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At least 109 records · Page 6

Bemnifosbuvir: An HCV NS5B Inhibitor With Multiple Modes of Action

Bemnifosbuvir (BEM) is a potent, pan-genotypic inhibitor targeting the hepatitis C virus (HCV) NS5B polymerase. Its antiviral activity was evaluated in an ascending dose phase I clinical trial involving 30 patients treated once a day for 7 days. After treatment initiation, plasma HCV RNA declined in a biphasic manner with a mean reduction of 2.3 log 10 IU/mL after 24 hours and 4.4 log10 IU/mL by day 7 for the highest dose. Alanine aminotransferase (ALT) also normalized in most patients. We employed a multiscale mathematical model fitted to the HCV RNA and ALT dynamics to quantify the antiviral activity and evaluate the modes of action of BEM. We found that models in which BEM only acted as a typical HCV RNA polymerase inhibitor and reduced the intracellular production of HCV RNA did not fit the data as well as models in which BEM had multiple modes of action, including suppressing viral assembly and secretion and enhancing intracellular HCV RNA degradation. BEM's effectiveness in inhibiting intracellular HCV RNA production increased with dose (150 mg/day: 88.2%, 300 mg/day: 98.8%, 600 mg/day: 99.5%), while inhibition of viral assembly and release was ~95% effective regardless of dose. We observed a dose-dependent enhancement in the degradation of intracellular HCV RNA, with degradation rates 1.5-fold higher in patients receiving 300 mg/day and 2.7-fold higher in those receiving 600 mg/day than in patients receiving 150 mg/day. No significant differences in antiviral activity were detected between HCV genotypes 1b and 3 or between patients with and without compensated cirrhosis.

59 BASIC BIOLOGICAL SCIENCES↗

Anomalous hydrodynamics effective actions from holography

We derive an effective action for charged plasmas with an anomalous (abelian) global current charge current using holography. The holographic description is captured by the dynamics of an Einstein-Maxwell-Chern-Simons theory in an asymptotically AdS spacetime. The ’t Hooft anomaly contribution, which is encoded in the Chern-Simons term, contributes at the Gaussian order in the effective action only in the momentum diffusion sector, where it leads to chiral shear waves. However, as we demonstrate, beyond the Gaussian order, there is non-trivial imprint of the parity-violating anomaly term in sound and charge diffusion dynamics as well.

79 ASTRONOMY AND ASTROPHYSICS↗

A numerical approach for detecting switch-like bistability in mass action chemical reaction networks with conservation laws

Theoretical analysis of signaling pathways can provide a substantial amount of insight into their function. One particular area of research considers signaling pathways capable of assuming two or more stable states given the same amount of signaling ligand. This phenomenon of bistability can give rise to switch-like behavior, a mechanism that governs cellular decision making. Investigation of whether or not a signaling pathway can confer bistability and switch-like behavior, without knowledge of specific kinetic rate constant values, is a mathematically challenging problem. Recently a technique based on optimization has been introduced, which is capable of finding example parameter values that confer switch-like behavior for a given pathway. Although this approach has made it possible to analyze moderately sized pathways, it is limited to reaction networks that presume a uniterminal structure. It is this limited structure we address by developing a general technique that applies to any mass action reaction network with conservation laws. In this paper we developed a generalized method for detecting switch-like bistable behavior in any mass action reaction network with conservation laws. The method involves (1) construction of a constrained optimization problem using the determinant of the Jacobian of the underlying rate equations, (2) minimization of the objective function to search for conditions resulting in a zero eigenvalue, (3) computation of a confidence level that describes if the global minimum has been found and (4) evaluation of optimization values, using either numerical continuation or directly simulating the ODE system, to verify that a bistability region exists. The generalized method has been tested on three motifs known to be capable of bistability. We have developed a variation of an optimization-based method for the discovery of bistability, which is not limited to uniterminal chemical reaction networks. Successful completion of the method provides an S-shaped bifurcation diagram, which indicates that the network acts as a bistable switch for the given optimization parameters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Guide for Creating a Building-Level Action Plan to Improve Energy Efficiency and Reduce Carbon Emissions

