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At least 415 records · Page 23

Harmonizing direct and indirect anthropogenic land carbon fluxes indicates a substantial missing sink in the global carbon budget since the early 20th century

Inconsistencies in the calculation of the two anthropogenic land flux terms of the global carbon cycle are investigated. The two terms—the direct anthropogenic flux (caused by direct human disturbance in anthromes, currently a carbon source to the atmosphere) and the indirect anthropogenic flux (caused indirectly by human activities that lead to global change and affecting all biomes, currently an atmospheric carbon sink)—are typically calculated independently, resulting in inconsistent underlying assumptions. We harmonize the estimation of the two anthropogenic land flux terms by incorporating previous estimates of these inconsistencies. We recalculate the global carbon budget (GCB) and apply change-point analysis to the cumulative budget imbalance. Cumulative over 1850–2018 (1959–2018), harmonization results in a 13% lesser (4% greater) land use source from anthromes and a 20% (23%) lesser land sink. This recalculation yields a greater non-closure of the GCB, indicating a missing carbon sink averaging 0.65 Pg C year -1 since the early 20th century. The imbalance likely results from a combination of method discontinuity and structural errors in the assessment of the direct anthropogenic land use flux, greater ocean carbon uptake, structural errors in land models, and in how these land terms are quantified for the budget. We caution against overconfidence in considering the GCB a solved problem and recommend further study of methodological discontinuities in budget terms. We strongly recommend studies that quantify the direct and indirect anthropogenic land fluxes simultaneously to ensure consistency, with a deeper understanding of human disturbance and legacy effects in anthromes.

54 ENVIRONMENTAL SCIENCES↗

Velocity Extraction Using Complete Time-Domain Waveform Data and Audio Machine Learning

We developed a new machine learning-based tool for extracting information from interferometry measurements: MIDWAZE (Modular Interferometry Direct Waveform AnalyZEr). This paper showcases MIDWAZE’s ability to extract an object’s velocity information from Photonic Doppler Velocimetry (PDV) data at near-human accuracy with little to no human intervention. MIDWAZE can extract velocities roughly 350 times as fast as a human analyst "rushing" to complete their extractions, with similar extraction accuracy. MIDWAZE’s most outstanding feature is that it operates directly in waveform/temporal space, freeing analysis from certain limitations imposed by traditional spectrogram-based approaches and opening the way to "phase aware" PDV analysis. MIDWAZE also has limited ability to discriminate between different solid objects, which we develop as a first step towards automated discrimination of different kinds of objects such as ejecta clouds.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Activity-Based Protein Profiling to Probe Relationships between Cytochrome P450 Enzymes and Early-Age Metabolism of Two Polycyclic Aromatic Hydrocarbons (PAHs): Phenanthrene and Retene

A growing body of literature has linked early life exposures to polycyclic aromatic hydrocarbons (PAH) with adverse neurodevelopmental effects. Once in the body, metabolism serves as a powerful mediator of PAH toxicity by bioactivating and detoxifying PAH metabolites. Since enzyme expression and activity varies considerably throughout human development, we evaluated infant metabolism of PAHs as a potential contributing factor to PAH susceptibility. Here, we measured and compared rates of phenanthrene and retene (two primary PAH constituents of woodsmoke) metabolism in human hepatic microsomes from individuals ≤21 months of age to a pooled sample (n = 200) consisting primarily of adults. We used activity-based protein profiling (ABPP) to characterize cytochrome P450 enzymes (CYPs) in the same hepatic microsome samples. Once incubated in microsomes, phenanthrene demonstrated rapid depletion. Best fit models for phenanthrene metabolism demonstrated either 1 or 2 phases, depending on the sample, indicating that multiple enzymes could metabolize phenanthrene. We observed no statistically significant differences in phenanthrene metabolism as a function of age, although samples from the youngest individuals had the slowest phenanthrene metabolism rates. We observed slower rates of retene metabolism compared to phenanthrene also in multiple phases. Rates of retene metabolism increased in an age-dependent manner until adult (pooled) levels were achieved at ~12 mo. ABPP identified 28 unique CYPs among all samples, and we observed lower amounts of active CYPs in individuals ≤21 months of age compared to the pooled sample. Phenanthrene metabolism correlated to CYPs 1A1, 1A2, 2C8, 4A22, 3A4, and 3A43 and activities and retene metabolism correlated to CYPs 1A1, 1A2, and 2C8 activities measured by ABPP and vendor-supplied substrate marker activities. These results will aid efforts to determine human health risk and susceptibility to PAHs exposures during early life.

