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At least 217 records · Page 12

Yes, No, Maybe So: Human Factors Considerations for Fostering Calibrated Trust in Foundation Models Under Uncertainty

High-stakes analytical environments require analysts to evaluate evidence and generate conclusions to inform critical decisions often under conditions of uncertainty. Probabilistic decision-making based on incomplete or inaccurate information can reduce productivity, compromise national interests, and endanger public safety. Researchers are developing expert systems built on foundation models (FMs) to support analysts’ decision-making processes by enabling human-artificial intelligence (AI) teaming, in part through the quantification and expression of uncertainty information. As FMs continue to mature, it is imperative to correspondingly consider analysts’ needs for appropriately interpreting and using uncertainty information. However, prior research indicates that it remains unclear how analysts engage with FM-generated uncertainty information and the extent to which these interactions influence trust in, and reliance on, expert systems. We plan to review the state of the science and conduct an exploratory, qualitative study to (a) understand how properly communicated uncertainty can foster calibrated trust and appropriate reliance and (b) identify approaches for effectively conveying FM-generated uncertainty information during analytical workflows. We will administer semi-structured interviews with analysts from a specific high-stakes analytical environment to collect their current experiences with job-related uncertainty and their impressions when viewing FM-generated uncertainty information. During the interview protocol, participants will be presented with several different FM outputs and invited to discuss their thoughts and beliefs about the uncertainty information displayed. Participants may provide insights into how trust and reliance may be influenced by uncertainty. The results of this study will help us to better understand how analysts currently interpret and use uncertainty information. Our findings may inform human factors recommendations for effectively conveying uncertainty information to foster calibrated trust in, and appropriate reliance on, expert systems. Interaction designers and FM developers can use this knowledge to enhance human-AI teaming and ensure the responsible deployment of FM-based expert systems in analytical workflows.

97 MATHEMATICS AND COMPUTING↗

AI in Astrophysics: Tackling Domain Shift, Model Robustness and Uncertainty

Artificial Intelligence (AI) is revolutionizing physics research from probing the large-scale structure of the Universe to modeling subatomic interactions and fundamental forces. Yet, a major challenge persists: AI models trained on simulations or old experiment / astronomical survey often perform poorly when applied to new data exposing issues of dataset (domain) shift, model robustness, and uncertainty in predictions. This talk will introduce common challenges in applying AI across domains and present solutions based on domain adaptation a set of techniques designed to improve model generalization under domain shift. We will cover foundational ideas, practical strategies, and current research frontiers in this area. Through examples in astrophysics, we'll explore how domain adaptation can help bridge the gap between synthetic and real-world data, improve trust in model outputs, and advance scientific discovery.

Ciprijanvoic, Aleksandra [Fermilab] (ORCID:0000000↗

Shift Happens: Building Robust AI Models with Domain Adaptation

Artificial Intelligence (AI) is revolutionizing physics research—from probing the large-scale structure of the Universe to modeling subatomic interactions and fundamental forces. Yet, a major challenge persists: AI models trained on simulations or old experiment / astronomical survey often perform poorly when applied to new data—exposing issues of dataset (domain) shift, model robustness, and uncertainty in predictions. This summer school session will introduce students to common challenges in applying AI across domains and present solutions based on domain adaptation—a set of techniques designed to improve model generalization under domain shift. We will cover foundational ideas, practical strategies, and current research frontiers in this area. Through examples in astrophysics, we'll explore how domain adaptation can help bridge the gap between synthetic and real-world data, improve trust in model outputs, and advance scientific discovery. The concepts discussed are broadly applicable across physics and other scientific disciplines, making this a valuable topic for anyone interested in building robust, transferable AI models for science.