Action plans are tools for commercial building owners to create pathways for reducing energy use and decarbonize, hence reducing carbon emissions. This template and associated direction manual provides a method for creating an action plan. Originally created for the Better Buildings Low Carbon Pilot, it can also be applied to the Better Buildings Climate Challenge and for any building owner striving towards lower carbon footprints.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Non-Resource Conservation and Recovery Act Corrective Action Unit (CAU) Post-Closure Inspection Report, Nevada National Security Site, Nevada For Calendar Year 2025

This report includes visual inspection results, descriptions of maintenance and repair activities, and recommendations for CY 2025 for use restrictions (URs) at corrective action sites (CASs) located on the Nevada National Security Site and on the Nevada Test and Training Range (NTTR) that are accessed through the NNSS Main Gate. This document is arranged by project activity (i.e., Industrial Sites, Soils, and Defense Threat Reduction Agency [DTRA]); then by corrective action unit (CAU); and then by CAS. Post-closure UR inspections are performed on an annual basis, unless as noted in text. Post-closure UR inspections verify the condition of physical controls required by each UR, which may include the following activities: • Visual verification of the legibility of signs • Visual inspection of fencing, signs, monuments, and/or markers for indications of wear • Visual inspection of soil covers for indications of subsidence, erosion, or unauthorized use Deficiencies in UR requirements that were identified during CY 2024 inspections and not addressed in the CY 2024 report are addressed in this CY 2025 report.

54 ENVIRONMENTAL SCIENCES↗

From Quantum Time to Manifestly Covariant QFT: On the Need for a Quantum-Action-Based Quantization

In quantum time (QT) schemes, time is promoted to a degree of freedom, allowing Lorentz covariance to be made explicit for single particles. We ask whether this can be lifted to QFT so that Lorentz covariance becomes manifest at the Hilbert-space level, rather than being hidden as in the standard canonical formulation. We address this question by proposing a second-quantized approach in which the elementary particle is the QT particle itself, leading naturally to the notion of spacetime field algebras and of quantum action. We show, however, that a naive many-body construction runs into inconsistencies. To pinpoint their origin we introduce a classical counterpart of the second-quantized formalism, spacetime classical mechanics (SCM), and prove a no-go theorem: Dirac quantization of SCM collapses back to standard QFT and therefore hides covariance. We circumvent this problem by presenting a quantum-action-based quantization that yields a spacetime version of quantum mechanics (SQM), making covariance manifest for (interacting) QFTs. Finally, we show that this resolution is tied to a genuine spacetime generalization of the notion of a quantum state, required by causality and closely connected to recent “states over time” proposals and, in dS/CFT–motivated settings, to microscopic notions of timelike entanglement and emergent time.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

GIS-Based Modeling of Contaminated Soil Volumes at Multiple Sites in the Formerly Utilized Sites Remedial Action Program - 20149

