth cycles (> 3 years) in sugarcane—plant cane, PC; first ratoon cane, FRC; second ratoon cane, SRC—and in improved (IM) and semi‐native (SN) pastures, which make up ca. 37% of agricultural land in the region. Immediately following conversion, PC was a stronger net source of CO 2 than pastures, indicating the importance of CO 2 losses related to land disturbance. Sugarcane, however, shifted to a strong net sink of CO 2 after first regrowth, and overall sugarcane was a stronger net CO 2 sink than pastures. Both stand age and low water availability during cane emergence and tillering substantially decreased its potential gross CO 2 uptake. Accounting for all C gains and removals (i.e., NECB), greater frequency of burn events and repeated harvest increased removals and overall made sugarcane a stronger C source relative to pastures despite substantial C inputs from the previous land use and a stronger CO 2 sink strength. Time since conversion substantially reduced C losses from sugarcane, and the NECB of SRC was similar to that of IM pasture but lower than that of SN pasture, indicating a rapid shift in the NECB of cane. We conclude that the C‐balance implications following conversion will depend on the proportion of IM versus SN pastures converted to sugarcane. Furthermore, our findings suggest that no‐burn harvest management strategies will be critical to the development of a sustainable bioenergy landscape in SE US.

Gomez‐Casanovas, Nuria↗

Ethanol from Agriculture for Arkansas and America

The purpose of this project was to develop technology that would facilitate production of sugars from agricultural residues to enable biofuels and biobased product manufacturing. Our primary technology is to use genetic engineering to put bacterial and fungal cellulase genes into corn kernels, using the grain as the production system for the enzymes. At the beginning of this DoE funded program, we were producing two cellulases—E1 endocellulase from a bacterium found in a hot spring at Yellowstone National Park, and CBH I exocellulase from a wood rot fungus. Our team developed several new regulatory sequences (promoters) that increased enzyme protein accumulation in two kernel compartments (embryo and endosperm). We were also able to capitalize on the diverse genetics of corn to increase protein accumulation. High oil germplasm in particular was instrumental in this increase. A second task in the program was to produce enzymes and proteins that enhanced the activity of the E1 and CBH I enzymes. Our team produced CBH II, from the same wood rot fungus at a level that enabled highly enhanced deconstruction activity of E1 and CBH I in a synergistic manner. We analyzed an additional protein, expansin from cucumber that was expressed in the maize grain expression system. This protein had been previously shown to enhance cellulase activity (D. Cosgrove, Penn State University), and required a large-scale production platform. Our team showed that the corn production system allows industrial amounts of active expansin to be harvested from the grain. One of the challenges of any new production system is to maximize recovery of active ingredient from the raw materials at a cost compatible with its final use. Our team showed that low pH extraction of grain solubilized the enzymes without contamination of native corn protein and active product could be concentrated through ultrafiltration. The final outcomes of this project were the following: 3 cellulase enzymes and the synergistic protein expansin produced at high levels in corn grain, new promoters and combinations of promoters to enhance protein accumulation in grain, application of unique germplasm pools to enhance protein accumulation, and highly efficient processing enabling cost-effective production of cellulases that are highly active in biomass deconstruction.

09 BIOMASS FUELS↗

infrastore [SWR-26-077]

Infrastore is time-series storage for energy-systems simulations, backed by HDF5 + SQLite, with Rust, Python, Julia, gRPC, and CLI bindings. It is a Rust library for managing time-series data in power-systems and energy simulations. Numerical arrays are persisted in HDF5, and the metadata associating each array with its owning component lives in SQLite. Identical arrays are stored once and shared through content addressing. It ships native Rust, Python (PyO3), and Julia (C ABI) interfaces, the infrastore command-line tool, and a read-only gRPC server with a Rust client. Documentation: https://natlabrockies.github.io/infrastore/latest/ — start with the Quick Start or the Architecture.

