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DOE OSTI2020

Applying Two Active Acoustic Technologies to Document Presence of Large Marine Animal Targets at a Marine Renewable Energy Site

Coastal regions are highly used by humans. The growing marine renewable energy (MRE) industry will add to existing anthropogenic pressures in these regions. Regulatory bodies require animal risk assessment before new industrial activities can progress, and MRE is no exception. Preliminary data of marine mammal use of an MRE device deployment location could be informative to permitting. A combination of downlooking hydroacoustics using an echosounder and acoustic camera (imaging sonar) was used to provide a number of large targets (proxy for large fish and marine mammals) in an area of interest for MRE tidal turbine deployment in Western Passage, Maine, USA. Data were collected in May, June, August, and September of 2010 and 2011. Of the nine large targets confirmed to be animals, eight were porpoises and one was a shark. Few large targets were observed in May and June, with the majority (90%) being present in August and September of both years. The most large targets were observed when tidal current speed was less than 1 m·s−1. These data provide a preliminary assessment of large targets in a single location over sixteen 24-h surveys. The aforementioned methodology could be used for future pre- and post-installation assessments at MRE device deployment locations. Their use in concert with visual and passive acoustic monitoring can provide water depth usage by marine mammals, which is a metric that is difficult to assess with passive acoustic and visual techniques.

Staines, Garrett↗

DOE OSTI2021

Methods for attaching transmitters to animals

Methods for attaching a radio frequency (RF) transmitter to an animal are provided. The methods can include providing an RF transmitter and providing an injection device having a needle of gauge of 9 or smaller; providing the RF transmitter into the injection device; and providing the RF transmitter through the 9 gauge or smaller needle and into the animal.

Deng, Z. Daniel↗

DOE OSTI2022

Methods for attaching transmitters to animals

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2

To investigate the evolutionary history of the recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China, a total of 70 genomes of virus strains from China and elsewhere with sampling dates between 24 December 2019 and 3 February 2020 were analyzed. To explore the potential intermediate animal host of the SARS-CoV-2 virus, we reanalyzed virome data sets from pangolins and representative SARS-related coronaviruses isolates from bats, with particular attention paid to the spike glycoprotein gene. We performed phylogenetic, split network, transmission network, likelihood-mapping, and comparative analyses of the genomes. Additionally, based on Bayesian time-scaled phylogenetic analysis using the tip-dating method, we estimated the time to the most recent common ancestor and evolutionary rate of SARS-CoV-2, which ranged from 22 to 24 November 2019 and 1.19 to 1.31 × 10 -3 substitutions per site per year, respectively. Our results also revealed that the BetaCoV/bat/Yunnan/RaTG13/2013 virus was more similar to the SARS-CoV-2 virus than the coronavirus obtained from the two pangolin samples (SRR10168377 and SRR10168378). We also identified a unique peptide (PRRA) insertion in the human SARS-CoV-2 virus, which may be involved in the proteolytic cleavage of the spike protein by cellular proteases, and thus could impact host range and transmissibility. Interestingly, the coronavirus carried by pangolins did not have the RRAR motif. Therefore, we concluded that the human SARS-CoV-2 virus, which is responsible for the recent outbreak of COVID-19, did not come directly from pangolins.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Bio-inspired bistable piezoelectric energy harvester for powering animal telemetry tags: Conceptual design and preliminary experimental validation

Here, this paper presents the conceptual design, preliminary experimental validation, and performance evaluation of a novel bio-inspired bi-stable piezoelectric energy harvester for self-powered animal telemetry tags. The overall conceptual design, which includes a bio-inspired attachment and a bi-stable piezoelectric energy harvester, is introduced firstly with a specific application example of marine fish tracking. The self-powered telemetry tag can be externally deployed on fish (dorsal fin) to monitor fish habitats, population, and underwater environment. Inspired by the Venus flytrap's rapid shape transition, a bi-stable piezoelectric energy harvester is developed to scavenge energy from fish maneuvering and the surrounding fluid flow for a sustainable power supply. The bistability of the harvester is characterized by the measured force-displacement curve and double potential wells. A bluff body is integrated to the free end of the bistable piezoelectric energy harvester to enhance the structure-fluid interaction for the large-amplitude snap-through vibrations and higher voltage output. Controlled laboratory experiments are conducted in a water tank on the bio-inspired bi-stable piezoelectric energy harvester using a servo motor system to simulate fish swing motion at various conditions to evaluate the power generation performance. The preliminary underwater experimental results demonstrated that the proposed bio-inspired bi-stable piezoelectric energy harvester could effectively convert fish swing motions into electricity. The device collected 17.25 mJ of energy over 130 s under a peak-to-peak swing angle of 30° at 1.5 Hz in the capacitor charging experiments.