The remediation of hazardous, toxic, and radioactive waste (HTRW) sites produces cost-related risks associated with the estimation of contaminated soil or debris volumes. Historical risk-management techniques include cost contingencies to cover volume uncertainties that affect project budgeting and decision-making. The Buffalo District teamed with project partners to lessen volume uncertainty and reduce project risks at multiple HTRW sites managed under the Formerly Utilized Sites Remedial Action Program (FUSRAP). Historical remedial investigations under FUSRAP commonly identified the presence of radiological material in site media, the associated human health risk, and then areas of remediation. To manage remedial execution and reduce risk, pre-design or remediation-phase sampling essentially 'chased' contamination, which was not conducive to efficient predictive budgeting derived from Feasibility Study (FS) cost analyses. The Buffalo District first optimized their approach to better understand volume uncertainty by utilizing the Argonne National Laboratory's Bayesian Approaches for Adaptive Spatial Sampling (BAASS) software [1]. BAASS processed soft data (e.g., gamma walk-over data) and spatial sampling data to estimate the lateral extent of contaminated soil irrespective of depth (i.e., gross contamination extent) and define areas of contaminant uncertainty. The software performed a binary transformation of contaminant concentrations at all sampling points based upon remedial action goals or a sum of ratios approach (i.e., clean, impacted, or range of impacts in soil). The model produced two-dimensional (horizontal) contaminant probability contours and statistical uncertainty in the sampling coverage and resulting contaminant extents. This method was translated vertically by partitioning the sampling data into depth brackets that produced a stacked representation of contaminant extents and uncertainty in the subsurface (i.e., similar to construction lifts). The results commonly led to a better understanding of project uncertainty and the need for sampling strategies that produce high-confidence soil volumes, which control costs. The BAASS-based delineations were eventually replaced by Empirical Bayesian Kriging (EBK) methods available in ArcGIS Spatial or 3D Analysts [2]. The EBK method calculates contaminant probability zones derived from user-controlled semivariograms of the spatial datasets. The resulting probability zones (e.g., 50% or 80% of contaminant probability) represent the two-dimensional surface delineation of the overall horizontal remedial area, similarly to BAASS. However, unlike BAASS, the vertical sampling data within these probability zones became vertical control points to contour a subterranean surface that connects subsurface points to the land-surface delineations of contamination. The resulting representation of horizontal and vertical impacts within an enclosed envelop (volume) of soil included uncertainty distributions that are used to plan uncertainty-reduction sampling. These data-driven and math-based models of three-dimensional sampling results produced well-bounded remedial volumes for project planning and better uncertainty predictions during project budgeting. The EBK method was applied to several FUSRAP sites managed by the Buffalo District and compared to less rigorously modeled sites previously remediated by the District. The comparison of modeled to actual remediated volumes provide a basis for validating the volume-estimation method. This comparison is important to ensure modeled volumes match physical boundaries of site remediation. FUSRAP sites with denser investigative sampling and lesser volume uncertainty proved useful in remedial planning and contracting. The Buffalo District noted that historical sites with sparser sampling arrays had greater disparity between estimated volumes and final remedial volumes. The benefit achieved over the cost of detailed soil sampling appears positive for FUSRAP projects, especially where impacts vary widely and appear unbounded by investigation-phase sampling. The subsequent Empirical Bayesian Kriging of contamination coupled with vertical contouring for soil estimations reduces uncertainty in soil volumes or indicates where sampling is required to reduce uncertainty, which together optimize remedial planning and budgeting. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Spinning black hole scattering at $ \mathcal{O} $(G 3 S 2 )(G 3 S 2 ): Casimir terms, radial action and hidden symmetry

We resolve subtleties in calculating the post-Minksowskian dynamics of binary systems, as a spin expansion, from massive scattering amplitudes of fixed finite spin. In particular, the apparently ambiguous spin Casimir terms can be fully determined from the gradient of the spin-diagonal part of the amplitudes with respect to S 2 = −s(s+1)ħ 2 , using an interpolation between massive amplitudes with different spin representations. From two-loop amplitudes of spin-0 and spin-1 particles minimally coupled to gravity, we extract the spin Casimir terms in the conservative scattering angle between a spinless and a spinning black hole at $ \mathcal{O} $(G 3 S 2 ), finding agreement with known results in the literature. This completes an earlier study [Phys. Rev. Lett. 130 (2023), 021601] that calculated the non-Casimir terms from amplitudes. We also illustrate our methods using a model of spinning bodies in electrodynamics, finding agreement between scattering amplitude predictions and classical predictions in a root-Kerr electromagnetic background up to $ \mathcal{O} $(α 3 S 2 ). For both gravity and electrodynamics, the finite part of the amplitude coincides with the two-body radial action in the aligned spin limit, generalizing the amplitude-action relation beyond the spinless case. Surprisingly, the two-loop amplitude displays a hidden spin-shift symmetry in the probe limit, which was previously observed at one loop. We conjecture that the symmetry holds to all orders in the coupling constant and is a consequence of integrability of Kerr orbits in the probe limit at the first few orders in spin.

