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At least 289 records · Page 16

Imperfect slope measurements drive overestimation in a geometric cone model of lake and reservoir depth

Lake and reservoir (waterbody) depth is a critical characteristic that influences many important ecological processes. Unfortunately, depth measurements are labor-intensive to gather and are only available for a small fraction of waterbodies globally. Therefore, scientists have tried to predict depth from characteristics easily obtained for all waterbodies, such as surface area or the slope of the surrounding land. One approach for predicting waterbody depth simulates basins using a geometric cone model where the nearshore land slope and distance to the center of the waterbody are assumed to be representative proxies for in-lake slope and distance to the deepest point respectively. We tested these assumptions using bathymetry data from ~5000 lakes and reservoirs to examine whether differences in waterbody type or shape influenced depth prediction error. Here, we found that nearshore land slope was not representative of in-lake slope, and using it for prediction increases error substantially relative to models using true in-lake slope for all waterbody types and shapes. Predictions were biased toward overprediction in concave waterbodies (i.e., bowl-shaped; up to 18% of the study population) and reservoir waterbodies (up to 30% of the study population). Despite this systematic overprediction, model errors were fewer (in absolute and relative terms, irrespective of any specific slope covariate) for concave than convex waterbodies, suggesting the geometric cone model is an adequate representation of depth for these waterbodies. But because convex waterbodies are far more common (>72% of our study population), minimizing overall depth prediction error remains a challenge.

54 ENVIRONMENTAL SCIENCES↗

Individualized empirical baselines for evaluating the energy performance of existing buildings

The evaluation of building energy performance requires a baseline for comparison. Common empirical baselines are usually used for existing buildings since they are fast and convenient. However, the same type of building at the same location will receive the same baseline despite their difference in usage. Individualized baselines by creating building energy models are possible solutions, but it is labor intensive and time-consuming. To fill the gap, this study is to develop individualized empirical baselines for existing buildings in a fast way. First, common empirical baselines are created based on survey data. Then, to get training samples, building energy models for large-scale existing buildings are created and simulated. So finally, based on simulation results, mathematical models to get individualized empirical baselines in a fast way are created. U.S. medium office buildings were used as an example to demonstrate the method. We developed 30 mathematical models for medium office buildings in two vintages (constructed before 1980 and after 1980) and 15 climate zones. The mean absolute percentage errors (MAPE) between the individualized empirical baselines and the modeled baselines for those 30 mathematical models are all lower than 5.5%. An engineer can obtain the individualized empirical baseline for an existing building in a few seconds by using the open-source tool we developed.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Roadmap on emerging concepts in the physical biology of bacterial biofilms: from surface sensing to community formation

Abstract Bacterial biofilms are communities of bacteria that exist as aggregates that can adhere to surfaces or be free-standing. This complex, social mode of cellular organization is fundamental to the physiology of microbes and often exhibits surprising behavior. Bacterial biofilms are more than the sum of their parts: single-cell behavior has a complex relation to collective community behavior, in a manner perhaps cognate to the complex relation between atomic physics and condensed matter physics. Biofilm microbiology is a relatively young field by biology standards, but it has already attracted intense attention from physicists. Sometimes, this attention takes the form of seeing biofilms as inspiration for new physics. In this roadmap, we highlight the work of those who have taken the opposite strategy: we highlight the work of physicists and physical scientists who use physics to engage fundamental concepts in bacterial biofilm microbiology, including adhesion, sensing, motility, signaling, memory, energy flow, community formation and cooperativity. These contributions are juxtaposed with microbiologists who have made recent important discoveries on bacterial biofilms using state-of-the-art physical methods. The contributions to this roadmap exemplify how well physics and biology can be combined to achieve a new synthesis, rather than just a division of labor.

Wong, Gerard C. L. (ORCID:0000000308936383)↗

Estimated impacts of forest restoration scenarios on smoke exposures among outdoor agricultural workers in California

