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DOE OSTI2022

A Fish Out of Basin: Increased Stress Physiology and Reduced Performance of Salmon River Hatchery Chinook Salmon

Abstract Variation in rearing conditions across hatcheries and basins can affect the performance of hatchery salmonids in the wild. In 2008, the Shoshone-Bannock Tribes began planning an out-of-basin hatchery facility on the eastern Snake River Plain for rearing threatened Chinook Salmon Oncorhynchus tshawytscha for release in tributaries of the upper Salmon River, Idaho, USA. To help determine the viability of the planned out-of-basin hatchery, we reared 100,000 juvenile Chinook Salmon from the same genetic stock at one in-basin (Sawtooth Fish Hatchery on the Salmon River) and one out-of-basin (Springfield Fish Hatchery on the Snake River Plain) site in Idaho that are characterized by significant differences in water hardness and temperature regime. In October 2018 and April 2019, we tested whether fish condition, stress physiology, acute mortality, and downstream survival differed between the two groups at the parr and smolt life stages upon release in the Yankee Fork Salmon River, which is characterized by low water hardness. For both release groups, parr experienced low acute mortality during the 48 h after release; however, the out-of-basin group had a downstream survival rate through an unimpounded portion of the migration corridor that was an order of magnitude lower than that for the in-basin group. During the smolt release, the out-of-basin group showed signs of extreme physiological stress, acute mortality rates of 40–80%, and low survival in the unimpounded portion of the migratory corridor. The in-basin group recovered from the stress of transport and release, had no acute mortality, and survived through the unimpounded migratory corridor at a rate comparable to that of previous years’ releases. Based on the results of this comparative study, comanagers are evaluating alternatives to the proposed out-of-basin hatchery program. This case study highlights the effects of differences between rearing and release conditions on salmon physiology and survival as well as the value of conducting preliminary evaluations prior to implementing large-scale hatchery supplementation programs.

Ebel, Jonathan D.↗

DOE OSTI2023

A Review of Factors Affecting the Susceptibility of Juvenile Salmonids to Avian Predation

Abstract We reviewed studies of piscivorous colonial waterbird predation on juvenile salmonids to synthesize current knowledge of factors affecting fish susceptibility to avian predators. Specifically, we examined peer-reviewed publications and reports from academic, governmental, and nongovernmental agencies to identify commonalities and differences in susceptibility of salmonids to avian predation, with a focus on mark–recovery studies in the Columbia River basin. Factors hypothesized to influence salmonid susceptibility to avian predation were grouped into four general categories: (1) salmonid species and populations, (2) environmental factors, (3) prey density, predator density, and migration timing, and (4) prey characteristics. Our review focused on predation by Caspian terns Hydroprogne caspia, double-crested cormorants Nannopterum auritum, and gull species Larus spp. as these are the most well-studied avian predators of salmonids. Results indicated that predator–prey interactions varied across salmonid species and populations and species of avian predator. Inferences across studies supported multiple hypotheses regarding predator–prey dynamics, including environmental factors that influence prey exposure to predators (e.g., river flows, turbidity, alternative prey), variation in predator and prey abundances, predator characteristics (e.g., foraging behavior, colony location), and prey characteristics (e.g., fish length, condition). Mark–recovery studies of avian predation on fish populations have greatly improved our understanding of the factors affecting fish susceptibility to avian predation, the relative contributions of abiotic and biotic factors to predation susceptibility, and the extent to which avian predation affects fish survival and the viability of prey populations. Future studies that jointly model predation and survival and the factors affecting those processes will further broaden our understanding of predator–prey dynamics and directly evaluate the effects of predation on prey population dynamics.