Classical Theories of Gravity↗

Comparing Transcriptomic Points of Departure to Apical Effect Concentrations For Larval Fathead Minnow Exposed to Chemicals with Four Different Modes Of Action

It is postulated that below a transcriptomic-based point of departure, adverse effects are unlikely to occur, thereby providing a chemical concentration to use in screening level hazard assessment. The present study extends previous work describing a high-throughput fathead minnow assay that can provide full transcriptomic data after exposure to a test chemical. One-day post-hatch fathead minnows were exposed to ten concentrations of three representatives of four chemical modes of action: organophosphates, ecdysone receptor agonists, plant photosystem II inhibitors, and estrogen receptor agonists for 24 h. Concentration response modeling was performed on whole body gene expression data from each exposure, using measured chemical concentrations when available. Transcriptomic points of departure in larval fathead minnow were lower than apical effect concentrations across fish species but not always lower than toxic effect concentrations in other aquatic taxa like crustaceans and insects. The point of departure was highly dependent on measured chemical concentration which were often lower than the nominal concentration. Differentially expressed genes between chemicals within modes of action were compared and often showed statistically significant overlap. In addition, reproducibility between identical exposures using a positive control chemical (CuSO 4 ) and variability associated with the transcriptomic point of departure using in silico sampling were considered. Results extend a transcriptomic-compatible fathead minnow high-throughput assay for possible use in ecological hazard screening.

59 BASIC BIOLOGICAL SCIENCES↗

Exploiting Kronecker structure in exponential integrators: Fast approximation of the action of φ $-$functions of matrices via quadrature

Here, in this article, we propose an algorithm for approximating the action of φ $-$ functions of matrices against vectors, which is a key operation in exponential time integrators. In particular, we consider matrices with Kronecker sum structure, which arise from problems admitting a tensor product representation. The method is based on quadrature approximations of the integral form of the φ $-$ functions combined with a scaling and modified squaring method. Owing to the Kronecker sum representation, only actions of 1D matrix exponentials are needed at each quadrature node and assembly of the full matrix can be avoided. Additionally, we derive a priori bounds for the quadrature error, which show that, as expected by classical theory, the rate of convergence of our method is supergeometric. Guided by our analysis, we construct a fast and robust method for estimating the optimal scaling factor and number of quadrature nodes that minimizes the total cost for a prescribed error tolerance. We investigate the performance of our algorithm by solving several linear and semilinear time-dependent problems in 2D and 3D. The results show that our method is accurate and orders of magnitude faster than the current state-of-the-art.

97 MATHEMATICS AND COMPUTING↗

A Typology for Characterizing Human Action in MultiSector Dynamics Models

The role of individual and collective human agency is increasingly recognized as a prominent and arguably paramount determinant in shaping the behavior, trajectory, and vulnerability of multisector systems. This human influence operates at multiple scales: from short-term (hourly to daily) to long-term (annually to centennial) timescales, and from the local to the global, pushing systems towards either desirable or undesirable outcomes. However, the effort to represent human systems in multisector models has been fragmented across philosophical, methodological, and disciplinary lines. To cohere insights across diverse modeling approaches, we present a new typology for classifying how human actors are represented in the broad suite of coupled human-natural system models that are applied in MultiSector Dynamics (MSD) research. The typology conceptualizes a “sector” as a system-of-systems that includes a diverse group of human actors, defined across individual to collective social levels, involved in governing, provisioning, and utilizing products, goods, or services towards some human end. We trace the salient features of modeled representations of human systems by organizing the typology around three key questions: 1) Who are the modeled actors in MSD systems? 2) What are their modeled actions? 3) How and for what purpose are these actors and actions operationalized in a computational model? The typology is used to critically examine existing models and chart the frontier of future human systems modeling for MSD research.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Update on Our Action Plan for Equity, Inclusion, and Diversity in Publishing at JGR: Biogeosciences

