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At least 955 records · Page 53

Comparison of point cloud and image-based models for calorimeter fast simulation

Score based generative models are a new class of generative models that have been shown to accurately generate high dimensional calorimeter datasets. Recent advances in generative models have used images with 3D voxels to represent and model complex calorimeter showers. Point clouds, however, are likely a more natural representation of calorimeter showers, particularly in calorimeters with high granularity. Furthermore, point clouds preserve all of the information of the original simulation, more naturally deal with sparse datasets, and can be implemented with more compact models and data files. In this work, two state-of-the-art score based models are trained on the same set of calorimeter simulation and directly compared.

47 OTHER INSTRUMENTATION↗

Climate change impacts on the energy system: a model comparison

Increasing renewable energy use is an essential strategy for mitigating climate change. Nevertheless, the sensitivity of renewable energy to climatic conditions means that the energy system’s vulnerability to climate change can also become larger. In this research, we used two integrated assessment models and data from four climate models to analyse climate change impacts on primary energy use at a global and regional scale under a low-level (RCP2.6) and a medium-level (RCP6.0) climate change scenario. The impacts are analysed on the energy system focusing on four renewable sources (wind, solar, hydropower, and biomass). Globally, small climate impacts on renewable primary energy use are found in both models (5% for RCP2.6 and 6% for RCP6.0). These impacts lead to a decrease in the use of fossil sources for most regions, especially for North America and Europe under the RCP60 scenario. Overall, IMAGE and GCAM provide a similar signal impact response for most regions. E.g. in Asia (excluding China and India), climate change induces an increase in wind and hydropower use under the RCP6.0 scenarios; however, for India, a decrease in solar energy use can be expected under both scenarios and models.

54 ENVIRONMENTAL SCIENCES↗

Available land for cellulosic biofuel production: a supply chain centered comparison

The land that is potentially available to produce dedicated cellulosic bioenergy crops, often referred to as 'marginal' land, depends heavily on the underlying assumptions used to classify and identify it. In this study we compare three definitions and types of marginal land to identify the interactions between the bioenergy landscape and the logistics networks needed for the biofuel supply chain. Typical studies of the scale, cost, and greenhouse gas (GHG) mitigation potential of cellulosic biofuel take a land-centered approach which may neglect to account for the trade-offs between establishing bioenergy crops and the supply chain design decisions needed to allow those crops to be converted to liquid fuel. A mathematical programming approach is used to minimize the total annualized cost of a large-scale field-to-product system producing bioethanol in the USA midwest. Results show that a high concentration of marginal land leads to efficient systems and that the bioenergy landscape design becomes increasingly important with a higher emphasis on GHG mitigation. Additionally, targeted landscape design (including fertilization) with a focus on fields with high soil carbon sequestration potential can greatly reduce the system-wide GHG emissions for only a small increase in the unit cost of biofuel.

09 BIOMASS FUELS↗

Lack of clear standards and usable comparisons of downscaled climate projections pose a roadblock for US climate discovery and adaptation

Abstract The release of global climate projections coupled with the demand for local-resolution climate-forced meteorology has prompted many research groups to downscale these projections using various statistical, dynamical, and current machine learning techniques. Such downscaled datasets are being used to plan infrastructure and other community needs over the coming decades. Faced with roughly a dozen available US downscaled datasets, many practitioners ask, ‘What are the relevant differences between datasets?’ This work highlights the difficulty of comparing downscaled datasets and illustrates ways in which datasets differ even when using identical climate model input data. We show that substantial variability in precipitation projections arises from downscaling alone and that the downscaled dataset agreement varies depending on global climate projection. This analysis emphasizes the need for greater coordination and movement toward rigorous benchmarking of downscaling strategies within the downscaling research community, à la the land-modeling community, to better quantify downscaling dataset differences, strengths, and weaknesses for practitioners.