59 BASIC BIOLOGICAL SCIENCES↗

Land Resources for Wind Energy Development Requires Regionalized Characterizations

Estimates of the land area occupied by wind energy differ by orders of magnitude due to data scarcity and inconsistent methodology. Here, we developed a method that combines machine learning-based imagery analysis and geographic information systems and examined the land area of 318 wind farms (15,871 turbines) in the U.S. portion of the Western Interconnection. We found that prior land use and human modification in the project area are critical for land-use efficiency and land transformation of wind projects. Projects developed in areas with little human modification have a land-use efficiency of 63.8 ± 8.9 W/m 2 (mean ±95% confidence interval) and a land transformation of 0.24 ± 0.07 m 2 /MWh, while values for projects in areas with high human modification are 447 ± 49.4 W/m 2 and 0.05 ± 0.01 m 2 /MWh, respectively. We show that land resources for wind can be quantified consistently with our replicable method, a method that obviates >99% of the workload using machine learning. To quantify the peripheral impact of a turbine, buffered geometry can be used as a proxy for measuring land resources and metrics when a large enough impact radius is assumed (e.g., >4 times the rotor diameter). Our analysis provides a necessary first step toward regionalized impact assessment and improved comparisons of energy alternatives.

17 WIND ENERGY↗

Early Career Perspectives to Broaden the Scope of Critical Zone Science

Abstract Critical Zone (CZ) scientists have advanced understanding of Earth's surface through process‐based research that quantifies water, energy, and mass fluxes in predominantly undisturbed systems. However, the CZ is being increasingly altered by humans through climate and land use change. Expanding the scope of CZ science to include both human‐ and non‐human controls on the CZ is important for understanding anthropogenic impacts to Earth's surface processes and ecosystem services. Here, we share perspectives from predominantly U.S.‐based, early career CZ scientists centered around broadening the scope of CZ science to focus on societally relevant science through a transdisciplinary science framework. We call for increased training on transdisciplinary methods and collaboration opportunities across disciplines and with stakeholders to foster a scientific community that values transdisciplinary science alongside physical science. Here, we build on existing transdisciplinary research frameworks by highlighting the need for institutional support to include and educate graduate students throughout the research processes. We also call for graduate‐student‐led initiatives to increase their own exposure to transdisciplinary science through activities such as transdisciplinary‐focused seminars and symposiums, volunteering with local conservation groups, and participating in internships outside academia.

Warix, Sara [University of Utah Department of Geol↗

Developing Scenario‐Based Strategies for Health, Climate, and Environmental Preparedness: The One Health, One Earth Approach

Climate change amplifies many threats to human health. Despite advances in understanding climate change dynamics and impacts, there remains a critical gap in translating scientific knowledge into equitable, and community-driven health interventions. The inaugural One Earth, One Health workshop sought to explore this gap through human-centered design exercises involving interdisciplinary researchers from climate and Earth sciences, engineering, epidemiology, microbiology, and environmental health. Although participants did not co-develop solutions with affected communities, they used stakeholder role-playing to guide ideation and lay groundwork for actionable plans. Through these methods, participants identified community needs and proposed prototype solutions to alleviate health threats exacerbated by global environmental change. Prototypes were organized around infectious diseases, extreme weather, and air quality, as illustrative themes rather than an exhaustive set of risks. Key solutions included strategies for anticipatory systems and early warning (e.g., integrating environmental signals with health data), inclusive communication and infrastructure needs for responding to extreme weather events, and integrated platforms visualizing air quality trends to support tailored, context-aware guidance beyond one-size-fits-all alerts. The workshop highlighted opportunities such as leveraging machine learning, Earth observation, and real-time surveillance to protect communities, but also noted barriers including data quality, technological redundancy, privacy, and governance challenges. Additionally, participants emphasized the need for interdisciplinary teams capable of collaborating across sectors, breaking down silos and addressing gaps in training and education. Overall, the workshop illustrates how process-driven, human-centered approaches can help surface user needs and generate testable prototype concepts, while underscoring the importance of direct community partnership for implementation.