Hostetter, Nathan J. (ORCID:0000000160752157)↗

DOE OSTI2023

Genetic monitoring of steelhead in the Klickitat River to estimate productivity, straying, and migration timing

Abstract Objective Salmonids with a complex life history variation present challenges for conservation management, but genetic approaches alongside fisheries monitoring can address questions regarding the viability of the natural populations. Methods We genotyped adult (n = 3108) and juvenile (n = 2624) samples of steelhead Oncorhynchus mykiss that were collected in the Klickitat River, Washington, USA at traps in the lower drainage to examine tributary level productivity, straying from outside sources, and variation in adult migration timing. Result Genetic assignment of steelhead from this system indicated that the majority were produced within or near tributaries of the middle Klickitat River (juvenile mean = 72.8%; adult mean = 87.3%). Analyses with parentage-based tagging identified that most hatchery-origin adults were assigned to the Skamania Hatchery (80.8%), as expected, since this has been the release stock for decades within the Klickitat River drainage. Hatchery-origin adults were also identified from programs operating outside the Klickitat River, which were primarily strays from Snake River hatcheries. Most natural-origin steelhead were assigned to the Klickitat River, but there were also natural-origin fish identified as strays from other regions of the Columbia River (22.3% of natural returns). We also examined genes known to be associated with migration timing in adult steelhead observed at the trap and observed a strong relationship between migration date and alleles for early and late migration, but individual outliers were detected across seasons. Conclusion Our results indicate that genetic variation of steelhead in the Klickitat River has been influenced by hatchery programs as well as natural-origin straying from other subbasins, but genetic diversity remains high throughout the subbasin, and both early and late migration alleles are maintained. The genetic diversity present in Klickitat River steelhead may enable this Endangered Species Act listed (threatened) species to better adapt to stochastic environmental conditions compared to less diverse populations.

Collins, Erin E. (ORCID:0000000260978479)↗

DOE OSTI2022

Manning condensation in ion exchange membranes: A review on ion partitioning and diffusion models

Here, the rational design of ion exchange membranes (IEMs) is becoming more pertinent as their usage becomes broader and as their staple applications (i.e., electrodialysis, flow batteries, and fuel cells) improve in commercial viability. Such efforts would be catalyzed by an improved fundamental understanding of ion transport in IEMs. This review discusses recent progress in modeling ion partitioning and diffusion in IEMs in an effort to relate IEM performance metrics to fundamental membrane properties over which researchers and membrane manufacturers possess direct and sometimes precise control. Central focus is given to the Donnan-Manning model for ion partitioning and the Manning-Meares model for ion diffusion in IEMs. These two frameworks, which are derived from Manning's counter-ion condensation theory for polyelectrolyte solutions, have been widely used within the IEM literature since their recent introduction. To explore this topic, the mathematical derivation of both models is revisited, followed by a survey of experimental and computational discussions of counter-ion condensation in IEMs. Alternative models which fulfill similar roles in predicting IEM transport properties are compared. This review concludes by highlighting the uniquely favorable positions of the Donnan-Manning and Manning-Meares models and discussing their prospects as leading predictors of IEM partitioning and diffusive properties.

25 ENERGY STORAGE↗

DOE OSTI2022

Crystal structure of Campylobacter jejuni lipoprotein Cj1090c

In Gram-negative bacteria, lipopolysaccharide (LPS) is an essential component of the asymmetric outer membrane (OM). LptE is an OM lipoprotein that forms a complex with the β-barrel OM protein, LptD. Incorporation of LPS into the OM outer leaflet is essential for bacterial viability, and mediated by the LptD/E complex. The genome of Campylobacter jejuni, a major foodborne pathogen, contains over 20 putative lipoproteins including Cj1090c. Here, we report the crystal structure of Cj1090c at 2.4 Å resolution, revealing structural evidence for LptE in C. jejuni. The analysis of this crystal structure, along with the genomic context, allows us to propose the C. jejuni LPS transport system for the first time, and also permits for discussion of the features of the LptD/E complex of C. jejuni.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Temporal Sampling of Enzymes from Live Cells by Localized Electroporation and Quantification of Activity by SAMDI Mass Spectrometry

Abstract Measuring changes in enzymatic activity over time from small numbers of cells remains a significant technical challenge. In this work, a method for sampling the cytoplasm of cells is introduced to extract enzymes and measure their activity at multiple time points. A microfluidic device, termed the live cell analysis device (LCAD), is designed, where cells are cultured in microwell arrays fabricated on polymer membranes containing nanochannels. Localized electroporation of the cells opens transient pores in the cell membrane at the interface with the nanochannels, enabling extraction of enzymes into nanoliter‐volume chambers. In the extraction chambers, the enzymes modify immobilized substrates, and their activity is quantified by self‐assembled monolayers for matrix‐assisted laser desorption/ionization (SAMDI) mass spectrometry. By employing the LCAD‐SAMDI platform, protein delivery into cells is demonstrated. Next, it is shown that enzymes can be extracted, and their activity measured without a loss in viability. Lastly, cells are sampled at multiple time points to study changes in phosphatase activity in response to oxidation by hydrogen peroxide. With this unique sampling device and label‐free assay format, the LCAD with SAMDI enables a powerful new method for monitoring the dynamics of cellular activity from small populations of cells.