Hartke, Samantha H. (ORCID:0000000202394723)↗

Variability in modelled reservoir greenhouse gas emissions: comparison of select US hydropower reservoirs against global estimates

Abstract Greenhouse gas (GHG) emissions from reservoirs have most often been evaluated on a global extent through areal scaling or linear-regression models. These models typically rely on a limited number of characteristics such as age, size, and average temperature to estimate per reservoir or areal flux. Such approaches may not be sufficient for describing conditions at all types of reservoirs. Emissions from hydropower reservoirs have received increasing attention as industry and policy makers seek to better understand the role of hydropower in sustainable energy solutions. In the United States (US), hydropower reservoirs span a wide range of climate regions and have diverse design and operational characteristics compared to those most heavily represented in model literature (i.e., large, tropical reservoirs). It is not clear whether estimates based on measurements and modeling of other subsets of reservoirs describe the diverse types of hydropower reservoirs in the US. We applied the Greenhouse Gas from Reservoirs (G‐res) emissions model to 28 hydropower reservoirs located in a variety of ecological, hydrological, and climate settings that represent the range of sizes and types of facilities within the US hydropower fleet. The dominant pathways for resulting GHG emissions estimates in the case-study reservoirs were diffusion of carbon dioxide, followed by methane ebullition. Among these case-study reservoirs, total post-impoundment areal flux of carbon ranges from 84 to 767 mgCm −2 d −1 , which is less variable than what has been reported through measurements at other US and global reservoirs. The net GHG reservoir footprint was less variable and towards the lower end of the range observed from modeling larger global reservoirs, with a range of 138 to 1,052 g CO 2 eq m −2 y −1 , while the global study reported a range of 115 to 145,472 g CO 2 eq m −2 y −1 . High variation in emissions normalized with respect to area and generation highlights the need to be cautious when using area or generation in predicting or communicating emissions footprints for reservoirs relative to those of other energy sources, especially given that many of the hydropower reservoirs in the US serve multiple purposes beyond power generation.

54 ENVIRONMENTAL SCIENCES↗

Torrefaction of almond shell as a renewable reinforcing agent for plastics: techno-economic analyses and comparison to bioethanol process

Abstract In 2016, the US state of California alone produced nearly 3.5 billion kilograms of almonds, accounting for approximately 84% of the world’s almond production. This generated about 2.58 million metric tons (MTs) of almond residues. Almond shells are currently either burned to generate power or disposed of in landfill. Valorizing almond shells and hulls provides an opportunity to replace petroleum-derived products and divert organic material from landfill. Here we demonstrate a detailed techno-economic analysis (TEA) of an almond shell torrefaction process capable of utilizing the 520 000 MTs of almond shells produced annually in California. Our process also includes preprocessing the torrefied biomass to exploit it as a reinforcing agent for plastics. We further compared the revenue generated from the torrefied biomass and bioethanol derived from the same quantity of almond shells. We considered three different torrefaction facility scales to evaluate trade-offs between economies of scale at the facility and trucking costs to deliver almond shells. A facility that takes in 200 000 MT yr –1 of almond shells results in lower per-unit-output basis capital and operating cost relative to other smaller-scale torrefaction facilities, including 10 000 MT yr –1 and 50 000 MT yr –1 , considered for analysis in this study. The large-sale facility results in a minimum selling price (MSP) of the torrefied biomass of $311.4 MT –1 . An analogous TEA on converting almond residues into bioethanol is also investigated. The MSP of almond shell derived ethanol ($1.71 kg −1 ) is higher than that of corn ($0.48 kg −1 ) or cellulosic biomass ($0.88 kg −1 ) derived ethanol. Compared with the bioethanol route, the torrefied almond shells result in three times more revenue if utilized as a reinforcing agent for plastics.

