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At least 289 records · Page 16

Advancing the central role of non-model biorepositories in predictive modeling of emerging pathogens

The COVID-19 pandemic demonstrated the insufficiency of a reactive approach to emerging zoonotic pathogens. With spillover increasing in frequency as environments change and the human footprint continues to grow, pandemic prevention will require predictive models that can identify (i) potential zoonoses with a high likelihood of emergence and (ii) environmental or other features that may trigger a shift in host, vector, or pathogen baselines associated with emergence and/or spillover. Artificial intelligence (AI), and particularly its machine learning and deep learning branches, holds enormous potential for detecting shifts in large-scale biodiversity and disease datasets (genomic, ecological, geospatial, etc.). Such algorithms can be trained to identify subtle patterns in large volumes of data to yield insights into complex phenomena for which we have limited knowledge of the true cause(s) or predictor(s), as is the case for emerging infectious diseases.

59 BASIC BIOLOGICAL SCIENCES↗

Modeling the emergence of viral resistance for SARS-CoV-2 during treatment with an anti-spike monoclonal antibody

To mitigate the loss of lives during the COVID-19 pandemic, emergency use authorization was given to several anti-SARS-CoV-2 monoclonal antibody (mAb) therapies for the treatment of mild-to-moderate COVID-19 in patients with a high risk of progressing to severe disease. Monoclonal antibodies used to treat SARS-CoV-2 target the spike protein of the virus and block its ability to enter and infect target cells. Monoclonal antibody therapy can thus accelerate the decline in viral load and lower hospitalization rates among high-risk patients with variants susceptible to mAb therapy. However, viral resistance has been observed, in some cases leading to a transient viral rebound that can be as large as 3–4 orders of magnitude. As mAbs represent a proven treatment choice for SARS-CoV-2 and other viral infections, evaluation of treatment-emergent mAb resistance can help uncover underlying pathobiology of SARS-CoV-2 infection and may also help in the development of the next generation of mAb therapies. Although resistance can be expected, the large rebounds observed are much more difficult to explain. We hypothesize replenishment of target cells is necessary to generate the high transient viral rebound. Thus, we formulated two models with different mechanisms for target cell replenishment (homeostatic proliferation and return from an innate immune response antiviral state) and fit them to data from persons with SARS-CoV-2 treated with a mAb. We showed that both models can explain the emergence of resistant virus associated with high transient viral rebounds. We found that variations in the target cell supply rate and adaptive immunity parameters have a strong impact on the magnitude or observability of the viral rebound associated with the emergence of resistant virus. Both variations in target cell supply rate and adaptive immunity parameters may explain why only some individuals develop observable transient resistant viral rebound. Our study highlights the conditions that can lead to resistance and subsequent viral rebound in mAb treatments during acute infection.

60 APPLIED LIFE SCIENCES↗

Development of a Conceptual Chum Salmon Emergence Model for Ives Island

The objective of the study described herein was to develop a conceptual model of chum salmon emergence that was based on empirical water temperature of the riverbed and river in specific locations where chum salmon spawn in the Ives Island area. The conceptual model was developed using water temperature data that have been collected in the past and are currently being collected in the Ives Island area. The model will be useful to system operators who need to estimate the complete distribution of chum salmon emergence (first emergence through final emergence) in order to balance chum salmon redd protection and power system operation.

Murray, Christopher J.↗

Chemical Imaging and Dynamical Studies of Reactivity and Emergent Behavior in Complex Interfacial Systems. Final Technical Report