Ciprijanovic, A. [Fermilab] (ORCID:000000031281719↗

Quantum Plasmonic Sensors

The extraordinary sensitivity of plasmonic sensors is well-known in the optics and photonics community. These sensors exploit simultaneously the enhancement and the localization of electromagnetic fields close to the interface between a metal and a dielectric. This enables, for example, the design of integrated biochemical sensors at scales far below the diffraction limit. Despite their practical realization and successful commercialization, the sensitivity and associated precision of plasmonic sensors are starting to reach their fundamental classical limit given by quantum fluctuations of light—known as the shot-noise limit. To improve the sensing performance of these sensors beyond the classical limit, quantum resources are increasingly being employed. This area of research has become known as “quantum plasmonic sensing”, and it has experienced substantial activity in recent years for applications in chemical and biological sensing. This review aims to cover both plasmonic and quantum techniques for sensing, and it shows how they have been merged to enhance the performance of plasmonic sensors beyond traditional methods. We discuss the general framework developed for quantum plasmonic sensing in recent years, covering the basic theory behind the advancements made, and describe the important works that made these advancements. We also describe several key works in detail, highlighting their motivation, the working principles behind them, and their future impact. The intention of the review is to set a foundation for a burgeoning field of research that is currently being explored out of intellectual curiosity and for a wide range of practical applications in biochemistry, medicine, and pharmaceutical research.

47 OTHER INSTRUMENTATION↗

End-of-Century Changes in Orographic Precipitation with the Intermediate Complexity Atmospheric Research Model over the Western United States

Abstract Downscaled precipitation projections were created using the Intermediate Complexity Atmospheric Research (ICAR) model over the western United States to increase the physical realism in orographic precipitation changes. End-of-century simulations from eight models in phase 5 of the Coupled Model Intercomparison Project (CMIP5) were downscaled with ICAR and compared to the widely utilized statistically downscaled dataset, localized constructed analogs (LOCAs), to understand where and why projections of cool-season (September–May) precipitation differed. ICAR and LOCA precipitation projections were similar, but their sign differed in hydrologically relevant regions likely due to ICAR’s simulation of microphysics and mesoscale dynamics with high-resolution topography (6 km). In the Pacific Northwest, cool-season precipitation projections from ICAR showed an increase on the windward side of the Cascades and no significant change within the lee. This difference between the windward and leeward side was attributed to reduced zonal wind speeds, allowing more time for microphysical processes within ICAR. This contrast is enhanced by rain’s faster fall speed compared to snow, limiting transport into the lee. Meanwhile, LOCA projected an increase in precipitation across the Cascades. In the Upper Colorado River basin, LOCA projected an increase in precipitation in high elevation regions (>3000 m), but ICAR projected no significant change or a decrease in precipitation. High elevation differences were most evident in the spring and fall and were also attributed to a snow-to-rain transition and dynamical processes that impacted orographic enhancement within ICAR. Idealized, controlled studies are needed to better isolate individual processes, but these results underscore the importance of including microphysics and mesoscale dynamics within regional-scale precipitation projections. Significance Statement A set of global climate model simulations was downscaled using an atmospheric model that contains key physical equations, referred to as Intermediate Complexity Atmospheric Research (ICAR). ICAR was used to examine projected changes in end-of-century cool-season precipitation over mountains in the western United States. Precipitation projections from ICAR were similar to projections that used statistical relationships to downscale climate projections. However, projections differed between ICAR and statistically downscaled datasets in whether they increased, decreased, or stayed the same in specific, hydrologically relevant regions such as the eastern Cascades and high elevation areas of the Upper Colorado River basin. These differences were attributed to the simulation of physical processes in ICAR. The results highlight the importance of kilometer-scale atmospheric processes in regional climate projections.

Currier, William Ryan [NOAA/Physical Sciences Labo↗

Hydropower Geotechnical Foundations: Current Practice and Innovation Opportunities for Low-Head Applications