We made a commitment to better include underrepresented members of our community in the publication pipeline of JGR: Biogeosciences. This commitment consists of regular updates on our policies and practices, and concrete actions we intend to implement over the next year. So far, our progress to tackle biases and ensure equitable research in the biogeosciences has focused on improving diversity of our associate editor and reviewer pools, increasing awareness of unconscious bias in peer-review, and promoting inclusion in global collaborations. In this update, we explore manuscript submissions and manuscript decisions by gender, and we present a pilot that aims to promote ethical and equitable global collaborations in resource-poor settings. Here, we end our editorial by presenting our next set of actions that we plan on completing over the next year, which include a more thorough analysis of reviewer demographics.

99 GENERAL AND MISCELLANEOUS↗

Advancing the Representation of Human Actions in Large‐Scale Hydrological Models: Challenges and Future Research Directions

Characterizing the impact of human actions on terrestrial water fluxes and storages at multi-basin, continental, and global scales has long been on the agenda of scientists engaged in climate science, hydrology, and water resources systems analysis. This need has resulted in a variety of modeling efforts focused on the representation of water infrastructure operations. Yet, the representation of human-water interactions in large-scale hydrological models is still relatively crude, fragmented across models, and often achieved at coarse resolutions (~10–100 km) that cannot capture local water management decisions. In this commentary, we argue that the concomitance of four drivers and innovations is poised to change the status quo: “hyper-resolution” hydrological models (~0.1–1 km), multi-sector modeling, satellite missions able to monitor the outcome of human actions, and machine learning are creating a fertile environment for human-water research to flourish. We then outline four challenges that chart future research in hydrological modeling: (a) creating hyper-resolution global data sets of water management practices, (b) improving the characterization of anthropogenic interventions on water quantity, stream temperature, and sediment transport, (c) improving model calibration and diagnostic evaluation, and (d) reducing the computational requirements associated with the successful exploration of these challenges. Overcoming them will require addressing modeling, computational, and data development needs that cut across the hydrology community, thereby requiring a major communal effort.

catchment hydrology↗

A Continuous Action Space Tree search for INverse desiGn (CASTING) framework for materials discovery

Abstract Material properties share an intrinsic relationship with their structural attributes, making inverse design approaches crucial for discovering new materials with desired functionalities. Reinforcement Learning (RL) approaches are emerging as powerful inverse design tools, often functioning in discrete action spaces. This constrains their application in materials design problems, which involve continuous search spaces. Here, we introduce an RL-based framework CASTING (Continuous Action Space Tree Search for inverse design), that employs a decision tree-based Monte Carlo Tree Search (MCTS) algorithm with continuous space adaptation through modified policies and sampling. Using representative examples like Silver (Ag) for metals, Carbon (C) for covalent systems, and multicomponent systems such as graphane, boron nitride, and complex correlated oxides, we showcase its accuracy, convergence speed, and scalability in materials discovery and design. Furthermore, with the inverse design of super-hard Carbon phases, we demonstrate CASTING’s utility in discovering metastable phases tailored to user-defined target properties and preferences.

36 MATERIALS SCIENCE↗

Mass action model of solution activity via speciation by solvation and ion pairing equilibria

Abstract Solutes and their concentrations influence many natural and anthropogenic solution processes. Electrolyte and solution models are used to quantify and predict such behavior. Here we present a mechanistic solution model based on mass action equilibria. Solvation and ion pairing are used to model speciated solute and solvent concentrations such that they correlate to a solution’s vapor pressure (solvent activity) according to Raoult’s law from dilute conditions to saturation. This model introduces a hydration equilibrium constant ( K ha ) that is used with either an ion dissociation constant ( K id ) or a hydration modifier ( m ) with an experimentally determined ion dissociation constant, as adjustable parameters to fit vapor–liquid equilibrium data. The modeled solvation equilibria are accompanied by molecular dynamics (MD) studies that support a decline in the observed degree of solvation with increased concentration. MD calculations indicate this finding is a combination of a solvent that solvates multiple solutes, and changes in a solute’s solvation sphere, with the dominant factor changing with concentration. This speciation-based solution model is lateral to established electrostatics-based electrolyte theories. With its basis in mass action, the model can directly relate experimental data to the modeled solute and solvent speciated concentrations and structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Encouraging voluntary government action via a solar-friendly designation program to promote solar energy in the United States