This research program explored the efficacy of using molecular-level manipulation, imaging and scanning tunneling spectroscopy in conjunction with supersonic molecular beam gas-surface scattering to significantly enhance our understanding of chemical processes occurring on well-characterized interfaces. One program focus was on the spatially-resolved emergent behavior of complex reaction systems as a function of the local geometry and density of adsorbate-substrate systems under reaction conditions. Another focus was on elucidating the emergent electronic and related reactivity characteristics of intentionally constructed single and multicomponent atom- and nanoparticle-based materials. We also examined emergent chirality and self-organization in adsorbed molecular systems where collective interactions between adsorbates and the supporting interface lead to spatial symmetry breaking. In many of these studies we combined the advantages of scanning tunneling (STM) and atomic force (AFM) imaging, scanning tunneling local electronic spectroscopy (STS), and reactive supersonic molecular beams to elucidate precise details of interfacial reactivity that had not been observed by more traditional surface science methods. Using these methods, it was possible to examine, for example, the differential reactivity of molecules adsorbed at different bonding sites in conjunction with how reactivity is modified by the local configuration of nearby adsorbates. At the core of this effort was the goal of significantly extending our understanding of interfacial atomic-scale interactions to create, with intent, molecular assemblies and materials with advanced chemical and physical properties. This ambitious program addressed several key topics in DOE Grand Challenge Science, including emergent chemical and physical properties in condensed phase systems, novel uses of chemical imaging, and the development of advanced reactivity concepts in combustion and catalysis including carbon management. These activities directly benefitted national science objectives in the areas of chemical energy production and advanced materials development.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Alternative and Emerging Technologies for an Energy-Efficient, Water-Efficient, and Low-Pollution Textile Industry

Emerging energy-efficiency, greenhouse gas (GHG), and pollution mitigation technologies will be crucial for the textile industry as it responds to population and economic growth that is expected to spur a rapid increase in textile consumption over the coming decades and a corresponding increase in the industry’s absolute energy use and GHG and other pollutant emissions. This report gives an overview of textile industry processes and compiles available information on the energy savings, environmental and other benefits, costs, commercialization status, and references for 18 emerging technologies to reduce the industry’s energy use and environmental emissions. Although studies from around the world identify a variety of sector specific and cross-cutting energy-efficiency technologies that have already been commercialized for the textile industry, information is scarce and/or scattered regarding emerging or advanced energy-efficiency and low-carbon technologies that are not yet commercialized or at the very early stage of adoption. This report is intended to be a resource on these emerging technologies for engineers, researchers, investors, textile manufacturers, policy makers, and other interested parties.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Emergency Response Capability Baseline Needs Assessment - Compliance Assessment

This document was prepared by John A. Sharry, LLNL Fire Marshal and Division Leader for Fire Protection and was reviewed by LLNL Emergency Management Department Head, James Colson. This document is the second of a two-part analysis on Emergency Response Capabilities of Lawrence Livermore National Laboratory. The first part, 2016 Baseline Needs Assessment Requirements Document established the minimum performance criteria necessary to meet mandatory requirements. This second part analyses the performance of Lawrence Livermore Laboratory Emergency Management Department to the contents of the Requirements Document. The document was prepared based on an extensive review of information contained in the 2016 BNA, a review of Emergency Planning Hazards Assessments, a review of building construction, occupancy, fire protection features, dispatch records, LLNL alarm system records, fire department training records, and fire department policies and procedures. The 2013 BNA was approved by NNSA’s Livermore Field Office on January 22, 2014.

99 GENERAL AND MISCELLANEOUS↗

Emergency Management Situation Report (April 2019)

After a major disaster, federal assistance will not be available for up to 72 hours. The Federal Emergency Management Agency recommends that everybody have an emergency kit ready for an unforeseen disaster. FEMA has published a checklist of recommended items here, but it is important to remember that this is your emergency kit - this is just a basic list of suggestions that should be modified to your personal needs. FEMA recommends that everyone have a three-day kit at home, a one-day kit at work, and a one-day kit in the car. An earthquake cannot be predicted, but it can be prepared for - during an emergency, you will be thankful you took the time to prepare beforehand.

58 GEOSCIENCES↗

Adapting to a Changing World: Managing the Promise and Peril of Emerging Technologies and the Nuclear Nexus [Slides]

The Promise and Peril of Emerging Technologies: New and emerging technologies offer countless advances for just above everything; They also have the potential to be used for more destructive purposes; These technologies remain largely ungoverned by laws or norms; and, The nexus of emerging technologies with nuclear threats demands special attention. Overview, questions: How should we be thinking about these issues? What can we do to reduce the risk that accidents or miscalculation will lead to inadvertent escalation—especially at the nuclear nexus? This talk will examine emerging threats, the state of play of international discussions on these issues, and offer recommendations for the future.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Emergency Management Overview [Slides]

Introdution: LANL's Emergency Management Program is designed and managed in accordance with standards and requirements mandated by the DOE. LANL's primary driver and foundation of this course is DOE O 151.1D, Comprehensive Emergency Management System ; Established the requirements for emergency preparedness, response, and recovery for DOE facilities; Implemented by Emergency Management Division (EMD) on behalf of the Laboratory.