Hydropower is a renewable energy resource that produces electricity from flowing water under pressure. Engineered hydropower structures, such as dams, are used to create a hydraulic head, enabling a turbinegenerator unit to convert pressurized flow into electricity. While hydropower has been a source of renewable energy since antiquity, new development in the United States has slowed in recent decades. Based on recent resource assessments, the largest opportunity to expand hydropower in the United States is from new stream-reach development (i.e., new hydropower development along stream-reaches that do not currently have hydroelectric facilities or other forms of infrastructure, such as dams). Roughly 75% of identified new stream-reach development potential is from low-head sites (less than 30 ft of head), which typically suffer from smaller power densities and higher normalized costs, given economies of scale. Hydropower developers and other stakeholders are thus interested in strategies to reduce initial capital costs while practicing sustainable development to maximize environmental compatibility with minimal disruption to natural aquatic life, sediment, and water flows. Historically, civil works have represented a significant cost driver for new hydropower development, with the foundation system representing a major cost component and source of uncertainty. The foundation system is the collection of engineered structural features (e.g. cutoff trenches, walls, grouting, anchors) constructed at or below the preconstruction ground surface that interfaces between the overlying structures (superstructures) and the bed material below (subsurface). Development of a hydropower foundation system must consider the various characteristics of the surrounding stream environment and subsurface while adhering to the engineering requirements of the superstructure that it supports. The care of water, excavation, and other construction activities are important features of foundation design and construction. The design and construction cost of the foundation system is largely dependent on the site geology and riverbed composition and is influenced by the level of geotechnical assessment required and conducted. Thus, a hydropower facility’s geotechnical foundation is often highly site-specific, with proper site selection and assessment being important to project success. The foundation system is designed to provide structural stability (of the foundation and dam), limit seepage, ensure public safety, and maintain functionality for the project life, during both construction and facility operations. Inadequate foundation or dam design can result in dam failure and the uncontrolled release of significant volumes of water, which could cause a high number of casualties and extensive property damage downstream of the failure. According to the Association of State Dam Safety Officials, approximately 30% of all historical dam failures in the United States are attributed to foundation or abutment defects, and another 20% are attributed to piping or seepage through the embankment, foundation, or abutment. To ameliorate these safety considerations, foundations often require massive amounts of construction material (e.g., grout, concrete, engineered dam fill) and long construction times. Foundation design also requires significant analysis prior to construction because the initial in-stream and abutment subsurface conditions are site-specific, and sufficient data for them often are lacking. Current practice requires on-site assessment, using expensive drilling and invasive and non-invasive investigation methods, to determine the expected cost of foundation material and treatment. Additionally, foundation construction often requires site dewatering (and other care of water activities), which involves constructing temporary diversion structures upstream and often downstream, called cofferdams, and water diversion systems that route water around the construction site. Cofferdams and water diversion systems can drastically increase construction costs and contribute to environmental disruption, including modification of flow patterns and benthic habitats. Given the technical, economic, and environmental challenges associated with hydropower foundations, opportunities exist to improve the current state of practice and to develop new and innovative solutions to Hydropower is a renewable energy resource that produces electricity from flowing water under pressure. Engineered hydropower structures, such as dams, are used to create a hydraulic head, enabling a turbinegenerator unit to convert pressurized flow into electricity. While hydropower has been a source of renewable energy since antiquity, new development in the United States has slowed in recent decades. Based on recent resource assessments, the largest opportunity to expand hydropower in the United States is from new stream-reach development (i.e., new hydropower development along stream-reaches that do not currently have hydroelectric facilities or other forms of infrastructure, such as dams). Roughly 75% of identified new stream-reach development potential is from low-head sites (less than 30 ft of head), which typically suffer from smaller power densities and higher normalized costs, given economies of scale. Hydropower developers and other stakeholders are thus interested in strategies to reduce initial capital costs while practicing sustainable development to maximize environmental compatibility with minimal disruption to natural aquatic life, sediment, and water flows. Historically, civil works have represented a significant cost driver for new hydropower development, with the foundation system representing a major cost component and source of uncertainty. The foundation system