Mukherjee, Prithvijit↗

DOE OSTI2024

Review of Technical Photovoltaic Key Performance Indicators and the Importance of Data Quality Routines

Technical key performance indicators (KPIs) are important metrics used to assess and quantitatively summarize various aspects of photovoltaic (PV) systems, including long-term performance, economic viability, and carbon footprint. Herein, a group of experts of the International Energy Agency's Photovoltaic Power Systems Programme Task 13 collect and describ the most important technical KPIs used in the industry. Thereby, a set of best practices for reliably handling PV system data is presented and the impact of data quality and climatic variability on KPI calculation is investigated. Further, the effective use of technical KPIs allows triggering data-driven and informed decisions to optimize PV systems and providing a comprehensive overview of how PV systems operate across different conditions and climates. With the worldwide growth of the PV industry, more companies operate/own PV systems in different regions, where the climatic and seasonal profiles differ. This requires context-aware evaluation of KPIs, or the judicious application of multiple KPIs, to ensure that each asset is evaluated correctly. Beyond that, there is untapped potential in the utilization of KPIs through geospatial mapping and extrapolation of fleet KPIs. This study demonstrates that the uncertainty in KPI estimation is not well understood and depends on data quality, climatic variability, and system configuration.

14 SOLAR ENERGY↗

DOE OSTI2022

National-scale impacts on wind energy production under curtailment scenarios to reduce bat fatalities

Wind energy often plays a major role in meeting renewable energy policy objectives; however, increased deployment can raise concerns regarding the impacts of wind plants on certain wildlife. Particularly, estimates suggest hundreds of thousands of bat fatalities occur annually at wind plants across North America, with potential implications for the viability of several bat species. One approach to reducing bat fatalities is shutting down (or curtailing) turbines when bats are most at risk, such as at night during relatively low wind speed periods throughout summer and early autumn. While curtailment has consistently been shown to reduce bat fatalities, the lost power production reduces revenues for wind plants. This study conducted simulations with a range of curtailment scenarios across the contiguous United States to examine sensitivities of annual energy production (AEP) loss and potential impacts on economic metrics for future wind energy deployment. We found that AEP reduction can vary across the country from less than 1% to more than 10% for different curtailment scenarios. From an estimated 2891 gigawatts (GW) of simulated economically viable wind capacity (measured by a positive net present value), we found the mid curtailment scenario (6.0 m/s wind speed cut-in from July 1 through October 31) reduced the quantity of economic wind capacity by 274 GW or 9.5%. Our results indicate that high levels of curtailment could substantially reduce the future footprint of financially viable wind energy. In this context, future work that illuminates cost-effective strategies to minimize curtailment while reducing bat fatalities would be of value.

17 WIND ENERGY↗

DOE OSTI2021

Chapter 3: New Developments on Ionic Liquid-Tolerant Microorganisms Leading Toward a More Sustainable Biorefinery

The growing concerns about climate change and energy security are driving the development of bio-based technologies to produce renewable liquid fuels and chemicals. Ionic liquids (ILs) have demonstrated to be promising solvents to pretreat lignocellulosic residues, promoting efficient enzymatic hydrolysis of lignocellulosic carbohydrates into sugars, which can be further used by microorganisms to produce biofuels and other value-added chemicals. Despite their unique properties to effectively deconstruct plant cell walls, ILs show strong interactions with the pretreated biomass, and their presence is often inhibitory to cellulolytic enzymes and microorganisms. The most advanced biorefinery concepts based on IL pretreatments focus on the development of more biocompatible ILs and more robust microbial strains with higher tolerance to ILs. This chapter provides an overview and a discussion over the main efforts performed on the screening and development of IL-tolerant microbial strains, as well as in more biocompatible IL pretreatment methods. These early research advancements in this field offer a baseline and a platform for future research with the goal of improving the sustainability and economic viability of IL pretreatment-based biorefineries.