Liu, Dupeng (ORCID:0000000269514064)↗

Evaluation of present-day extreme precipitation over the United States: an inter-comparison of convection and dynamic permitting configurations of E3SMv1

Abstract Accurate simulation of the present-day characteristics of mean and extreme precipitation at regional scales remains a challenge for Earth system models, which is due in part to deficiencies in model physics such as convective parameterization (CP), and coarse resolution. High horizontal resolution (HR, ∼25 km) and multiscale modeling framework (MMF, i.e. replacing conventional CP with embedded km-scale cloud-resolving models) are two promising directions that could help improve the interaction between subgrid-scale physical processes and large-scale climate. Here, we evaluate simulated extreme precipitation over the United States (US) across three configurations (i.e. low-resolution [LR], HR, and MMF) of the Energy Exascale Earth System Model (E3SMv1) and intercompare them against two gridded observation datasets (climate prediction center daily US precipitation and integrated multi-satellite retrievals for global precipitation measurement). We assess the model’s ability to simulate very heavy seasonal precipitation (illustrated by the difference between the 99th and 90th percentile values) as well as the spatial distributions of several extreme precipitation indices defined by the expert team on climate change detection and indices. Our results show that both the dry (i.e. consecutive dry days (CDD)) and wet (i.e. consecutive wet days, maximum 5 day precipitation, and very wet days) extremes evaluated herein show some improvement as well as degradation with MMF and HR relative to LR. These results vary across seasons and US subregions. For instance, only the very heavy precipitation of winter is improved with MMF and HR. Both configurations alleviate the well-known drizzling bias evident in LR across both winter and summer in many parts of the US, largely due to the overall improvement in intensity and frequency of precipitation. Additionally, our results suggest that while E3SMv1-MMF has higher intensity rates when it does rain, it has too many CDD during the summer, contributing to a low mean precipitation bias.

54 ENVIRONMENTAL SCIENCES↗

Comparison of the Antiviral Activity of Remdesivir, Chloroquine, and Interferon-β as Single or Dual Agents Against the Human Beta-Coronavirus OC43

The human beta-coronavirus strain, OC43, provides a useful model for testing the antiviral activity of various agents. We compared the activity of several antiviral drugs against OC43, including remdesivir, chloroquine, interferon (IFN)-β, IFN-λ1, and IFN-λ4, in two distinct cell types: human colorectal carcinoma cell line (HCT-8 cells) and normal human bronchial epithelial (NHBE) cells. We also tested whether these agents mediate additive, synergistic, or antagonistic activity against OC43 infection when used in combination. When used as single agents, remdesivir exhibited stronger antiviral activity than chloroquine, and IFN-β exhibited stronger activity than IFN-λ1 or IFN-λ4 against OC43 in both HCT-8 and NHBE cells. Anakinra (IL-1 inhibitor) and tocilizumab (IL-6 inhibitor) did not mediate any antiviral activity. The combination of IFN-β plus chloroquine or remdesivir resulted in higher synergy scores and higher expression of IFN-stimulated genes than did IFN-β alone. In contrast, the combination of remdesivir plus chloroquine resulted in an antagonistic interaction in NHBE cells. Our findings indicate that the combined use of IFN-β plus remdesivir or chloroquine induces maximal antiviral activity against human coronavirus strain OC43 in primary human respiratory epithelial cells. Furthermore, our experimental OC43 virus infection model provides an excellent method for evaluating the biological activity of antiviral drugs.

60 APPLIED LIFE SCIENCES↗

Genome features of a novel hydrocarbonoclastic Chryseobacterium oranimense strain and its comparison to bacterial oil-degraders and to other C. oranimense strains

For the first time, we report the whole genome sequence of a hydrocarbonoclastic Chryseobacterium oranimense strain isolated from Trinidad and Tobago (COTT) and its genes involved in the biotransformation of hydrocarbons and xenobiotics through functional annotation. The assembly consisted of 11 contigs with 2,794 predicted protein-coding genes which included a diverse group of gene families involved in aliphatic and polycyclic hydrocarbon degradation. Comparative genomic analyses with 18 crude-oil degrading bacteria in addition to two C. oranimense strains not associated with oil were carried out. The data revealed important differences in terms of annotated genes involved in the hydrocarbon degradation process that may explain the molecular mechanisms of hydrocarbon and xenobiotic biotransformation. Notably, many gene families were expanded to explain COTT’s competitive ability to manage habitat-specific stressors. Gene-based evidence of the metabolic potential of COTT supports the application of indigenous microbes for the remediation of polluted terrestrial environments and provides a genomic resource for improving our understanding of how to optimize these characteristics for more effective bioremediation.