Thom, Daniel [National Laboratory of the Rockies (↗

Capturing the inherent structural dynamics of the HIV-1 envelope glycoprotein fusion peptide

The N-terminal fusion peptide (FP) of the human immunodeficiency virus (HIV)-1 envelope glycoprotein (Env) gp41 subunit plays a critical role in cell entry. However, capturing the structural flexibility in the unbound FP is challenging in the native Env trimer. Here, FP conformational isomerism is observed in two crystal structures of a soluble clade B transmitted/founder virus B41 SOSIP.664 Env with broadly neutralizing antibodies (bNAbs) PGT124 and 35O22 to aid in crystallization and that are not specific for binding to the FP. Large rearrangements in the FP and fusion peptide proximal region occur around M530, which remains anchored in the tryptophan clasp (gp41 W623, W628, W631) in the B41 Env prefusion state. Further, we redesigned the FP at position 518 to reinstate the bNAb VRC34.01 epitope. These findings provide further structural evidence for the dynamic nature of the FP and how a bNAb epitope can be restored during vaccine design.

59 BASIC BIOLOGICAL SCIENCES↗

Distinguishing the XUV-induced Coulomb explosion dynamics of iodobenzene using covariance analysis

The primary and secondary fragmentation dynamics of iodobenzene following its ionization at 120 eV were determined using three-dimensional velocity map imaging and covariance analysis. Site-selective iodine 4d ionization was used to populate a range of excited polycationic parent states, which primarily broke apart at the carbon-iodine bond to produce I+ with phenyl or phenyl-like cations (C n H x + or C n H, with n = 1 – 6 and x = 1 – 5). The molecular products were produced with varying degrees of internal excitation and dehydrogenation, leading to stable and unstable outcomes. This further allowed the secondary dynamics of C 6 H x 2+ intermediates to be distinguished using native-frame covariance analysis, which isolated these processes in their own centre-of-mass reference frames. Furthermore, the mass resolution of the imaging mass spectrometer used for these measurements enabled the primary and secondary reaction channels to be specified at the level of individual hydrogen atoms, demonstrating the ability of covariance analysis to comprehensively measure the competing fragmentation channels of aryl cations, including those involving intermediate steps.

74 ATOMIC AND MOLECULAR PHYSICS↗

Charge-carrier behavior in Ba-, Sr- and Yb-filled $\mathrm{CoSb_3}$: NMR and transport studies

Here, we report $\mathrm{^{59}Co}$ NMR and transport measurements on n -type filled skutterudites $\mathrm{Ba}_x\mathrm{Yb}_y \mathrm{Co_4Sb_{12}}$ and $A_x \mathrm{Co_4Sb_{12}}$ $(A = \mathrm{Ba}$ or Sr), promising thermoelectric materials. The results demonstrate consistently that a shallow defect level near the conduction-band minimum dominates the electronic behavior, in contrast to the behavior of unfilled $\mathrm{CoSb_3}$. To analyze the results, we modeled the defect as having a single peak in the density of states, occupied at low temperatures due to donated charges from filler atoms. We fitted the NMR shifts and spin-lattice relaxation rates allowing for arbitrary carrier densities and degeneracies. The results provide a consistent picture for the Hall data, explaining the temperature dependence of the carrier concentration. Furthermore, without adjusting model parameters, we calculated Seebeck coefficient curves, which also provide good consistency. In agreement with recently reported computational results, it appears that composite native defects induced by the presence of filler atoms can explain this behavior. These results provide a better understanding of the balance of charge carriers, which is of crucial importance for designing improved thermoelectric materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Attacking the Opioid Epidemic: Determining the Epistatic and Pleiotropic Genetic Architectures for Chronic Pain and Opioid Addiction