Abadi, Azar M. [University of Alabama, Birmingham,↗

Reimagining How Flood Warnings Can Inform Decision‐Making and Community Actions

Society faces increasingly severe flood hazards, intensifying demand for flood early warning systems (FEWS) that deliver accurate and actionable information. However, most existing FEWS remain prediction‐centric, treating decision‐making as a downstream consumer of hazard forecasts while offering limited support for uncertainty interpretation, risk communication, and real‐world response. This Perspective presents a vision and blueprint for a novel inland FEWS‐decision‐making (FEWS‐DM) framework that repositions decision‐making as an equal partner in the forecasting process—not a passive recipient of its outputs. The framework is built on three tightly coupled, co‐evolving thrusts: Physical Science (T1), which advances flood prediction with quantified uncertainty informed by decision relevance; Human Science (T2), which incorporates psychology, behavior, and cultural and institutional context; and Decision Science (T3), which unifies physical predictions and human factors through principled, utility‐based decision support with end‐to‐end uncertainty management. Rather than treating T1 as a solved problem, FEWS‐DM recognizes that forecast development itself must be shaped by decision needs through continuous bidirectional feedback. We identify key scientific, behavioral, and operational challenges limiting such integration and discuss the enabling role of AI, while emphasizing human‐centered design and community feedback as essential for building trust and improving flood risk management.

54 ENVIRONMENTAL SCIENCES↗

Air, surface, and wastewater surveillance of SARS-CoV-2; a multimodal evaluation of COVID-19 detection in a built environment

Environmental surveillance of infectious organisms holds tremendous promise to reduce human-to-human transmission in indoor spaces through early detection. In this study we determined the applicability and limitations of wastewater, indoor high-touch surfaces, in-room air, and rooftop exhaust air sampling methods for detecting SARS-CoV-2 in a real world building occupied by residents recently diagnosed with COVID-19. We concurrently examined the results of three 24-hour environmental surveillance techniques, indoor surface sampling, exhaust air sampling and wastewater surveillance, to the known daily census fluctuations in a COVID-19 isolation dormitory. Additionally, we assessed the ability of aerosol samplers placed in the large volume lobby to detect SARS-CoV-2 multiple times per day. Our research reveals an increase in the number of individuals confirmed positive with COVID-19 as well as their estimated human viral load to be associated with statistically significant increases in viral loads detected in rooftop exhaust aerosol samples (p = 0.0413), wastewater samples (p = 0.0323,), and indoor high-touch surfaces (p < 0.001)). We also report that the viral load detected in lobby aerosol samples was statistically higher in samples collected during presence of occupants whose COVID-19 diagnostic tests were confirmed positive via qPCR compared to periods when the lobby was occupied by either contact-traced (suspected positive) individuals or during unoccupied periods (p = 0.0314 and <2e–16). We conclude that each daily (24h) surveillance method, rooftop exhaust air, indoor high-touch surfaces, and wastewater, provide useful detection signals for building owner/operator(s). Furthermore, we demonstrate that exhaust air sampling can provide spatially resolved signals based upon ventilation exhaust zones. Additionally, we find that indoor lobby air sampling can provide temporally resolved signals useful during short duration sampling periods (e.g., 2-4 hours) even with intermittent occupancy by occupants diagnosed with COVID-19.