Animal tracking↗

DOE OSTI2021

The regulation of animal behavior by cellular stress responses

Cellular stress responses exist to detect the effects of stress on cells, and to activate protective mechanisms that promote resilience. As well as acting at the cellular level, stress response pathways can also regulate whole organism responses to stress. One way in which animals facilitate their survival in stressful environments is through behavioral adaptation; this review considers the evidence that activation of cellular stress responses plays an important role in mediating the changes to behavior that promote organismal survival upon stress.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Reburning of Animal Waste Based Biomass with Coals for NO x Reduction, Part II: Dairy Biomass (DB) and Coal–DB Blends

Concentrated animal feeding operations (both slaughter and dairy cattle) lead to land, water, and air pollution if waste storage and handling systems are not effectively managed. At the same time, cattle biomass (CB), which includes both slaughter/feedlot biomass (FB) and dairy biomass (DB), have the potential to be a source of green energy at coal-fired power plants. Part I presented results on NOx reductions with pure FB or Coal: FB blends as reburn fuels. Part II deals with results from reburning with pure DB or Coal: DB blends as reburn fuels. A mixture of NG with a small amount of NH3 was used to generate the baseline NOx of 400–420 ppm (or 185–194 g/GJ). NOx emissions were found to be reduced by as much as 96% when reburning with FB. The effects of reburn fuel type, equivalence ratio (ER RBZ ) in the reburn zone, vitiated air, several injection configurations of reburn fuel and initial NO concentrations on NOx emissions were investigated. The ER RBZ shows a significant effect on the NOx reduction. The 20% heat input by reburning was the better operating condition for the long-term operation due to its ash production. The results reveal that reburn with DB fuels is an effective technology for NOx emission control when the initial NOx emission is higher than 275 ppm (or 127 g/GJ or 0.3 lb/MMBtu).

09 BIOMASS FUELS↗

DOE OSTI2023

Aggregation of Leslie matrix models with application to ten diverse animal species

Some grouping is necessary when constructing a Leslie matrix model because it involves discretizing a continuous process of births and deaths. Here, the level of grouping is determined by the number of age classes and frequency of sampling. It is largely unknown what is lost or gained by using fewer age classes, and I address this question using aggregation theory. I derive an aggregator for a Leslie matrix model using weighted least squares, determine what properties an aggregated matrix inherits from the original matrix, evaluate aggregation error, and measure the influence of aggregation on asymptotic and transient behaviors. To gauge transient dynamics, I employ reactivity of the standardized Leslie matrix. I apply the aggregator to 10 Leslie models developed for animal populations drawn from a diverse set of species. Several properties are inherited by the aggregated matrix: (a) it is a Leslie matrix; (b) it is irreducible whenever the original matrix is irreducible; (c) it is primitive whenever the original matrix is primitive; and (d) its stable population growth rate and stable age distribution are consistent with those of the original matrix if the least squares weights are equal to the original stable age distribution. In the application, depending on the population modeled, when the least squares weights do not follow the stable age distribution, the stable population growth rate of the aggregated matrix may or may not be approximately consistent with that of the original matrix. Transient behavior is lost with high aggregation.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

The toughest animals of the Earth versus global warming: Effects of long‐term experimental warming on tardigrade community structure of a temperate deciduous forest