59 BASIC BIOLOGICAL SCIENCES↗

A comparison of free-living and sponge-associated bacterial communities from a remote oceanic island with a focus on calcareous sponges

Abstract Calcareous sponges are an often overlooked element of sponge communities. In contrast to most other sponges, calcareous sponges produce calcium carbonate spicules, as opposed to the siliceous spicules of most sponges. Here, we investigated the bacterial communities of 17 sponge species, including type and paratype specimens of recently described calcareous species, sampled off the remote island of Rodrigues, in the Indian Ocean. The main axis of variation in a PCO analysis of all samples separated noncalcareous sponge species, including Axinyssa aplysinoides, Cinachyrella aff. australiensis, Petrosia seychellensis, Ircinia aff. variabilis, Spongia ceylonensis, Plakinastrella aff. clipptertonensis, Agelas aff. ceylonica, Agelas aff. mauritiana, and Hyrtios erectus from calcareous sponges, the noncalcareous Biemna tubulata, sediment, and seawater. Overall, the bacterial communities of calcareous sponges revealed unique prokaryotic profiles with low abundances of several bacterial phyla, and relatively high abundances of other taxa, for example, the phyla Fibrobacterota, Proteobacteria, and the SAR324 clade, the class Alphaproteobacteria, and orders Cytophagales and Cyanobacteriales, although there was considerable variation among species. Calcareous sponges also had a high dominance of unknown bacterial operational taxonomic units (OTUs). Considering the unique nature of these communities, further studies are needed to better understand the environmental and ecological drivers of calcareous sponge-associated bacterial communities and their relevance as potential sources of novel microbes of biotechnological interest.

Cleary, D. F. R. (ORCID:0000000261433390)↗

Taxonomic and functional restoration of tallgrass prairie soil microbial communities in comparison to remnant and agricultural soils

Abstract Restoring ecosystems requires the re-establishment of diverse soil microbial communities that drive critical ecosystem functions. In grasslands, restoration and management require the application of disturbances like fire and grazing. Disturbances can shape microbial taxonomic composition and potentially functional composition as well. We characterized taxonomic and functional gene composition of soil communities using whole genome shotgun metagenomic sequencing to determine how restored soil communities differed from pre-restoration agricultural soils and original remnant soils, how management affects soil microbes, and whether restoration and management affect the number of microbial genes associated with carbohydrate degradation. We found distinct differences in both taxonomic and functional diversity and composition among restored, remnant, and agricultural soils. Remnant soils had low taxonomic and functional richness and diversity, as well as distinct composition, indicating that restoration of agricultural soils does not re-create soil microbial communities that match remnants. Prescribed fire management increased functional diversity, which also was higher in more recently planted restorations. Finally, restored and post-fire soils included high abundances of genes encoding cellulose-degrading enzymes, so restorations and their ongoing management can potentially support functions important in carbon cycling.

Mason, Cayla N. (ORCID:0000000345983824)↗

Comparison of stress tolerance mechanisms between Saccharomyces cerevisiae and the multistress-tolerant Pichia kudriavzevii

Yeasts play a vital role in both research and industrial biomanufacturing. Saccharomyces cerevisiae has been extensively utilized as a model system. However, its application is often constrained by limited tolerance to the diverse stress conditions encountered in bioprocesses. These challenges have driven increasing interest in nonconventional, multistress-tolerant yeasts as alternative biomanufacturing hosts. This review highlights Pichia kudriavzevii as a promising nonconventional yeast for industrial applications. Unlike S. cerevisiae, P. kudriavzevii exhibits exceptional tolerance to high temperatures, elevated concentrations of furanic and phenolic inhibitors, osmotic stress, salinity, and extreme pH. These traits make it an attractive candidate for industrial processes without requiring extensive genetic modifications to enhance stress resistance. As a result, P. kudriavzevii has emerged as a flagship species for advancing bioeconomy. Despite its industrial potential, the molecular mechanisms underlying P. kudriavzevii's superior stress tolerance remain poorly understood. This review compiles current knowledge on P. kudriavzevii and compares its stress tolerance mechanisms with those of S. cerevisiae, providing insights into its innate resilience. By expanding our understanding of nonconventional yeasts, this review aims to facilitate their broader adoption as robust microbial platforms for industrial biomanufacturing.