bioconversion↗

DOE OSTI2021

Continuum-mediated self-interacting dark matter

Dark matter may self-interact through a continuum of low-mass states. This happens if dark matter couples to a strongly-coupled nearly-conformal hidden sector. This type of theory is holographically described by brane-localized dark matter interacting with bulk fields in a slice of 5D anti-de Sitter space. The long-range potential in this scenario depends on a non-integer power of the spatial separation, in contrast to the Yukawa potential generated by the exchange of a single 4D mediator. The resulting self-interaction cross section scales like a non-integer power of velocity. We identify the Born, classical and resonant regimes and investigate them using state-of-the-art numerical methods. We demonstrate the viability of our continuum-mediated framework to address the astrophysical small-scale structure anomalies. Investigating the continuum-mediated Sommerfeld enhancement, we demonstrate that a pattern of resonances can occur depending on the non-integer power. We conclude that continuum mediators introduce novel power-law scalings which open new possibilities for dark matter self-interaction phenomenology.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Collinear expansion for color singlet cross sections

We demonstrate how to efficiently expand cross sections for color-singlet production at hadron colliders around the kinematic limit of all final state radiation being collinear to one of the incoming hadrons. This expansion is systematically improvable and applicable to a large class of physical observables. We demonstrate the viability of this technique by obtaining the first two terms in the collinear expansion of the rapidity distribution of the gluon fusion Higgs boson production cross section at next-to-next-to leading order (NNLO) in QCD perturbation theory. Furthermore, we illustrate how this technique is used to extract universal building blocks of scattering cross section like the N-jettiness and transverse momentum beam function at NNLO.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Submicron immunoglobulin particles exhibit FcγRII-dependent toxicity linked to autophagy in TNFα-stimulated endothelial cells

In intravenous immunoglobulins (IVIG), and some other immunoglobulin products, protein particles have been implicated in adverse events. Role and mechanisms of immunoglobulin particles in vascular adverse effects of blood components and manufactured biologics have not been elucidated. We have developed a model of spherical silica microparticles (SiMPs) of distinct sizes 200–2000 nm coated with different IVIG- or albumin (HSA)-coronas and investigated their effects on cultured human umbilical vein endothelial cells (HUVEC). IVIG products (1–20 mg/mL), bare SiMPs or SiMPs with IVIG-corona, did not display significant toxicity to unstimulated HUVEC. In contrast, in TNFα-stimulated HUVEC, IVIG-SiMPs induced decrease of HUVEC viability compared to HSA-SiMPs, while no toxicity of soluble IVIG was observed. 200 nm IVIG-SiMPs after 24 h treatment further increased ICAM1 (intercellular adhesion molecule 1) and tissue factor surface expression, apoptosis, mammalian target of rapamacin (mTOR)-dependent activation of autophagy, and release of extracellular vesicles, positive for mitophagy markers. Toxic effects of IVIG-SiMPs were most prominent for 200 nm SiMPs and decreased with larger SiMP size. Using blocking antibodies, toxicity of IVIG-SiMPs was found dependent on FcγRII receptor expression on HUVEC, which increased after TNFα-stimulation. Similar results were observed with different IVIG products and research grade IgG preparations. In conclusion, submicron particles with immunoglobulin corona induced size-dependent toxicity in TNFα-stimulated HUVEC via FcγRII receptors, associated with apoptosis and mTOR-dependent activation of autophagy. Testing of IVIG toxicity in endothelial cells prestimulated with proinflammatory cytokines is relevant to clinical conditions. Our results warrant further studies on endothelial toxicity of sub-visible immunoglobulin particles.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Microbial Enrichments Contribute to Characterization Of Desert Tortoise Gut Microbiota