is the collection of engineered structural features (e.g. cutoff trenches, walls, grouting, anchors) constructed at or below the preconstruction ground surface that interfaces between the overlying structures (superstructures) and the bed material below (subsurface). Development of a hydropower foundation system must consider the various characteristics of the surrounding stream environment and subsurface while adhering to the engineering requirements of the superstructure that it supports. The care of water, excavation, and other construction activities are important features of foundation design and construction. The design and construction cost of the foundation system is largely dependent on the site geology and riverbed composition and is influenced by the level of geotechnical assessment required and conducted. Thus, a hydropower facility’s geotechnical foundation is often highly site-specific, with proper site selection and assessment being important to project success. The foundation system is designed to provide structural stability (of the foundation and dam), limit seepage, ensure public safety, and maintain functionality for the project life, during both construction and facility operations. Inadequate foundation or dam design can result in dam failure and the uncontrolled release of significant volumes of water, which could cause a high number of casualties and extensive property damage downstream of the failure. According to the Association of State Dam Safety Officials, approximately 30% of all historical dam failures in the United States are attributed to foundation or abutment defects, and another 20% are attributed to piping or seepage through the embankment, foundation, or abutment. To ameliorate these safety considerations, foundations often require massive amounts of construction material (e.g., grout, concrete, engineered dam fill) and long construction times. Foundation design also requires significant analysis prior to construction because the initial in-stream and abutment subsurface conditions are site-specific, and sufficient data for them often are lacking. Current practice requires on-site assessment, using expensive drilling and invasive and non-invasive investigation methods, to determine the expected cost of foundation material and treatment. Additionally, foundation construction often requires site dewatering (and other care of water activities), which involves constructing temporary diversion structures upstream and often downstream, called cofferdams, and water diversion systems that route water around the construction site. Cofferdams and water diversion systems can drastically increase construction costs and contribute to environmental disruption, including modification of flow patterns and benthic habitats. Given the technical, economic, and environmental challenges associated with hydropower foundations, opportunities exist to improve the current state of practice and to develop new and innovative solutions to challenges frequently encountered with traditional approaches. With this understanding, it is critically important to understand and document the current state of practice for hydropower geotechnical foundations, identify key challenges, and define opportunities for innovative solutions. To this end, this report documents the current state of practice across the three main phases of geotechnical foundation development: (1) geotechnical site assessment, (2) design, and (3) construction for hydropower systems. It also describes the major challenges with conventional approaches and identifies opportunities for innovation to reduce hydropower foundations costs, timelines, and risks. Key takeaways from this report include the following: Approximately 80% of available low-head sites are expected to have foundations on soil beds rather than rock beds, suggesting that rockfill and earthfill dams may be the most cost-effective conventional dam type for new projects.; Geotechnical and geologic investigation activities are time-consuming and expensive but are essential to define the parameters and criteria needed for foundation design.; Certain riverbed soil and bedrock types present significant technical challenges or require expensive foundation construction, which can prove financially prohibitive for low-head project development.; Modular hydropower design and prefabricated modular foundations represent a promising but unproven paradigm for new hydropower development. Design and construction approaches using optimized and highly repeatable, reliable components would benefit project cost, time, and risk but require additional research and development.; Temporary construction features for foundations, including cofferdams, water diversion, and water control systems, can prove costly and have inherent construction risk.; For economically viable development, hydropower geotechnical foundations should be limited to 4 to 15% of the project’s total initial capital costs. Many proposed projects have experienced cost overruns attributable to foundation difficulties or surprises during construction. These overruns may have been due to inadequate investigations, lack of adequate engineering effort to tailor the structures to site geology and topography, and/or contractual terms, among other considerations.; Challenges for hydropower foundations and opportunities for innovative technology solutions are identified in the following areas (consistent with the three main phases of foundation development): Geotechnical site assessment, Foundation design and materials, Construction methods and technology. Ultimately, this report aims to provide information about geotechnical foundations for low-head hydropower and to motivate transformative technologies to support hydropower growth.