60 APPLIED LIFE SCIENCES↗

A giant virus infecting the amoeboflagellate Naegleria

Giant viruses (Nucleocytoviricota) are significant lethality agents of various eukaryotic hosts. Although metagenomics indicates their ubiquitous distribution, available giant virus isolates are restricted to a very small number of protist and algal hosts. Here we report on the first viral isolate that replicates in the amoeboflagellate Naegleria. This genus comprises the notorious human pathogen Naegleria fowleri, the causative agent of the rare but fatal primary amoebic meningoencephalitis. We have elucidated the structure and infection cycle of this giant virus, Catovirus naegleriensis (a.k.a. Naegleriavirus, NiV), and show its unique adaptations to its Naegleria host using fluorescence in situ hybridization, electron microscopy, genomics, and proteomics. Naegleriavirus is only the fourth isolate of the highly diverse subfamily Klosneuvirinae, and like its relatives the NiV genome contains a large number of translation genes, but lacks transfer RNAs (tRNAs). NiV has acquired genes from its Naegleria host, which code for heat shock proteins and apoptosis inhibiting factors, presumably for host interactions. Notably, NiV infection was lethal to all Naegleria species tested, including the human pathogen N. fowleri. This study expands our experimental framework for investigating giant viruses and may help to better understand the basic biology of the human pathogen N. fowleri.

59 BASIC BIOLOGICAL SCIENCES↗

Substrate binding plasticity revealed by Cryo-EM structures of SLC26A2

SLC26A2 is a vital solute carrier responsible for transporting essential nutritional ions, including sulfate, within the human body. Pathogenic mutations within SLC26A2 give rise to a spectrum of human diseases, ranging from lethal to mild symptoms. The molecular details regarding the versatile substrate-transporter interactions and the impact of pathogenic mutations on SLC26A2 transporter function remain unclear. Here, using cryo-electron microscopy, we determine three high-resolution structures of SLC26A2 in complexes with different substrates. These structures unveil valuable insights, including the distinct features of the homodimer assembly, the dynamic nature of substrate binding, and the potential ramifications of pathogenic mutations. This structural-functional information regarding SLC26A2 will advance our understanding of cellular sulfate transport mechanisms and provide foundations for future therapeutic development against various human diseases.

59 BASIC BIOLOGICAL SCIENCES↗

Science acceleration and accessibility with self-driving labs

In the evolving landscape of scientific research, the complexity of global challenges demands innovative approaches to experimental planning and execution. Self-Driving Laboratories (SDLs) automate experimental tasks in chemical and materials sciences and the design and selection of experiments to optimize research processes and reduce material usage. This perspective explores improving access to SDLs via centralized facilities and distributed networks. We discuss the technical and collaborative challenges in realizing SDLs’ potential to enhance human–machine and human–human collaboration, ultimately fostering a more inclusive research community and facilitating previously untenable research projects.

Canty, Richard B. [North Carolina State University↗

Operating advanced scientific instruments with AI agents that learn on the job

Advanced scientific user facilities, such as next generation X-ray light sources and self-driving laboratories, are revolutionizing scientific discovery by automating routine tasks and enabling rapid experimentation and characterizations. However, these facilities must continuously evolve to support new experimental workflows, adapt to diverse user projects, and meet growing demands for more intricate instruments and experiments. This continuous development introduces significant operational complexity, necessitating a focus on usability, reproducibility, and intuitive human-instrument interaction. In this work, we explore the integration of agentic AI, powered by Large Language Models (LLMs), as a transformative tool to achieve this goal. We present our approach to developing a human-in-the-loop pipeline for operating advanced instruments including an X-ray nanoprobe beamline and an autonomous robotic station dedicated to the design and characterization of materials. Specifically, we evaluate the potential of various LLMs as trainable scientific assistants for orchestrating complex, multi-task workflows, which also include multimodal data, optimizing their performance through optional human input and iterative learning. We demonstrate the ability of AI agents to bridge the gap between advanced automation and user-friendly operation, paving the way for more adaptable and intelligent scientific facilities.