Abstract Desert tortoises play ecologically significant roles, including plant seed dispersal and mineral cycling, and yet little is known about microbial members that are critical to their gut and overall health. Tortoises consume recalcitrant plant material, which their gut microbiota degrades and converts into usable metabolites and nutrients for the tortoise. Findings from tortoise gut microbiomes may translate well into biotechnological applications as these microbes have evolved to efficiently degrade recalcitrant substrates and generate useful products. In this study, we cultivated microbial communities from desert tortoise fecal samples following a targeted anaerobic enrichment for microbes involved in deconstruction and utilization of plant biomass. We employed 16S rRNA amplicon sequencing to compare cultivated communities to initial fecal source material and found high abundances of Firmicutes and Bacteroidota typically associated with biomass deconstruction in all cultivated samples. Significantly decreased microbial diversity was observed in the cultivated microbial communities, yet several key taxa thrived in lignocellulose enrichments, includingLachnospiraceaeandEnterococcus. Additionally, cultivated communities produced short-chain fatty acids under anaerobic conditions, and their growth and metabolic output provide evidence of their viability in the initial fecal communities. Overall, this study adds to the limited understanding of reptilian herbivore microbiota, and offers a path towards biotechnological translation based on the ability of the cultivated communities to convert lignocellulose directly to acetate, propionate, and butyrate.

Environmental Sciences & Ecology↗

DOE OSTI2025

Heterogeneous Mixtures of Dictionary Functions to Approximate Subspace Invariance in Koopman Operators: Why Deep Koopman Operators Work

Abstract Koopman operators model nonlinear dynamics as a linear dynamic system acting on a nonlinear function as the state. This nonstandard state is often called a Koopman observable and is usually approximated numerically by a superposition of functions drawn from a dictionary . In a widely used algorithm, extended dynamic mode decomposition (EDMD), the dictionary functions are drawn from a fixed class of functions. Deep learning combined with EDMD has been used to learn novel dictionary functions in an algorithm called deep dynamic mode decomposition (deepDMD). The learned representation both (1) accurately models and (2) scales well with the dimension of the original nonlinear system. In this paper, we analyze the learned dictionaries from deepDMD and explore the theoretical basis for their strong performance. We explore State-Inclusive Logistic Lifting (SILL) dictionary functions to approximate Koopman observables. Error analysis of these dictionary functions show they satisfy a property of subspace approximation, which we define as uniform finite approximate closure. Typically, a Koopman dictionary’s nonlinear functions are homogeneous. In this paper, we discover that structured mixing of heterogeneous dictionary functions drawn from different classes of nonlinear functions achieve the same accuracy and dimensional scaling as the deep-learning-based deepDMD algorithm Yeung et al. ( In: 2019 American Control Conference (ACC), 2019). We specifically show this by building a heterogeneous dictionary comprised of SILL functions and conjunctive radial basis functions (RBFs). This mixed dictionary achieves similar accuracy and dimensional scaling to deepDMD with an order of magnitude reduction in parameters, while maintaining geometric interpretability. These results strengthen the viability of dictionary-based Koopman models to solving high-dimensional nonlinear learning problems.

Johnson, Charles A.↗

DOE OSTI2024

Shear and extensional rheology of polyethylenes recycled using a solvent dissolution process

There is high market demand for increasing the viability of current plastic recycling processes. In this work rheology is used to evaluate the mechanical properties of a solvent dissolution recycled polymer compared to its virgin untreated precursor. Solvent dissolution and precipitation are used to target multi-layer, multi-component, industry films, which cannot be mechanically recycled. Polyethylene was chosen as the primary polymer of interest. Polymer thermal stability was monitored via time-resolved rheology; consecutive frequency sweeps over the course of an hour while under isothermal conditions. Additional rheological experiments were performed within the identified thermally stable conditions. Small-angle oscillatory shear was complemented with steady shear viscosity experiments over a wide range of shear rates. Extensional rheology was used to determine changes in molecular weight and cross link density. As a result, rheological characterization is supplemented with gas chromatography–mass spectrometry of the solvent wash to determine components stripped from the virgin polymers during solvent treatment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

An overview of the Energy Modeling Forum 33rd study: Assessing large-scale global bioenergy deployment for managing climate change