13 HYDRO ENERGY↗

FORGE: Pre-Training Open Foundation Models for Science

Large language models (LLMs) are poised to revolutionize the way we conduct scientific research. However, both model complexity and pre-training cost are impeding effective adoption for the wider science community. Identifying suitable scientific use cases, finding the optimal balance between model and data sizes, and scaling up model training are among the most pressing issues that need to be addressed. In this study, we provide practical solutions for building and using LLM-based foundation models targeting scientific research use cases. We present an end-to-end examination of the effectiveness of LLMs in scientific research, including their scaling behavior and computational requirements on Frontier, the first Exascale supercomputer. We have also developed for release to the scientific community a suite of open foundation models called FORGE with up to 26B parameters using 257B tokens from over 200M scientific articles, with performance either on par or superior to other state-of-the-art comparable models. We have demonstrated the use and effectiveness of FORGE on scientific downstream tasks. Our research establishes best practices that can be applied across various fields to take advantage of LLMs for scientific discovery.

Yin, Junqi↗

Global rare earth element resources: A concise review

Deposits enriched in rare earth elements (REEs) are abundant and diverse in mineralogy, but those of current economic value have extremely limited geographic distribution. Due to rapidly increasing demand and concerns about supply chain security, new and improved methods of prospecting, beneficiation, separation, purification, and recycling are needed. By overviewing the types and geographic distribution of REE reserves globally, their petrogenesis and major mineralogic assemblages, this review aims to provide a foundation for posing new directions for research and development in these areas. In conclusion, our review also seeks to provide a concise summary of important background information that is accessible to researchers from a variety of disciplines who are seeking to engage in this rapidly expanding field.

58 GEOSCIENCES↗

Material Recovery Facilities (MRFs) in the United States: Operations, revenue, and the impact of scale

An analysis was conducted using nationwide survey data to evaluate how material recovery facilities (MRFs) operations vary regionally and with scale. The survey characterized materials, processes, and energy use involved with operations, and revenue for recyclables. This is the first nationwide analysis of MRFs in the US that accounts for mass processed, energy consumed, and revenue. Of a population of 521 MRFs, 48 responses representing MRFs from five US regions were received and analyzed (9.2 % response rate). Responses were analyzed by size according to yearly mass of inbound materials (small: <1,000 Mg/year, medium: 1,000–10,000 Mg/year, and large: >10,000 Mg/year). Most MRFs identify as single-stream; source from residences; utilize tipping floors, picking lines, baling and warehousing; and are powered by electricity. Most revenue and inbound mass (>50%) came from fiber (cardboard and paper). Glass had little revenue, and plastics were difficult to transition to market. Percent residue ranged from 1-39%, averaged <20%, and increased as the mass of inbound material increased. Large MRFs reported more sources of material, employed advanced sorting technology, had greater plastics revenue (33% versus 5% for small MRFs), and had more market access for plastics compared to small MRFs. Large MRFs had two orders of magnitude less annual electricity consumption per Mg recyclables than small MRFs (5–90 kWh/Mg versus ∼300–550 kWh/Mg). Results demonstrate environmental and economic benefits of larger-scale MRFs, which could be implemented more broadly in the US through regional hub-and-spoke arrangements for collecting and processing recyclables, lowering energy consumption and increasing revenue for recyclables.

Hub-and-Spoke↗

Strain Effect in Palladium Nanostructures as Nanozymes

While various effects of physicochemical parameters (e.g., size, facet, composition, and internal structure) on the catalytic efficiency of nanozymes (i.e., nanoscale enzyme mimics) have been studied, the strain effect has never been reported and understood before. Herein, we demonstrate the strain effect in nanozymes by using Pd octahedra and icosahedra with peroxidase-like activities as a model system. Strained Pd icosahedra were found to display 2-fold higher peroxidase-like catalytic efficiency than unstrained Pd octahedra. Theoretical analysis suggests that tensile strain is more beneficial to OH radical (a key intermediate for the catalysis) generation than compressive strain. Pd icosahedra are more active than Pd octahedra because icosahedra amplify the surface strain field. As a proof-of-concept demonstration, the strained Pd icosahedra were applied to immunoassay of biomarkers, outperforming both unstrained Pd octahedra and natural peroxidases. The findings in this research may serve as a strong foundation to guide the design of high-performance nanozymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A compendium of human gene functions derived from evolutionary modelling

A comprehensive, computable representation of the functional repertoire of all macromolecules encoded within the human genome is a foundational resource for biology and biomedical research. The Gene Ontology Consortium has been working towards this goal by generating a structured body of information about gene functions, which now includes experimental findings reported in more than 175,000 publications for human genes and genes in experimentally tractable model organisms 1,2 . Here, we describe the results of a large, international effort to integrate all of these findings to create a representation of human gene functions that is as complete and accurate as possible. Specifically, we apply an expert-curated, explicit evolutionary modelling approach to all human protein-coding genes. This approach integrates available experimental information across families of related genes into models that reconstruct the gain and loss of functional characteristics over evolutionary time. The models and the resulting set of 68,667 integrated gene functions cover approximately 82% of human protein-coding genes. The functional repertoire reveals a marked preponderance of molecular regulatory functions, and the models provide insights into the evolutionary origins of human gene functions. We show that our set of descriptions of functions can improve the widely used genomic technique of Gene Ontology enrichment analysis. The experimental evidence for each functional characteristic is recorded, thereby enabling the scientific community to help review and improve the resource, which we have made publicly available.