Large Language Models↗

A deep generative model for deciphering cellular dynamics and in silico drug discovery in complex diseases

Human diseases are characterized by intricate cellular dynamics. Single-cell transcriptomics provides critical insights, yet a persistent gap remains in computational tools for detailed disease progression analysis and targeted in silico drug interventions. Here we introduce UNAGI, a deep generative neural network tailored to analyse time-series single-cell transcriptomic data. This tool captures the complex cellular dynamics underlying disease progression, enhancing drug perturbation modelling and screening. When applied to a dataset from patients with idiopathic pulmonary fibrosis, UNAGI learns disease-informed cell embeddings that sharpen our understanding of disease progression, leading to the identification of potential therapeutic drug candidates. Validation using proteomics reveals the accuracy of UNAGI’s cellular dynamics analysis, and the use of the fibrotic cocktail-treated human precision-cut lung slices confirms UNAGI’s predictions that nifedipine, an antihypertensive drug, may have anti-fibrotic effects on human tissues. UNAGI’s versatility extends to other diseases, including COVID, demonstrating adaptability and confirming its broader applicability in decoding complex cellular dynamics beyond idiopathic pulmonary fibrosis, amplifying its use in the quest for therapeutic solutions across diverse pathological landscapes.

Neural Network↗

An expanded registry of candidate cis -regulatory elements

Mammalian genomes contain millions of regulatory elements that control the complex patterns of gene expression. Previously, the ENCODE consortium mapped biochemical signals across hundreds of cell types and tissues and integrated these data to develop a registry containing 0.9 million human and 300,000 mouse candidate cis-regulatory elements (cCREs) annotated with potential functions. Here we have expanded the registry to include 2.37 million human and 967,000 mouse cCREs, leveraging new ENCODE datasets and enhanced computational methods. This expanded registry covers hundreds of unique cell and tissue types, providing a comprehensive understanding of gene regulation. Functional characterization data from assays such as STARR-seq, massively parallel reporter assay, CRISPR perturbation and transgenic mouse assays have profiled more than 90% of human cCREs, revealing complex regulatory functions. We identified thousands of novel silencer cCREs and demonstrated their dual enhancer and silencer roles in different cellular contexts. Integrating the registry with other ENCODE annotations facilitates genetic variation interpretation and trait-associated gene identification, exemplified by the identification of KLF1 as a novel causal gene for red blood cell traits. This expanded registry is a valuable resource for studying the regulatory genome and its impact on health and disease.

Moore, Jill E. [Univ. of Massachusetts, Worchester↗

Heterogeneous estimations of non-pharmaceutical mitigation behavior during the COVID-19 pandemic

The COVID-19 pandemic highlighted the importance of human behavior in mitigating the spread of disease. Nonetheless, human behavior is often overlooked in models of disease spread, particularly by underutilizing real-world data. We address this by estimating probabilities that individuals engage in behaviors that influence SARS-CoV-2 transmission risk during the COVID-19 pandemic, between September 2020 and June 2022. These behaviors include wearing a mask, using public transportation, spending time with others, avoiding contact with others, and going to work. Our estimates account for the age and sex of individuals and are generated for every county in the United States. We utilized multiple open-source datasets and United States Census data to produce these estimates. Multiple datasets were used for validation, showing our estimates demonstrated comparable accuracy and robustness. Our estimates aid in understanding human behavior dynamics during the COVID-19 pandemic and could be used to inform monthly or longer-term behavior in simulations of COVID-19. Moreover, the methods presented can be applied to other behaviors and features for future simulations of infectious disease.