Previous studies have projected a significant role for bioenergy in decarbonizing the global economy and helping realize international climate goals such as limiting global average warming to 2°C or 1.5°C. However, with significant variability in bioenergy results and significant concerns about potential environmental and social implications, greater transparency and dedicated assessment of the underlying modeling and results and more detailed understanding of the potential role of bioenergy are needed. Stanford University’s Energy Modeling Forum (EMF) initiated a 33rd study (EMF-33) to explore the viability of large-scale bioenergy as part of a comprehensive climate management strategy. This special issue presents the papers of the EMF-33 study—a multi-year inter-model comparison project designed to understand and assess global, long-run, biomass supply and bioenergy deployment potentials and related uncertainties. Using a novel scenario design with independent biomass supply and bioenergy demand protocols, EMF-33 separately elucidates and explores the modeling of biomass feedstock supplies and bioenergy technologies and their deployment—revealing, comparing, and assessing the modeling that is suggesting that bioenergy could be a key climate containment strategy. This introduction provides an overview of the EMF-33 study design and the overview, thematic, and individual modeling team papers and types of insights that make up this special issue. By providing enhanced transparency and new detailed insights, we hope to inform policy dialogue about the potential role of bioenergy and facilitate new research.

Rose, Steven K.↗

DOE OSTI2022

Quantifying Firebrand Production and Transport Using the Acoustic Analysis of In-Fire Cameras

Firebrand travel and ignition of spot fires is a major concern in the Wildland-Urban Interface and in wildfire operations overall. Firebrands allow for the efficient breaching across fuel-free barriers such as roads, rivers and constructed fuel breaks. Existing observation-based knowledge on medium-distance firebrand travel is often based on single tree experiments that do not replicate the intensity and convective updraft of a continuous crown fire. Recent advances in acoustic analysis, specifically pattern detection, has enabled the quantification of the rate at which firebrands are observed in the audio recordings of in-fire cameras housed within fire-proof steel boxes that have been deployed on experimental fires. The audio pattern being detected is the sound created by a flying firebrand hitting the steel box of the camera. This technique allows for the number of firebrands per second to be quantified and can be related to the fire's location at that same time interval (using a detailed rate of spread reconstruction) in order to determine the firebrand travel distance. A proof of concept is given for an experimental crown fire that shows the viability of this technique. When related to the fire's location, key areas of medium-distance spotting are observed that correspond to regions of peak fire intensity. Trends on the number of firebrands landing per square metre as the fire approaches are readily quantified using low-cost instrumentation.

58 GEOSCIENCES↗

DOE OSTI2022

Structural characterization and biological activity of an α-glucan from the mollusk Marcia hiantina (Lamarck, 1818)

Marcia hiantina (Mollusca, Bivalvia) (Lamarck, 1818), is an edible clam mainly distributed along the tropical coastal regions. Recent researches have demonstrated that clams can possess compounds, including polysaccharides, with a wide range of biological actions including antioxidant, immunomodulatory and antitumor activities. Here an α-glucan was isolated from M. hiantina by hot water, purified by anion exchange chromatography, and its structure was characterized by a combination of multiple nuclear magnetic resonance (NMR) methods (1D 1 H, 1 H- 1 H COSY, 1 H- 1 H TOCSY, 1 H- 1 H NOESY, 1 H- 13 C HSQC and 1 H- 13 C HSQC-NOESY spectra), gas chromatography-mass spectrometry, and high performance size exclusion chromatography (HPSEC). The analysis from NMR, monosaccharide composition, methylation analyses and HPSEC combined with multi angle light scattering (MALS) of M. hiantina-derived α-glycan confirmed a branched polysaccharide exclusively composed of glucose (Glc), mostly 4-linked in its backbone, branched occasionally at 6-positions, and having a molecular weight of ~ 570 kDa. The mollusk α-glucan was subjected to four cell-based assays: (i) viability of three cell lines (RAW264.7, HaCaT, and HT-29), (ii) activity on lipopolysaccharide (LPS)-induced prostaglandin production in RAW264.7 cells, (iii) inhibitory activities of in H 2 O 2 - and LPS-induced reactive oxygen species (ROS) production in HMC3 cells, and (iv) HaCaT cell proliferation. Furthermore, results have indicated no cytotoxicity, potent inhibition of both H 2 O 2 - and LPS-induced ROS, and potent cell proliferative activity.

59 BASIC BIOLOGICAL SCIENCES↗