Abstract As wildfires continue to worsen across western United States, forest managers are increasingly employing prescribed burns as a way to reduce excess fuels and future wildfire risk. While the ecological benefits of these fuel treatments are clear, little is known about the smoke exposure tradeoffs of using prescribed burns to mitigate wildfires, particularly among at-risk populations. Outdoor agricultural workers are a population at increased risk of smoke exposure because of their time spent outside and the physical demands of their work. Here, we assess the smoke exposure impacts among outdoor agricultural workers resulting from the implementation of six forest management scenarios proposed for a landscape in the Central Sierra, California. We leverage emissions estimates from LANDIS-II to model daily PM 2.5 concentrations with the Hybrid Single Particle Lagrangian Integrated Trajectory Model (HYSPLIT) and link those to agricultural employment data from the Bureau of Labor Statistics. We find a u-shaped result, in that moderate amounts of prescribed burning result in the greatest reduction in total smoke exposure among outdoor agricultural workers, particularly during months of peak agricultural activity due to wildfire-specific smoke reductions. The reduction in total smoke exposure, relative to scenarios with the least amount of management, decreases as more prescribed burning is applied to the landscape due to the contributions of the fuel treatments themselves to overall smoke burden. The results of this analysis may contribute to preparedness efforts aimed at reducing smoke exposures among outdoor agricultural workers, while also informing forest management planning for this specific landscape.

Environmental Sciences & Ecology↗

Further adoption of conservation tillage can increase maize yields in the western US Corn Belt

Conservation tillage can reduce soil erosion, increase soil health, and decrease labor and fuel input costs. Despite these benefits, potential yield impacts remain an important concern for farmers considering adoption. Previous research suggests that conservation tillage is likely to have the largest yield benefits in more arid conditions, but a lack of field-level analyses across climatic, management and soil conditions limits confidence in such predictions. Satellite imagery provides the opportunity to monitor agricultural lands at sub-field resolution across large spatial scales and wide environmental gradients. Here we investigate the maize yield impacts of conservation tillage in the semi-arid western US Corn Belt, using sub-field resolution datasets on tillage practices and crop yields derived from satellite data spanning four states (Nebraska, Kansas, South Dakota, and North Dakota) between 2008 and 2020. On these datasets, we estimate heterogenous yield outcomes for several thousand maize fields across gradients in climate, soil quality and irrigation status by using a causal forests analysis, an adaptation of the random forests machine-learning algorithm for causal inference on observational data. We find that long-term adoption of conservation tillage increased rainfed maize yields by an average of 9.9% in the region. Impacts on irrigated yields were small and not statistically significant. These results, along with an analysis of variables related to greater than average yield benefits, indicate that improved water infiltration and retention are the primary reasons for conservation tillage benefits. Despite yield benefits, many fields estimated to see increased yields under long term low till have not adopted the practice. Therefore, we identify specific counties likely to benefit most from increased levels of adoption. Our results strengthen the understanding of the impacts of conservation agriculture on crop yields and help define environments and counties most likely to benefit from conservation tillage.

54 ENVIRONMENTAL SCIENCES↗

Implications of climate change impacts for emission and land use scenario development

Scenarios of future emissions and land use produced by integrated assessment models have traditionally been developed without accounting for how climate change impacts could affect the emissions and land use trajectories themselves. This omission risks skewing our assessments of the plausible range of future emission pathways and associated Earth system changes. Beyond the salience for emission scenario development, a better integrated representation of human and Earth system changes and feedbacks would enable better anticipation of the implications of alternative socio-economic development pathways. We use the Global Change Analysis Model to investigate whether endogenizing several impacts when generating its baseline emission scenario is warranted. We do so by comparing the emissions and land use change that result from the baseline scenario with and without impacts, where impacts are implemented as exogenous changes to water availability, crop and labor productivity, and energy demand and supply. Our results indicate that the effect on global emissions leads to less than 0.1 °C increase in warming by 2100 and therefore do not support endogenizing impacts. This conclusion is conditional on our modeling framework and the specific impact channels represented but is consistent with other studies that have addressed the magnitude of feedbacks by implementing a two-way coupling. However, we do find regional impacts indicating that local economies and well-being measures may be affected significantly.