We describe the CoMet application for large-scale epistatic Genome-Wide Association Studies (eGWAS) and pleiotropy studies. High performance is attained by transforming the underlying vector comparison methods into highly performant generalized distributed dense linear algebra operations. The 2-way and 3-way Proportional Similarity metric and Custom Correlation Coefficient are implemented using native or adapted GEMM kernels optimized for GPU architectures. By aggressive overlapping of communications, transfers and computations, high efficiency with respect to single GPU kernel performance is maintained up to the full Titan and Summit systems. Nearly 300 quadrillion element comparisons per second and over 2.3 mixed precision ExaOps are reached on Summit by use of Tensor Core hardware on the Nvidia Volta GPUs. Performance is four to five orders of magnitude beyond comparable state of the art. CoMet is currently being used in projects ranging from bioenergy to clinical genomics, including for the genetics of chronic pain and opioid addiction.

Joubert, Wayne↗

Characterization of the In Vivo Deuteration of Native Phospholipids by Mass Spectrometry Yields Guidelines for Their Regiospecific Customization

Customization of deuterated biomolecules is vital for many advanced biological experiments including neutron scattering. However, because it is challenging to control the proportion and regiospecificity of deuterium incorporation in live systems, often only two or three synthetic lipids are mixed together to form simplistic model membranes. This limits the applicability and biological accuracy of the results generated with these synthetic membranes. Despite some limited prior examination of deuterating Escherichia coli lipids in vivo, this approach has not been widely implemented. In this report an extensive mass spectrometry-based profiling of E. coli phospholipid deuteration states with several different growth media was performed, and a computational method to describe deuterium distributions with a one-number summary is introduced. The deuteration states of 36 lipid species were quantitatively profiled in 15 different growth conditions, and tandem mass spectrometry was used to reveal deuterium localization. Regressions were employed to enable the prediction of lipid deuteration for untested conditions. Small-angle neutron scattering was performed on select deuterated lipid samples, which validated the deuteration states calculated from the mass spectral data. Based on these experiments, guidelines for the design of specifically deuterated phospholipids are described. This unlocks even greater capabilities from neutron-based techniques, enabling experiments that were formerly impossible.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Origin of replication discovery for environmentally isolated Pantoea strain enables expression of heterologous proteins, pathways and products

Leveraging predicted origin sequences from a previously characterized groundwater plasmidome, we constructed a barcoded plasmid library to screen for previously unknown origins. Testing this library against a panel of representative bacterial strains led to the identification of 3 previously unknown origins that replicate in gram-negative bacteria not previously associated with these origin sequences. Experimental validation confirmed that a plasmid bearing origin 6911 as the sole origin could replicate with a copy number of 9 (±2) in Pantoea sp. MT58, a fast growing and metal tolerant, environmentally important bacterium. Plasmids based on this new origin were used to express the reporter protein GFP, and non-native metabolite pathways for the natural product indigoidine and the terpenoid compound isoprenol. Functional previously unknown origins of replication in such non-model organisms can expand the toolkit for genetic manipulations of both model and less-studied bacteria.

molecular biology↗

Structural basis for the allosteric modulation of rhodopsin by nanobody binding to its extracellular domain

Rhodopsin is a prototypical G protein-coupled receptor (GPCR) critical for vertebrate vision. Research on GPCR signaling states has been facilitated using llama-derived nanobodies (Nbs), some of which bind to the intracellular surface to allosterically modulate the receptor. Extracellularly binding allosteric nanobodies have also been investigated, but the structural basis for their activity has not been resolved to date. Here, we report a library of Nbs that bind to the extracellular surface of rhodopsin and allosterically modulate the thermodynamics of its activation process. Crystal structures of Nb2 in complex with native rhodopsin reveal a mechanism of allosteric modulation involving extracellular loop 2 and native glycans. Nb2 binding suppresses Schiff base deprotonation and hydrolysis and prevents intracellular outward movement of helices five and six – a universal activation event for GPCRs. Nb2 also mitigates protein misfolding in a disease-associated mutant rhodopsin. Our data show the power of nanobodies to modulate the photoactivation of rhodopsin and potentially serve as therapeutic agents for disease-associated rhodopsin misfolding.