Sustainable development requires an accelerated transition toward renewable energy. In particular, substantially scaling up solar photovoltaics (PV) adoption is a crucial component of reducing the impacts of climate change and promoting sustainable development. However, it is challenging to convince local governments to take action. This study uses a combination of propensity score matching (PSM) and difference-in-differences (DID) models to assess the effectiveness of a voluntary environmental program (VEP) called SolSmart that targets local governments to engage in solar-friendly practices to promote the local solar PV market in the United States. Via specific designation requirements and technical assistance, SolSmart simplifies the process of acting on interest in being solar friendly, has a wide coverage of basic solar-friendly actions with flexible implementation, and motivates completion with multiple levels of designation. We find that a local government’s participation in SolSmart is associated with an increased installed capacity of 18 to 19%/mo or with less statistical significance, an increased number of installations of 17%/mo in its jurisdiction. However, SolSmart has not shown a statistically significant impact on soft cost reductions to date. In evaluating the impact of the SolSmart program, this study improves our understanding of the causation between a VEP that encourages solar-friendly local government practices and multiple solar market outcomes. VEPs may be able to promote shifts toward sustainable development at the local level. Our findings have several implications for the design of VEPs that promote local sustainability.

14 SOLAR ENERGY↗

Dual-action kinase inhibitors influence p38α MAP kinase dephosphorylation

Reversible protein phosphorylation directs essential cellular processes including cell division, cell growth, cell death, inflammation, and differentiation. Because protein phosphorylation drives diverse diseases, kinases and phosphatases have been targets for drug discovery, with some achieving remarkable clinical success. Most protein kinases are activated by phosphorylation of their activation loops, which shifts the conformational equilibrium of the kinase toward the active state. To turn off the kinase, protein phosphatases dephosphorylate these sites, but how the conformation of the dynamic activation loop contributes to dephosphorylation was not known. To answer this, we modulated the activation loop conformational equilibrium of human p38α ΜΑP kinase with existing kinase inhibitors that bind and stabilize specific inactive activation loop conformations. From this, we identified three inhibitors that increase the rate of dephosphorylation of the activation loop phospho-threonine by the PPM serine/threonine phosphatase WIP1. Hence, these compounds are “dual-action” inhibitors that simultaneously block the active site and promote p38α dephosphorylation. Our X-ray crystal structures of phosphorylated p38α bound to the dual-action inhibitors reveal a shared flipped conformation of the activation loop with a fully accessible phospho-threonine. In contrast, our X-ray crystal structure of phosphorylated apo human p38α reveals a different activation loop conformation with an inaccessible phospho-threonine, thereby explaining the increased rate of dephosphorylation upon inhibitor binding. These findings reveal a conformational preference of phosphatases for their targets and suggest a unique approach to achieving improved potency and specificity for therapeutic kinase inhibitors.

Science & Technology - Other Topics↗

Effective action approach for preheating

Abstract We present a semiclassical non-perturbative approach for calculating the preheating process at the end of inflation. Our method involves integrating out the decayed particles within the path integral framework and subsequently determining world-line instanton solutions in the effective action. This enables us to obtain the effective action of the inflaton, with its imaginary part linked to the phenomenon of particle creation driven by coherent inflaton field oscillations. Additionally, we utilize the Bogoliubov transformation to investigate the evolution of particle density within the medium after multiple inflaton oscillations. We apply our approach to various final state particles, including scalar fields, tachyonic fields, and gauge fields. The non-perturbative approach provides analytical results for preheating that are in accord with previous methods.

Astronomy & Astrophysics↗