climate impacts↗

Development of wind turbine blade recycling baselines in the United States

Over the past several years, the wind energy industry has received scrutiny regarding wind turbine blade (WTB) recycling due to the landfilling of WTBs caused by a lack of industrially viable recycling solutions. The amount of WTBs that will need to be recycled is set to increase in the United States as the deployment of wind energy is expected to rapidly grow to meet the nation's energy goals by 2035. While significant progress has been made worldwide, it is still unclear which WTB recycling solutions would be the most cost and energy effective within the United States for the existing fleet of wind turbines. To guide researchers and industry with a clear path forward, a range of options for WTB recycling in the United States are modeled through development of baseline scenarios and the use of formal life cycle assessment (LCA). Model data have been collected through literature review, industry engagement, and expert opinion regarding current end of life practices and considerations surrounding equipment, labor, and logistics. A detailed baseline for WTB decommissioning processes has been developed and used to assess alternative approaches, such as on-site shredding to compare the impacts on greenhouse gas (GHG) emissions. The developed LCA model and baseline scenarios for WTB recycling is used to assess the current WTB decommissioning practices in the United States along with emerging recycling pathways, including cement kiln co-processing and pyrolysis. Initial findings indicate that there are different approaches to decommissioning WTBs in the United States, each of which has unique implications for recycling. In light of this finding, additional results from the modeling will be used to better understand decommissioning practices and assist in making educated decisions on recycling pathways for the future. Throughout the analysis, focus was given to where international efforts might differ from the United States. WTB recycling is occurring worldwide, and different countries have different drivers for creating markets for recycled WTB materials. The contrasts and similarities between the United States and other countries offer insight to areas of opportunity that the United States could investigate and areas that can be readily transferred from existing solutions. By modeling and characterizing the current decommissioning practices and potential recycling solutions for the United States, a clearer vision will be created for pathways forward as to how to handle end of life WTBs to enable more efficient and cost-effective opportunities for material recovery from end-of-life WTBs.

Korey, Matt↗

Machine learning for neutron reflectometry data analysis of two-layer thin films

Neutron reflectometry (NR) is a powerful tool for probing thin films at length scales down to nanometers. We investigated the use of a neural network to predict a two-layer thin film structure to model a given measured reflectivity curve. Application of this neural network to predict a thin film structure revealed that it was accurate and could provide an excellent starting point for traditional fitting methods. Employing prediction-guided fitting has considerable potential for more rapidly producing a result compared to the labor-intensive but commonly-used approach of trial and error searches prior to refinement. A deeper look at the stability of the predictive power of the neural network against statistical fluctuations of measured reflectivity profiles showed that the predictions are stable. We conclude that the approach presented here can provide valuable assistance to users of NR and should be further extended for use in studies of more complex n-layer thin film systems. This result also opens up the possibility of developing adaptive measurement systems in the future.

36 MATERIALS SCIENCE↗

Comparative Performance Evaluation of Large Language Models for Extracting Molecular Interactions and Pathway Knowledge

Understanding the interactions and regulatory relationships among biomolecules is essential for deciphering complex biological systems and elucidating the mechanisms behind diverse biological functions. Traditionally, the collection of such molecular interaction data has relied on expert curation, a process that is both time-consuming and labor-intensive. To address these limitations, this study explores the use of large language models (LLMs) to automate the genome-scale extraction of molecular interaction knowledge. Here, we evaluate the performance of various LLMs on key biological tasks, including the identification of protein-protein interactions, detection of genes associated with pathways influenced by low-dose radiation, and inference of gene regulatory relationships. Our findings demonstrate that larger LLMs tend to perform better, particularly in extracting intricate gene and protein interactions. Despite their strengths, these models face challenges in recognizing functionally diverse gene groups and highly correlated regulatory relationships. Through a comprehensive analysis using established molecular interaction and pathway databases, we show that LLMs possess the potential to identify relevant biomolecules and predict their interactions, offering valuable insights and marking a significant step toward AI-driven biological knowledge discovery.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Integrating AlphaFold and deep learning for atomistic interpretation of cryo-EM maps

Abstract Interpretation of cryo-electron microscopy (cryo-EM) maps requires building and fitting 3D atomic models of biological molecules. AlphaFold-predicted models generate initial 3D coordinates; however, model inaccuracy and conformational heterogeneity often necessitate labor-intensive manual model building and fitting into cryo-EM maps. In this work, we designed a protein model-building workflow, which combines a deep-learning cryo-EM map feature enhancement tool, CryoFEM (Cryo-EM Feature Enhancement Model) and AlphaFold. A benchmark test using 36 cryo-EM maps shows that CryoFEM achieves state-of-the-art performance in optimizing the Fourier Shell Correlations between the maps and the ground truth models. Furthermore, in a subset of 17 datasets where the initial AlphaFold predictions are less accurate, the workflow significantly improves their model accuracy. Our work demonstrates that the integration of modern deep learning image enhancement and AlphaFold may lead to automated model building and fitting for the atomistic interpretation of cryo-EM maps.

59 BASIC BIOLOGICAL SCIENCES↗

CryoTransformer: a transformer model for picking protein particles from Cryo-EM micrographs

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of large protein complexes. Picking single protein particles from cryo-EM micrographs (images) is a crucial step in reconstructing protein structures from them. However, the widely used template-based particle picking process requires some manual particle picking and is labor-intensive and time-consuming. Though machine learning and artificial intelligence (AI) can potentially automate particle picking, the current AI methods pick particles with low precision or low recall. The erroneously picked particles can severely reduce the quality of reconstructed protein structures, especially for the micrographs with low signal-to-noise-ratio (SNR).