Abstract Understanding how different taxa respond to global warming is essential for predicting future changes and elaborating strategies to buffer them. Tardigrades are well known for their ability to survive environmental stressors, such as drying and freezing, by undergoing cryptobiosis and rapidly recovering their metabolic function after stressors cease. Determining the extent to which animals that undergo cryptobiosis are affected by environmental warming will help to understand the real magnitude climate change will have on these organisms. Here, we report on the responses of tardigrades within a five‐year‐long, field‐based artificial warming experiment, which consisted of 12 open‐top chambers heated to simulate the projected effects of global warming (ranging from 0 to 5.5°C above ambient temperature) in a temperate deciduous forest of North Carolina (USA). To elucidate the effects of warming on the tardigrade community inhabiting the soil litter, three community diversity indices (abundance, species richness, and Shannon diversity) and the abundance of the three most abundant species ( Diphascon pingue , Adropion scoticum , and Mesobiotus sp.) were determined. Their relationships with air temperature, soil moisture, and the interaction between air temperature and soil moisture were tested using Bayesian generalized linear mixed models. Despite observed negative effects of warming on other ground invertebrates in previous studies at this site, long‐term warming did not affect the abundance, richness, or diversity of tardigrades in this experiment. These results are in line with previous experimental studies, indicating that tardigrades may not be directly affected by ongoing global warming, possibly due to their thermotolerance and cryptobiotic abilities to avoid negative effects of stressful temperatures, and the buffering effect on temperature of the soil litter substrate.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Towards replacement of animal tests with in vitro assays: a gene expression biomarker predicts in vitro and in vivo estrogen receptor activity

High-throughput transcriptomics (HTTr) has the potential to support efforts to reduce or replace some animal tests. In past studies, we described a computational approach utilizing a gene expression biomarker consisting of 46 genes to predict estrogen receptor (ER) activity after chemical exposure in ER-positive human breast cancer cells including the MCF-7 cell line. We hypothesized that the biomarker model could identify ER activities of chemicals examined by Endocrine Disruptor Screening Program (EDSP) Tier 1 screening assays in which transcript profiles of the same chemicals were examined in MCF-7 cells. For the 62 chemicals examined including 5 chemicals examined in this study using RNA-Seq, the ER biomarker model accuracy was 1) 97% for in vitro reference chemicals, 2) 76–85% for guideline uterotrophic assays, and 3) 87–88% for guideline and nonguideline uterotrophic assays. For the same chemicals, these accuracies were similar or slightly better than those of the ToxCast ER model based on 18 in vitro assays. The performance of the ER biomarker model indicates that HTTr interpreted using the ER biomarker correctly identifies active and inactive ER reference chemicals. Finally, as part of the HTTr screening program the approach could rapidly identify chemicals with potential ER bioactivities for additional screening and testing.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Classification of animal sounds in a hyperdiverse rainforest using convolutional neural networks with data augmentation

To protect tropical forest biodiversity, we need to be able to detect it reliably, cheaply, and at scale. Automated detection of sound producing animals from passively recorded soundscapes via machine-learning approaches is a promising technique towards this goal, but it is constrained by the necessity of large training data sets. Using soundscapes from a tropical forest in Borneo and a Convolutional Neural Network model (CNN), we investigate i) the minimum viable training data set size for accurate prediction of call types (‘sonotypes’), and ii) the extent to which data augmentation and transfer learning can overcome the issue of small and imbalanced training data sets. We found that even relatively high sample sizes (>80 per sonotype) lead to mediocre accuracy, which however improved significantly with data augmentation and transfer learning, including at extremely small sample sizes (3 per sonotype), regardless of taxonomic group or call characteristics. Neither transfer learning nor data augmentation alone achieved high accuracy. Our results suggest that transfer learning and data augmentation could make the use of CNNs to classify species’ vocalizations feasible even for small soundscape-based projects with many rare species. Retraining our open-source model requires only basic programming skills which makes it possible for individual conservation initiatives to match their local context, in order to enable more evidence-informed management of biodiversity.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Small Animal IMRT Using 3D-Printed Compensators

Preclinical radiation replicating clinical intensity modulated radiation therapy (IMRT) techniques can provide data translatable to clinical practice. For this work, treatment plans were created for oxygen-guided dose-painting in small animals using inverse-planned IMRT. Spatially varying beam intensities were achieved using 3-dimensional (3D)-printed compensators.