97 MATHEMATICS AND COMPUTING↗

Global peak water limit of future groundwater withdrawals

Over the past 50 years, humans have extracted the Earth’s groundwater stocks at a steep rate, largely to fuel global agro-economic development. Given society’s growing reliance on groundwater, we explore ‘peak water limits’ to investigate whether, when and where humanity might reach peak groundwater extraction. Using an integrated global model of the coupled human–Earth system, we simulate groundwater withdrawals across 235 water basins under 900 future scenarios of global change over the twenty-first century. Here we find that global non-renewable groundwater withdrawals exhibit a distinct peak-and-decline signature, comparable to historical observations of other depletable resources (for example, minerals), in nearly all (98%) scenarios, peaking on average at 625 km 3 yr -1 around mid-century, followed by a decline through 2100. The peak and decline occur in about one-third (82) of basins, including 21 that may have already peaked, exposing about half (44%) of the global population to groundwater stress. Most of these basins are in countries with the highest current extraction rates, including the United States, Mexico, Pakistan, India, China, Saudi Arabia and Iran. Furthermore, these groundwater-dependent basins will probably face increasing costs of groundwater and food production, suggesting important implications for global agricultural trade and a diminished role for groundwater in meeting global water demands during the twenty-first century.

58 GEOSCIENCES↗

Consistent and reproducible computation of the glass transition temperature from molecular dynamics simulations

In many fields, from semiconductors for opto-electronic applications to ionic liquids (ILs) for separations, the glass transition temperature (Tg) of a material is a useful gauge for its potential use in practical settings. As a result, there is a great deal of interest in predicting Tg using molecular simulations. However, the uncertainty and variation in the trend shift method, a common approach in simulations to predict Tg, can be high. This is due to the need for human intervention in defining a fitting range for linear fits of density with temperature assumed for the liquid and glass phases across the simulated cooling. The definition of such fitting ranges then defines the estimate for the Tg as the intersection of linear fits. We eliminate this need for human intervention by leveraging the Shapiro–Wilk normality test and proposing an algorithm to define the fitting ranges and, consequently, Tg. Through this integration, we incorporate into our automated methodology that residuals must be normally distributed around zero for any fit, a requirement that must be met for any regression problem. Consequently, fitting ranges for realizing linear fits for each phase are statistically defined rather than visually inferred, obtaining an estimate for Tg without any human intervention. The method is also capable of finding multiple linear regimes across density vs temperature curves. We compare the predictions of our proposed method across multiple IL and semiconductor molecular dynamics simulation results from the literature and compare other proposed methods for automatically detecting Tg from density–temperature data. We believe that our proposed method would allow for more consistent predictions of Tg. We make this methodology available and open source through GitHub.

Chemistry↗

Tertiary folds of the SL5 RNA from the 5 ' proximal region of SARS-CoV-2 and related coronaviruses

Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5' genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure of SL5 is predicted to contain a four-way junction of helical stems, some of which are capped with UUYYGU hexaloops. Here, using cryogenic electron microscopy (cryo-EM) and computational modeling with biochemically determined secondary structures, we present three-dimensional structures of SL5 from six coronaviruses. The SL5 domain of betacoronavirus severe-acute-respiratory-syndrome-related coronavirus 2 (SARS-CoV-2), resolved at 4.7 Å resolution, exhibits a T-shaped structure, with its UUYYGU hexaloops at opposing ends of a coaxial stack, the T’s “arms.” Further analysis of SL5 domains from SARS-CoV-1 and MERS (7.1 and 6.4 to 6.9 Å resolution, respectively) indicate that the junction geometry and inter-hexaloop distances are conserved features across these human-infecting betacoronaviruses. The MERS SL5 domain displays an additional tertiary interaction, which is also observed in the non-human-infecting betacoronavirus BtCoV-HKU5 (5.9 to 8.0 Å resolution). SL5s from human-infecting alphacoronaviruses, HCoV-229E and HCoV-NL63 (6.5 and 8.4 to 9.0 Å resolution, respectively), exhibit the same coaxial stacks, including the UUYYGU-capped arms, but with a phylogenetically distinct crossing angle, an X-shape. As such, all SL5 domains studied herein fold into stable tertiary structures with cross-genus similarities and notable differences, with implications for potential protein-binding modes and therapeutic targets.

59 BASIC BIOLOGICAL SCIENCES↗