59 BASIC BIOLOGICAL SCIENCES↗

Robust, versatile DNA FISH probes for chromosome-specific repeats in Caenorhabditis elegans and Pristionchus pacificus

Repetitive DNA sequences are useful targets for chromosomal fluorescence in situ hybridization. We analyzed recent genome assemblies of Caenorhabditis elegans and Pristionchus pacificus to identify tandem repeats with a unique genomic localization. Based on these findings, we designed and validated sets of oligonucleotide probes for each species targeting at least 1 locus per chromosome. These probes yielded reliable fluorescent signals in different tissues and can easily be combined with the immunolocalization of cellular proteins. Synthesis and labeling of these probes are highly cost-effective and require no hands-on labor. The methods presented here can be easily applied in other model and nonmodel organisms with a sequenced genome.

59 BASIC BIOLOGICAL SCIENCES↗

Reporter genes confer new-to-nature ornamental traits in plants

Ornamental plants (trees, shrubs, and herbs) beautify our urban and rural environments, enrich the quality of human life, and represent a vital component of the horticultural industry. The introduction of novel plant varieties and cultivars is critical to the ornamental horticultural industry [1]. To develop ornamental plants with desirable traits, different approaches, such as ploidy manipulation, interspecific hybridization, and physical/chemical mutagenesis, have been used for decades [2, 3]. However, the breeding of new ornamental varieties of trees and shrubs is a time- and labor-consuming process, because these plants may have a long juvenile growth period, large physical size, or altered floral structures, and consequently require long-term observations, large areas for progeny testing, and/or special equipment for pollination and/or seed collection [4].

59 BASIC BIOLOGICAL SCIENCES↗

A synthetic co-culture for bioproduction of ammonia from methane and air

Abstract Fixed nitrogen fertilizers feed 50% of the global population, but most fixed nitrogen production occurs using energy-intensive Haber–Bosch-based chemistry combining nitrogen (N2) from air with gaseous hydrogen (H2) from methane (CH4) at high temperatures and pressures in large-scale facilities sensitive to supply chain disruptions. This work demonstrates the biological transformation of atmospheric N2 into ammonia (NH3) using CH4 as the sole carbon and energy source in a single vessel at ambient pressure and temperature, representing a biological “room-pressure and room-temperature” route to NH3 that could ultimately be developed to support compact, remote, NH3 production facilities amenable to distributed biomanufacturing. The synthetic microbial co-culture of engineered methanotroph Methylomicrobium buryatense (now Methylotuvimicrobium buryatense) and diazotroph Azotobacter vinelandii converted three CH4 molecules to l-lactate (C3H6O3) and powered gaseous N2 conversion to NH3. The design used division of labor and mutualistic metabolism strategies to address the oxygen sensitivity of nitrogenase and maximize CH4 oxidation efficiency. Media pH and salinity were central variables supporting co-cultivation. Carbon concentration heavily influenced NH3 production. Smaller-scale NH3 production near dispersed, abundant, and renewable CH4 sources could reduce disruption risks and capitalize on untapped energy resources. One-Sentence Summary Co-culture of engineered microorganisms Methylomicrobium buryatense and Azotobacter vinelandii facilitated the use of methane gas as a sole carbon feedstock to produce ammonia in an ambient temperature, atmospheric pressure, single-vessel system.

Biotechnology & Applied Microbiology↗

Enhancing lipid production in plant cells through automated high-throughput genome engineering and phenotyping

Plant bioengineering is a time-consuming and labor-intensive process with no guarantee of achieving desired traits. Here, we present a fast, automated, scalable, high-throughput pipeline for plant bioengineering (FAST-PB) in maize (Zea mays) and Nicotiana benthamiana. FAST-PB enables genome editing and product characterization by integrating automated biofoundry engineering of callus and protoplast cells with single-cell matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). We first demonstrated that FAST-PB could streamline Golden Gate cloning, with the capacity to construct 96 vectors in parallel. Using FAST-PB in protoplasts, we found that PEG2050 increased transfection efficiency by over 45%. For proof-of-concept, we established a reporter-gene-free method for CRISPR editing and phenotyping via mutation of high chlorophyll fluorescence 136. We show that diverse lipids were enhanced up to 6-fold using CRISPR activation of lipid controlling genes. In callus cells, an automated transformation platform was employed to regenerate plants with enhanced lipid traits through introducing multigene cassettes. Lastly, FAST-PB enabled high-throughput single-cell lipid profiling by integrating MALDI-MS with the biofoundry, protoplast, and callus cells, differentiating engineered and unengineered cells using single-cell lipidomics. Furthermore, these innovations massively increase the throughput of synthetic biology, genome editing, and metabolic engineering and change what is possible using single-cell metabolomics in plants.