3D PRINTING↗

DOE OSTI2023

Glycosyltransferase family 47 (GT47) proteins in plants and animals

Glycosyltransferases (GTs) are carbohydrate-active enzymes that are encoded by the genomes of organisms spanning all domains of life. GTs catalyze glycosidic bond formation, transferring a sugar monomer from an activated donor to an acceptor substrate, often another saccharide. GTs from family 47 (GT47, PF03016) are involved in the synthesis of complex glycoproteins in mammals and insects and play a major role in the synthesis of almost every class of polysaccharide in plants, with the exception of cellulose, callose, and mixed linkage β-1,3/1,4-glucan. GT47 enzymes adopt a GT-B fold and catalyze the formation of glycosidic bonds through an inverting mechanism. Unlike animal genomes, which encode few GT47 enzymes, plant genomes contain 30 or more diverse GT47 coding sequences. With our current knowledge of the GT47 family across plant species brings us an interesting view, showcasing how members exhibit a great diversity in both donor and acceptor substrate specificity, even for members that are classified in the same phylogenetic clade. Thus, we discuss how plant GT47 family members represent a great case to study the relationship between substrate specificity, protein structure, and protein evolution. Most of the plant GT47 enzymes that are identified to date are involved in biosynthesis of plant cell wall polysaccharides, including xyloglucan, xylan, mannan, and pectins. This indicates unique and crucial roles of plant GT47 enzymes in cell wall formation. The aim of this review is to summarize findings about GT47 enzymes and highlight new challenges and approaches on the horizon to study this family.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Structure-based discovery of potent WD repeat domain 5 inhibitors that demonstrate efficacy and safety in preclinical animal models

WD repeat domain 5 (WDR5) is a core scaffolding component of many multiprotein complexes that perform a variety of critical chromatin-centric processes in the nucleus. WDR5 is a component of the mixed lineage leukemia MLL/SET complex and localizes MYC to chromatin at tumor-critical target genes. As a part of these complexes, WDR5 plays a role in sustaining oncogenesis in a variety of human cancers that are often associated with poor prognoses. Thus, WDR5 has been recognized as an attractive therapeutic target for treating both solid and hematological tumors. Previously, small-molecule inhibitors of the WDR5-interaction (WIN) site and WDR5 degraders have demonstrated robust in vitro cellular efficacy in cancer cell lines and established the therapeutic potential of WDR5. However, these agents have not demonstrated significant in vivo efficacy at pharmacologically relevant doses by oral administration in animal disease models. We have discovered WDR5 WIN-site inhibitors that feature bicyclic heteroaryl P 7 units through structure-based design and address the limitations of our previous series of small-molecule inhibitors. Importantly, our lead compounds exhibit enhanced on-target potency, excellent oral pharmacokinetic (PK) profiles, and potent dose-dependent in vivo efficacy in a mouse MV4:11 subcutaneous xenograft model by oral dosing. Furthermore, these in vivo probes show excellent tolerability under a repeated high-dose regimen in rodents to demonstrate the safety of the WDR5 WIN-site inhibition mechanism. Collectively, our results provide strong support for WDR5 WIN-site inhibitors to be utilized as potential anticancer therapeutics.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

A Predictive Model for Survival of Escherichia coli O157:H7 and Generic E. coli in Soil Amended with Untreated Animal Manure