59 BASIC BIOLOGICAL SCIENCES↗

Fort Yukon wood Energy Program Wood Boiler Deployment (Final Report)

The Fort Yukon Gwitchyaa Zhee Corporation (GZ) worked with partners on the development of an Integrated Biomass Energy Program for Fort Yukon. This integrated approach linked sustainable forest management with an in- village for -profit wood harvest and delivery business to displace diesel energy with wood energy for heat and power. The program was based on the concept of ecological, economic and social sustainability with a goal of displacing as much diesel and fuel oil as is technically feasible and sustainable; essentially systematically converting a village to significant amounts of wood use. Additionally, GZ worked with the Alaska Energy Authority (AEA) on the development of a rural power system upgrade (RPSU) project that replaced GZ’s existing antiquated diesel power plant and provided upgrades to the existing electrical distribution system. Due to the synergy of the two projects, the Biomass and RPSU projects were combined to provide improved operating efficiency, economy of scale and increased benefits to GZ, the Council of Athabascan Tribal Governments (CATG) and the community of Fort Yukon. The combined project is referred to as the Fort Yukon Combined heat and power (CHP) project. The purpose of the DOE Tribal Energy Program award was to support the preconstruction tasks and installation of wood boilers at the CATG clinic, and at the new GZ diesel power plant as part of an overall program to create a for- profit wood energy utility in Native Village of Fort Yukon. The CHP project provides biomass and diesel generation recovered heat via a new district heating system to the major commercial buildings in Fort Yukon. The CATG clinic will receive heat from a separate biomass boiler to their heating needs. The award from the Department of Energy (DOE) Tribal Energy Program was divided into two phases: Design/Permitting (phase 1) and Construction (phase 2). Phase 1 (Design & Permitting) is cost shared using State of Alaska Renewable Energy Funding (REF) funds through the Alaska Energy Authority (AEA). Phase 2 (Construction) was funded by DOE, AEA and US Department of Agriculture Rural Utility Service (USDA-RUS). Phase 1 of this grant, along with a separate grant from the Denali Commission provided funding for development of the wood delivery infrastructure necessary to support the CHP project. Under phase 2, This DOE grant supported final design of the boiler, bidding, purchase and transport of boilers, installation, technical support and engineering. The AEA and RUS grants supported permitting, final design, material and equipment purchase, and construction and installation of the new diesel power plant and district heating distribution system.

09 BIOMASS FUELS↗

Predicting Patterns of Solar Energy Buildout to Identify Opportunities for Biodiversity Conservation

The construction of solar energy facilities can have positive or negative impacts on biodiversity depending on siting and associated land use transitions. We identified drivers of solar siting and quantified patterns of buildout in states surrounding the Chesapeake Bay watershed – a biodiversity hotspot with numerous ecosystem services. Using a convolutional neural network, we mapped the footprints of ground-mounted solar arrays present in satellite imagery annually from 2017 to 2021 in Delaware, Maryland, Pennsylvania, New York, Virginia, and West Virginia. As of 2021, we identified 958 solar arrays covering 52.3 km2 built primarily on previously cultivated land, while avoiding natural landcover. We fit a binomial-Weibull model to these solar timeseries data in a hierarchical, Bayesian framework to quantify the relationship between geospatial covariates and rate of solar development. Solar array construction rate increased in cultivated areas, areas of lower agricultural suitability, lower slope, lower forest cover, lower biodiversity protection, and greater distances from roads. We also estimated changes in the rate of solar construction over time and found differences among states: acceleration in Virginia and deceleration in New York. We used parameter estimates to map the relative likelihood of future solar development across the study area. This methodology can be used to anticipate where solar is likely to be built in different landscapes and how these patterns align with conservation goals. Around the Chesapeake Bay watershed, the selection of lower quality agricultural areas for solar energy minimizes removal of important habitat and provides opportunities for native plant and pollinator restoration.

Artificial Intelligence↗