59 BASIC BIOLOGICAL SCIENCES↗

Synergizing superwetting and architected electrodes for high-rate water splitting

Water splitting is one of the most promising technologies for generating green hydrogen. To meet industrial demand, it is essential to boost the operation current density to industrial levels, typically in the hundreds of mA cm -2 . However, operating at these high current densities presents significant challenges, with bubble formation being one of the most critical issues. Efficient bubble management is crucial as it directly impacts the performance and stability of the water splitting process. Superwetting electrodes, which can enhance aerophobicity, are particularly favorable for facilitating bubble detachment and transport. By reducing bubble contact time and minimizing the size of detached bubbles, these electrodes help prevent blockage and maintain high catalytic efficiency. Here, in this review, we aim to provide an overview of recent advancements in tackling bubble-related issues through the design and implementation of superwetting electrodes, including surface modification techniques and structural optimizations. We will also share our insights into the principles and mechanisms behind the design of superwetting electrodes, highlighting the key factors that influence their performance. Our review aims to guide future research directions and provides a solid foundation for developing more efficient and durable superwetting electrodes for high-rate water splitting.

36 MATERIALS SCIENCE↗

Fluid modeling of low-temperature plasmas

Fluid models are essential for understanding and predicting low-temperature plasma (LTP) behavior in various scientific and industrial settings. This paper provides an introductory tutorial on fluid modeling of LTPs, covering model formulation, implementation, and computational simulations. The tutorial focuses on five main components of the formulation of LTP fluid models: fluid flow, energy, chemistry, electromagnetism, and material properties, as well as in essential aspects of model implementations, including multiscale phenomena, multiphysics coupling, and numerical convergence. Designed for students and early-career researchers, this work offers a practical foundation for developing and using fluid models, from in-house computational codes to commercial software, bridging fundamental theory with real-world applications.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Analysis of MHD stability and active mode control on KSTAR for high confinement, disruption-free plasma

Long-pulse plasma operation at high normalized beta, $β_N$, above the $\textit{n}$= 1 ideal MHD no-wall stability limit in KSTAR is presently limited by tearing instabilities rather than resistive wall modes. H-mode plasma operation during the recent KSTAR device campaign produced discharges having strong $\textit{m/n}$= 2/1 tearing instabilities at $β_N$ lower than the ideal MHD no-wall beta limit. The unstable tearing mode consequently reduced plasma confinement and toroidal plasma rotation significantly. We report the experiment confirmed that an extended duration of electron cyclotron heating (ECH) at the initial phase of the discharge plays a critical role in mode destabilization. To study destabilizing mechanisms that affect the mode growth, the stability of the observed tearing modes from plasmas with significantly different $β_N$ is computed by using the resistive DCON code and the M3D-C 1 code. Equilibrium reconstructions that include constraints from internal profile diagnostics, and computed fast particle pressure are used as input for reliable computation of stability. The classical tearing stability index, Δ', from resistive DCON is computed to be unstable when the island is fully saturated with large amplitude, while the unstable mode is not computed by M3D-C 1 . The modified Rutherford equation (MRE) describing the evolution of the island width has been constructed for KSTAR plasmas by using plasma parameters computed by the TRANSP code. The MRE model estimates a saturated island width corresponding to ~10% of the plasma minor radius for equilibrium at high $β_N$ 3 having a stable Δ' from the resistive DCON. In preparation for long-pulse plasma operation at higher beta utilizing increased plasma heating power, a resistive wall mode (RWM) active feedback control algorithm has been completed and enabled on KSTAR. To accurately determine the $\textit{n}$= 1component produced by RWMs, an algorithm has been developed that includes magnetic sensor compensation of the prompt applied field and the field from the induced current on the passive conductors. Use of multiple toroidal sensor arrays is enabled by modifying the sensor toroidal angles assumed in mode decomposition to include the effect of varied mode helicities in the outboard region where the mode measurement is made. This analysis on stability, transport, and control provides the required foundation for disruption prediction and avoidance research on KSTAR.