Abstract This study aimed at developing a predictive model that captures the influences of a variety of agricultural and environmental variables and is able to predict the concentrations of enteric bacteria in soil amended with untreated Biological Soil Amendments of Animal Origin (BSAAO) under dynamic conditions. We developed and validated a Random Forest model using data from a longitudinal field study conducted in mid‐Atlantic United States investigating the survival of Escherichia coli O157:H7 and generic E. coli in soils amended with untreated dairy manure, horse manure, or poultry litter. Amendment type, days of rain since the previous sampling day, and soil moisture content were identified as the most influential agricultural and environmental variables impacting concentrations of viable E. coli O157:H7 and generic E. coli recovered from amended soils. Our model results also indicated that E. coli O157:H7 and generic E. coli declined at similar rates in amended soils under dynamic field conditions.The Random Forest model accurately predicted changes in viable E. coli concentrations over time under different agricultural and environmental conditions. Our model also accurately characterized the variability of E. coli concentration in amended soil over time by providing upper and lower prediction bound estimates. Cross‐validation results indicated that our model can be potentially generalized to other geographic regions and incorporated into a risk assessment for evaluating the risks associated with application of untreated BSAAO. Our model can be validated for other regions and predictive performance also can be enhanced when data sets from additional geographic regions become available.

Pang, Hao↗

DOE OSTI2021

Bio-inspired Bistable Piezoelectric Energy Harvester for Powering Animal Telemetry Tags: Concept Design and Preliminary Experimental Validation

This paper presents the concept design, preliminary experimental validation, and performance evaluation of a novel bio-inspired bi-stable piezoelectric energy harvester for self-powered animal telemetry tags. The overall concept design, which includes a bio-inspired attachment and a bi-stable piezoelectric energy harvester, is introduced firstly with a specific application example of marine fish tracking. The self-powered telemetry tag can be externally deployed on fish (dorsal fin) to monitor fish habitats, population, and underwater environment. Inspired by the Venus flytrap’s rapid shape transition, a bistable piezoelectric energy harvester is developed to scavenge energy from fish maneuvering and the surrounding fluid flow for a sustainable power supply. The bistability of the harvester is characterized by the measured force-displacement curve and double potential wells. A bluff body is integrated to the free end of the bistable piezoelectric energy harvester to enhance the structure-fluid interaction for the large-amplitude snap-through vibrations and higher voltage output. Controlled laboratory experiments are conducted in a water tank on the bio-inspired bi-stable piezoelectric energy harvester using a servo motor system to simulate fish swing motion at various conditions to evaluate the power generation performance. The preliminary underwater experimental results demonstrated that the proposed bio-inspired bi-stable piezoelectric could effectively converter fish swing motions into electricity. 17.25 mJ energy was obtained within 130 s under the peak-to-peak swing angle of 30o at 1.5 Hz in the capacitor charging experiments.

Qian, Feng↗

DOE OSTI2020

Preserving Contextual Awareness during Selection of Moving Targets in Animated Stream Visualizations

In many types of dynamic interactive visualizations, it is often desired to interact with moving objects. Stopping moving objects can make selection easier, but pausing animated content can disrupt perception and understanding of the visualization. To address such problems, we explore selection techniques that only pause a subset of all moving targets in the visualization. We present various designs for controlling pause regions based on cursor trajectory or cursor position. We then report a dual-task experiment that evaluates how different techniques affect both target selection performance and contextual awareness of the visualization. Our findings indicate that all pause techniques significantly improved selection performance as compared to the baseline method without pause, but the results also show that pausing the entire visualization can interfere with contextual awareness. However, the problem with reduced contextual awareness was not observed with our new techniques that only pause a limited region of the visualization. Thus, our research provides evidence that region-limited pause techniques can retain the advantages of selection in dynamic visualizations without imposing a negative effect on contextual awareness.

Ragan, Eric↗

DOE OSTI2020

2020 State of the Science Report, Chapter 3: Collision Risk for Animals around Turbines

The potential for marine animals to encounter and collide with turbines, especially tidal and river turbines, along with the biological, ecological, and regulatory consequences of any such interactions, remain active areas of research and topics of global interest. Uncertainty and knowledge gaps associated with collision risk continue to present challenges within consenting/permitting (hereafter consenting) processes for turbine developments. Consequently, collision risk continues to be the focus of significant research effort, which in recent years has included environmental monitoring of operational devices and arrays. This chapter addresses the overall progress and growth in knowledge across this topic area, and specific progress related to marine mammals, fish, and seabirds. https://tethys.pnnl.gov/publications/state-of-the-science-2020-chapter-3-collision

13 HYDRO ENERGY↗