Frousnoon, Thasneem Banu↗

Comparison of linear regression, k-nearest neighbour and random forest methods in airborne laser-scanning-based prediction of growing stock

Abstract In this study, for five sites around the world, we look at the effects of different model types and variable selection approaches on forest yield modelling performances in an area-based approach (ABA). We compared ordinary least squares regression (OLS), k-nearest neighbours (kNN) and random forest (RF). Our objective was to test if there are systematic differences in accuracy between OLS, kNN and RF in ABA predictions of growing stock volume. The analyses are based on a 5-fold cross-validation at five study sites: an eucalyptus plantation, a temperate forest and three different boreal forests. Two completely independent validation datasets were also available for two of the boreal sites. For the kNN, we evaluated multiple measures of distance including Euclidean, Mahalanobis, most similar neighbour (MSN) and an RF-based distance metric. The variable selection approaches we examined included a heuristic approach (for OLS, kNN and RF), exhaustive search among all combinations (OLS only) and all variables together (RF only). Performances varied by model type and variable selection approaches among sites. OLS and RF had similar accuracies and were more efficient than any of the kNN variants. Variable selection did not affect RF performance. Heuristic and exhaustive variable selection performed similarly for OLS. kNN fared the poorest amongst model types, and kNN with RF distance was prone to overfitting when compared with a validation dataset. Additional caution is therefore required when building kNN models for volume prediction though ABA, being preferable instead to opt for models based on OLS with some variable selection, or RF with all variables together.

Cosenza, Diogo N.↗

MultiPhATE2: code for functional annotation and comparison of phage genomes

To address a need for improved tools for annotation and comparative genomics of bacteriophage genomes, we developed multiPhATE2. As an extension of multiPhATE, a functional annotation code released previously, multiPhATE2 performs gene finding using multiple algorithms, compares the results of the algorithms, performs functional annotation of coding sequences, and incorporates additional search algorithms and databases to extend the search space of the original code. MultiPhATE2 performs gene matching among sets of closely related bacteriophage genomes, and uses multiprocessing to speed computations. MultiPhATE2 can be re-started at multiple points within the workflow to allow the user to examine intermediate results and adjust the subsequent computations accordingly. In addition, multiPhATE2 accommodates custom gene calls and sequence databases, again adding flexibility. MultiPhATE2 was implemented in Python 3.7 and runs as a command-line code under Linux or MAC operating systems. Full documentation is provided as a README file and a Wiki website.

59 BASIC BIOLOGICAL SCIENCES↗

Source scaling comparison and validation in Central Italy: data intensive direct S waves versus the sparse data coda envelope methodology

SUMMARY Robustness of source parameter estimates is a fundamental issue in understanding the relationships between small and large events; however, it is difficult to assess how much of the variability of the source parameters can be attributed to the physical source characteristics or to the uncertainties of the methods and data used to estimate the values. In this study, we apply the coda method by Mayeda et al. using the coda calibration tool (CCT), a freely available Java-based code (https://github.com/LLNL/coda-calibration-tool) to obtain a regional calibration for Central Italy for estimating stable source parameters. We demonstrate the power of the coda technique in this region and show that it provides the same robustness in source parameter estimation as a data-driven methodology [generalized inversion technique (GIT)], but with much fewer calibration events and stations. The Central Italy region is ideal for both GIT and coda approaches as it is characterized by high-quality data, including recent well-recorded seismic sequences such as L'Aquila (2009) and Amatrice–Norcia–Visso (2016–2017). This allows us to apply data-driven methods such as GIT and coda-based methods that require few, but high-quality data. The data set for GIT analysis includes ∼5000 earthquakes and more than 600 stations, while for coda analysis we used a small subset of 39 events spanning 3.5 < Mw < 6.33 and 14 well-distributed broad-band stations. For the common calibration events, as well as an additional 247 events (∼1.7 < Mw < ∼5.0) not used in either calibration, we find excellent agreement between GIT-derived and CCT-derived source spectra. This confirms the ability of the coda approach to obtain stable source parameters even with few calibration events and stations. Even reducing the coda calibration data set by 75 per cent, we found no appreciable degradation in performance. This validation of the coda calibration approach over a broad range of event size demonstrates that this procedure, once extended to other regions, represents a powerful tool for future routine applications to homogeneously evaluate robust source parameters on a national scale. Furthermore, the coda calibration procedure can homogenize the Mw estimates for small and large events without the necessity of introducing any conversion scale between narrow-band measures such as local magnitude (ML) and Mw, which has been shown to introduce significant bias.