99 GENERAL AND MISCELLANEOUS↗

Development of the Table of Initial Isolation and Protective Action Distances for the 2024 Emergency Response Guidebook

The transportation of hazardous materials creates numerous opportunities for the release of toxic substances into the environment, whether caused by traffic accidents, train derailments, equipment failures, or human error. Such releases can pose acute hazards to the general public and to emergency response personnel who are the first to arrive at the scene. To help first responders determine whether a shipment is potentially hazardous and decide what actions should be taken if a toxic spill does occur, the Emergency Response Guidebook (ERG) is published by the U.S. Department of Transportation (DOT), Transport Canada, and the Secretariat of Transport and Communications of Mexico; with contributions from Centro de Informaciòn Quìmica para Emergencias of Argentina. The most recent version is the 2024 edition of the ERG (ERG 2024), titled 2024 Emergency Response Guidebook (ERG2024). The ERG provides essential information about firefighting, spill response, and potential public health effects. For chemicals that are toxic by inhalation (TIH) and chemicals that produce TIH gases upon reaction with water (TIH by water reactivity or TIHWR), the ERG provides initial isolation distances (IIDs) and protective action distances (PADs). The IID defines the radius of the zone around the spill that should be accessed solely by people who are directly involved in emergency response. The PAD is the distance downwind of the source of the release within which persons should be either evacuated or sheltered in place, depending on the severity of the incident and the nature of the population (e.g., density, age, health).

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Energy Emergency and Preparedness Data: Frequently Asked Questions (FAQs) and Quick Guidance on Crisis Communications

State Energy Offices and Public Utility Commissions rely on timely, accurate, and actionable information to perform their energy emergency response duties and execute their roles as state energy security planners. In support of this need, the National Association of State Energy Officials (NASEO) and the National Association of Regulatory Utility Commissions (NARUC) hosted an Energy Security and Data Analysis Workshop in Washington, DC to identify energy security response and planning data sources; and to share successful methods of data use and integration in state, federal, and private sector tools. Following the workshop, NASEO and NARUC hosted two topical data-centric webinars based on state priorities to identify best practices in Geographic Information Systems (GIS) and Crisis Communications programs leveraged in energy assurance planning and response. The Crisis Communications webinar covered best practice tactics for how states can respond during energy emergencies and other crises. Based on the workshop and webinars, this document summarizes commonly used data sources and includes frequently asked questions which may be used by state energy officials (i.e., consisting of staff from Public Utility Commissions and Governor-designated State Energy Offices) to help guide them in developing or improving their Crisis Communications capabilities. A strong public information program is a key crisis management tool. Timely and accurate information helps prevent confusion and uncertainty and encourages public support and cooperation. As energy subject matter experts, state energy officials are vital in the distilling, clarifying, and conveying energy sector information and implications to decision-makers and the public. Other participants in an effective public information program include the Governor’s Office, other state agencies, local governments, energy providers, local businesses, state legislature, and the federal government. It is essential to provide stakeholders and the public with information about the nature, severity, and duration of an emergency because inadequate understanding and awareness can lead to undesirable actions that could further exacerbate the situation. Before a state government can provide information to the public, it must gather information, describe the emergency accurately, and develop recommendations to manage the situation.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Adapting Technology Learning Curves for Prospective Techno-Economic and Life Cycle Assessments of Emerging Carbon Capture and Utilization Pathways

Comparisons of emerging carbon capture and utilization (CCU) technologies with equivalent incumbent technologies are necessary to support technology developers and to help policy-makers design appropriate long-term incentives to mitigate climate change through the deployment of CCU. In particular, early-stage CCU technologies must prove their economic viability and environmental reduction potential compared to already-deployed technologies. These comparisons can be misleading, as emerging technologies typically experience a drastic increase in performance and decrease in cost and greenhouse gas emissions as they develop from research to mass-market deployment due to various forms of learning. These changes complicate the interpretation of early techno-economic assessments (TEAs) and life cycle assessments (LCAs) of emerging CCU technologies. The effects of learning over time or cumulative production themselves can be quantitatively described using technology learning curves (TLCs). While learning curve approaches have been developed for various technologies, a harmonized methodology for using TLCs in TEA and LCA for CCU in particular is required. To address this, we describe a methodology that incorporates TLCs into TEA and LCA to forecast the environmental and economic performance of emerging CCU technologies. This methodology is based on both an evaluation of the state of the art of learning curve assessment and a literature review of TLC approaches developed in various manufacturing and energy generation sectors. Additionally, we demonstrate how to implement this methodology using a case study on a CO 2 mineralization pathway. Finally, commentary is provided on how researchers, technology developers, and LCA and TEA practitioners can advance the use of TLCs to allow for consistent, high-resolution modeling of technological learning for CCU going forward and enable holistic assessments and fairer comparisons with other climate technologies.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