59 BASIC BIOLOGICAL SCIENCES↗

Low-Cost Screening of Algae for Extreme Tolerance to pH, Temperature, Salinity, and Light

AbstractBioprospecting algae strains with tolerance to extreme conditions such as pH, temperature, salinity, and light is crucial for advancing biotechnology and environmental applications. However, traditional screening methods often involve significant costs and labor, restricting their accessibility and practical use. In this study, we developed and validated low-cost, high-throughput screening techniques, predominantly employing agar plates and liquid culture assays, to effectively differentiate tolerance levels among various algae strains. The methodologies were optimized using the model microalgaChlamydomonas reinhardtiiand its closely related speciesChlamydomonas incertaand the recently discovered extremophilicChlamydomonas pacifica. We systematically evaluated the algae for tolerance to extremes by establishing precise gradients of pH (acidic to alkaline conditions), salinity (0 to 5 M NaCl), temperature (34–42°C), and light intensity (40 to 2977 μE·m⁻²·s⁻¹). Our results demonstrated that these cost-effective, agar plate-based methods effectively distinguished algae strains exhibiting superior tolerance to extreme environmental conditions. These screening techniques not only provided clear differentiation among the closely related strains but also delivered reproducible outcomes suitable for scaling up to larger bioprospecting efforts. Furthermore, the affordability and simplicity of these methods facilitate their implementation in resource-limited laboratories, thereby broadening participation in algae bioprospecting endeavors. This study highlights the potential of low-cost, accessible screening techniques to significantly enhance the discovery and characterization of algal strains with extreme traits. Ultimately, these methods support the development of robust algae-based resources, driving innovation in diverse industrial processes and environmental solutions.Graphical Abstract

Saucedo, Barbara (ORCID:0009000008860839)↗

Detecting anomalous SRF cavity behavior with unsupervised learning

We present an unsupervised learning framework for detecting anomalous superconducting radio-frequency (SRF) cavity behavior at the Continuous Electron Beam Accelerator Facility (CEBAF), emphasizing its initial performance and effectiveness. Key to the system’s success was the development of data acquisition systems (DAQs) that capture fast-sampled, information-rich signals, essential for detecting transient effects. The approach involves creating daily cavity-specific models using principal component analysis to handle variations in rf signal behavior and mitigate performance degradation from data drift. This unsupervised method eliminates the need for expensive labeling by continuously updating models with recent data. Deployed and operational for 3 months before a scheduled shutdown, the system successfully identified several issues with DAQ signals, confirming its effectiveness. Despite access to only a fraction of CEBAF’s SRF cavity signals, the framework efficiently detected several instances requiring intervention, demonstrating a significant improvement over traditional, labor-intensive methods of manual plot inspection. Published by the American Physical Society 2025

43 PARTICLE ACCELERATORS↗

Machine learning approaches for crystallographic classification from synthetic 2D X-ray diffraction data

Crystallographic structure identification is crucial for understanding material properties; however, current methodologies often depend on labor-intensive and time-consuming analyses of 2D X-ray diffraction (XRD) patterns. To address these limitations, this study employs synthetic 2D XRD patterns combined with deep learning (DL) techniques to enable automated and high-throughput classification of the seven crystal systems and 230 space groups. We introduce the novel Auto Diffraction Pipeline, designed to generate synthetic 2D XRD spot patterns from crystallographic information files under diverse conditions, including varying zone axes, atomic substitution, atomic depletion and mechanical loading. These conditions enhance the realism of synthetic data, mitigating the scarcity of experimental datasets and enabling the creation of large representative training sets. Convolutional neural networks were trained and validated on these synthetic datasets to classify crystallographic structures across multiple scenarios. Our results demonstrate that integrating synthetic 2D XRD patterns with DL facilitates rapid, accurate and automated crystallographic classification, promoting the wider adoption of data-driven approaches in materials science.

Shahnazari, Ayoub [Univ. of Rochester, NY (United ↗