Morasca, Paola (ORCID:0000000265254867)↗

Microbiome Comparison and Pathogen Identification for Three Migrating Passerines Captured During Spring Season in Jordan Using 16S rRNA Sequencing

Jordan is located on an important spot along the Mediterranean and Black Sea Flyway. Hundreds of migratory bird species have been identified stopping over in Jordan during spring and autumn migratory seasons. Compared to mammals and economically important birds, the microbiomes of wild bird species are severely understudied. Gut microbial composition is a valuable source of information that reflects food preferences, foraging behavior, and the risk of pathogen transmission to humans and other animals. In this study, we assessed the microbiome composition of three species of migrating passerines (willow warblers, lesser whitethroats, and common reed warblers) captured during the spring migration stopover in Jordan in 2023. A total of 59 fecal samples were selected evenly from the three species and subjected to 16S sequencing and microbiome analysis. Our objectives were to determine the diversity of bacteria in these three species, assess the amount of intra- and inter-specific variation, and detect pathogenic genera and species that could pose health risks to humans, domestic animals, and wildlife. Bacteria mainly belonged to the phyla Proteobacteria (62%), Actinobacteriota (18%), Firmicutes (13%), Cyanobacteria (5%), and Bacteroidota (1%). The results reveal that lesser whitethroats had the greatest variation in bacterial genus richness, Shannon diversity, and microbial composition compared to willow warblers and common reed warblers. The three bird species harbored several pathogenic genera and species, including Campylobacter, Enterococcus, Escherichia-Shigella, Mycoplasma, Rickettsia, Clostridium perfringens, and Vibrio cholerae. We suggest further investigation to understand the relationship between migratory behavior and their gut microbiome. We advocate for the use of advanced molecular techniques to characterize the pathogens found in migratory birds that might have public and environmental health impacts in addition to economic loss.

59 BASIC BIOLOGICAL SCIENCES↗

A Comparison of Solidification Structures and Submicroscale Cellular Segregation in Rapidly Solidified Stainless Steels Produced via Two-Piston Splat Quenching and Laser Powder Bed Fusion

Fusion-based additive manufacturing techniques leverage rapid solidification (RS) conditions to create parts with complex geometries, unique microscale/nanoscale morphological features, and elemental segregation. Three custom composition stainless steel alloys with varying chromium equivalence to nickel equivalence ratio (Cr eq /Ni eq ) between 1.53 and 1.95 were processed using laser powder bed fusion (LPBF) and/or two-piston splat quenching (SQ) to produce solidification rates estimated between 0.4 and 0.8 m/s. Both scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were utilized to collect high-resolution images, electron backscatter diffraction (EBSD) phase identification, and measure cellular segregation. Similar features were observed in both LPBF and SQ samples including phase and microstructure, nanoscale oxide particles, cell size, and segregation behavior. However, dislocation pileup was observed along the cell boundaries only in the LPBF austenite solidified microstructure. Targeted adjustment of the SQ feedstock Cr and Ni concentrations, within the ASTM A240 specification for 316L resulted in no observable impact on the cell size, oxide particle size, or magnitude of segregation. Also, the amount of Ni segregation in the ferrite solidified microstructures did not significantly differ, regardless of Cr/Ni eq or processing technique. Here, SQ is demonstrated as capable of simulating RS rates and microstructures similar to LPBF for use as an alternative screening tool for new RS alloy compositions.

42 ENGINEERING↗