THE COOL SURGE FOLLOWING FLUX EMERGENCE IN A RADIATION-MHD EXPERIMENT

Cool and dense ejections, typically Hα surges, often appear alongside EUV or X-ray coronal jets as a result of the emergence of magnetized plasma from the solar interior. Idealized numerical experiments explain those ejections as being indirectly associated with the magnetic reconnection taking place between the emerging and preexisting systems. However, those experiments miss basic elements that can importantly affect the surge phenomenon. In this paper we study the cool surges using a realistic treatment of the radiation transfer and material plasma properties. To that end, the Bifrost code is used, which has advanced modules for the equation of state of the plasma, photospheric and chromospheric radiation transfer, heat conduction, and optically thin radiative cooling. We carry out a 2.5D experiment of the emergence of magnetized plasma through (meso) granular convection cells and the low atmosphere to the corona. Through detailed Lagrange tracing we study the formation and evolution of the cool ejection and, in particular, the role of the entropy sources; this allows us to discern families of evolutionary patterns for the plasma elements. In the launch phase, many elements suffer accelerations well in excess of gravity; when nearing the apex of their individual trajectories, instead, the plasma elements follow quasi-parabolic trajectories with accelerations close to g{sub ⊙}. We show how the formation of the cool ejection is mediated by a wedge-like structure composed of two shocks, one of which leads to the detachment of the surge from the original emerged plasma dome.

79 ASTRONOMY AND ASTROPHYSICS↗

The Eruption of a Small-scale Emerging Flux Rope as the Driver of an M-class Flare and of a Coronal Mass Ejection

Solar flares and coronal mass ejections are the most powerful explosions in the Sun. They are major sources of potentially destructive space weather conditions. However, the possible causes of their initiation remain controversial. Using high-resolution data observed by the New Solar Telescope of Big Bear Solar Observatory, supplemented by Solar Dynamics Observatory observations, we present unusual observations of a small-scale emerging flux rope near a large sunspot, whose eruption produced an M-class flare and a coronal mass ejection. The presence of the small-scale flux rope was indicated by static nonlinear force-free field extrapolation as well as data-driven magnetohydrodynamics modeling of the dynamic evolution of the coronal three-dimensional magnetic field. During the emergence of the flux rope, rotation of satellite sunspots at the footpoints of the flux rope was observed. Meanwhile, the Lorentz force, magnetic energy, vertical current, and transverse fields were increasing during this phase. The free energy from the magnetic flux emergence and twisting magnetic fields is sufficient to power the M-class flare. These observations present, for the first time, the complete process, from the emergence of the small-scale flux rope, to the production of solar eruptions.

79 ASTRONOMY AND ASTROPHYSICS↗

Data-driven particle dynamics: Structure-preserving coarse-graining for emergent behavior in non-equilibrium systems

Multiscale systems are ubiquitous in science and technology, but are notoriously challenging to simulate as short spatiotemporal scales must be appropriately linked to emergent bulk physics. When expensive high-dimensional dynamical systems are coarse-grained into low-dimensional models, the entropic loss of information leads to emergent physics which are dissipative, history-dependent, and stochastic. To machine learn coarse-grained dynamics from time-series observations of particle trajectories, we propose a framework using the metriplectic bracket formalism that preserves these properties by construction; most notably, the framework guarantees discrete notions of the first and second laws of thermodynamics, conservation of momentum, and a discrete fluctuation-dissipation balance crucial for capturing non-equilibrium statistics. We introduce the mathematical framework abstractly before specializing to a particle discretization. As labels are generally unavailable for entropic state variables, we introduce a novel self-supervised learning strategy to identify emergent structural variables. We validate the method on benchmark systems and demonstrate its utility on two challenging examples: (1) coarse-graining star polymers at challenging levels of coarse-graining while preserving non-equilibrium statistics, and (2) learning models from high-speed video of colloidal suspensions that capture coupling between local rearrangement events and emergent stochastic dynamics. We provide open-source implementations in both PyTorch and LAMMPS, enabling large-scale inference and extensibility to diverse particle-based systems.