resistive wall mode (RWM)↗

Crystal structures of SARS-CoV-2 ADP-ribose phosphatase: from the apo form to ligand complexes

Among 15 nonstructural proteins (Nsps), the newly emerging Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) encodes a large, multidomain Nsp3. One of its units is the ADP-ribose phosphatase domain (ADRP; also known as the macrodomain, MacroD), which is believed to interfere with the host immune response. Such a function appears to be linked to the ability of the protein to remove ADP-ribose from ADP-ribosylated proteins and RNA, yet the precise role and molecular targets of the enzyme remain unknown. Here, five high-resolution (1.07–2.01 Å) crystal structures corresponding to the apo form of the protein and its complexes with 2-(N-morpholino)ethanesulfonic acid (MES), AMP and ADP-ribose have been determined. The protein is shown to undergo conformational changes to adapt to the ligand in the manner previously observed in close homologues from other viruses. A conserved water molecule is also identified that may participate in hydrolysis. This work builds foundations for future structure-based research on ADRP, including the search for potential antiviral therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗

Do woody vines use gelatinous fibers to climb?

Many plant movements are facilitated by contractile cells called gelatinous fibers (G-fibers), but how G-fibers function in the climbing movements of woody vines remains underexplored. In this report, we compare the presence and distribution of G-fibers in the stems of stem-twiners, which wrap around supports, with non-stem-twiners, which attach to supports via tendrils or adventitious roots. An examination of 164 species spanning the vascular plant phylogeny reveals that G-fibers are common in stem-twiners but scarce in non-stem-twiners, suggesting that G-fibers are preferentially formed in the organ responsible for movement. When present, G-fibers are in the xylem, phloem, pericycle, and/or cortex. We discuss the hypothesis that G-fibers are foundational to plant movement and highlight research opportunities concerning G-fiber development and function.

59 BASIC BIOLOGICAL SCIENCES↗

buhito

buhito is a Python library for graph analysis and machine learning. Graphs can represent networks with objects as nodes and their relationships as edges. buhito focuses on graphlet methods that study graphs through enumerating their component subgraphs to enable interpretable and fast models of complex systems. The package provides tools for different algorithmic designs for computing, analyzing, and applying graphlets to research problems such as machine learning, data compression, and anomaly detection in graph-structured data. A central feature is performing decomposition data analysis on graphs for machine learning models. Implemented in Python and built upon open-source scientific libraries such as NetworkX, NumPy, and SciPy, buhito provides high-performance methods for researchers exploring the mathematical and computational foundations of graphlet analysis applicable to systems of different sizes.

Pimonova, Yulia↗

Prediction of cccDNA dynamics in hepatitis B patients by a combination of serum surrogate markers

Quantification of intrahepatic covalently closed circular DNA (cccDNA) is a key for evaluating an elimination of hepatitis B virus (HBV) in infected patients. However, quantifying cccDNA requires invasive methods such as a liver biopsy, which makes it impractical to access the dynamics of cccDNA in patients. Although HBV RNA and HBV core-related antigens (HBcrAg) have been proposed as surrogate markers for evaluating cccDNA activity, they do not necessarily estimate the amount of cccDNA. Here, we employed a recently developed multiscale mathematical model describing intra- and intercellular viral propagation and applied it in HBV-infected patients under treatment. We developed a model that can predict intracellular HBV dynamics by use of extracellular viral markers, including HBsAg, HBV DNA, and HBcrAg in peripheral blood. Importantly, the model prediction of the amount of cccDNA in patients over time was confirmed to be well correlated with the data for quantified cccDNA by paired liver biopsy. Thus, our method combining classic and emerging surrogate markers enables us to predict the decay dynamics of cccDNA in patients undergoing treatment.

60 APPLIED LIFE SCIENCES↗