Computational Engineering, Finance, and Science (c↗

Spatial temporal cluster analysis to enhance awareness of disease re-emergence on a global scale

ObjectiveThe application of spatial analysis to improve the awareness and use of surveillance data.IntroductionThe re-emergence of an infectious disease is dependent on social, political, behavioral, and disease-specific factors. Global disease surveillance is a requisite of early detection that facilitates coordinated interventions to these events. Novel informatics tools developed from publicly available data are constantly evolving with the incorporation of new data streams. Re-emerging Infectious Disease (RED) Alert is an open-source tool designed to help analysts develop a contextual framework when planning for future events, given what has occurred in the past. Geospatial methods assist researchers in making informed decisions by incorporating the power of place to better explain the relationships between variables.MethodsDisease incidence and indicator data derived for the RED Alert project were analyzed for spatial associations. Using aggregate country-level data, spatial and spatiotemporal clusters were identified in ArcMap 10.5.1. The identified clusters were then used as the outcome for a series of binary logistic regression models to determine significant covariates that help explain global hotspots. These methods will continue to evolve and be incorporated into the RED Alert decision support ecosystem to provide analysts with a global perspective on potential re-emergence.ResultsHotspots of high disease incidence in relation to neighboring countries were identified for measles, cholera, dengue, and yellow fever between 2000 and 2014. Disease-specific predictors were identified using aggregate estimates from World Bank indicator dataset. Data was imputed where possible to enhance the validity of the Gi * statistic for clustering. In the future, as data streams become more readily available, hotspot modeling at a finer resolution will help to improve the precision of spatial epidemiology.ConclusionsSpatial methods enhance the capability of understanding complex population and disease relationships, which in turn improves surveillance and the ability to predict re-emergence. With tools like RED Alert, public health analysts can better prepare to respond rapidly to future re-emerging disease threats.

Altherr, Forest M.↗

Emergence of catalytic function in prebiotic information-coding polymers

Life as we know it relies on the interplay between catalytic activity and information processing carried out by biological polymers. Here we present a plausible pathway by which a pool of prebiotic information-coding oligomers could acquire an early catalytic function, namely sequence-specific cleavage activity. Starting with a system capable of non-enzymatic templated replication, we demonstrate that even non-catalyzed spontaneous cleavage would promote proliferation by generating short fragments that act as primers. Furthermore, we show that catalytic cleavage function can naturally emerge and proliferate in this system. Specifically, a cooperative catalytic network with four subpopulations of oligomers is selected by the evolution in competition with chains lacking catalytic activity. The cooperative system emerges through the functional differentiation of oligomers into catalysts and their substrates. The model is inspired by the structure of the hammerhead RNA enzyme as well as other DNA- and RNA-based enzymes with cleavage activity that readily emerge through natural or artificial selection. We identify the conditions necessary for the emergence of the cooperative catalytic network. In particular, we show that it requires the catalytic rate enhancement over the spontaneous cleavage rate to be at least 10 2 –10 3 , a factor consistent with the existing experiments. The evolutionary pressure leads to a further increase in catalytic efficiency. The presented mechanism provides an escape route from a relatively simple pairwise replication of oligomers toward a more complex behavior involving catalytic function. This provides a bridge between the information-first origin of life scenarios and the paradigm of autocatalytic sets and hypercycles, albeit based on cleavage rather than synthesis of reactants.

59 BASIC BIOLOGICAL SCIENCES↗

Emergence of catalytic function in prebiotic information-coding polymers

Life as we know it relies on the interplay between catalytic activity and information processing carried out by biological polymers. Here we present a plausible pathway by which a pool of prebiotic information-coding oligomers could acquire an early catalytic function, namely sequence-specific cleavage activity. Starting with a system capable of non-enzymatic templated replication, we demonstrate that even non-catalyzed spontaneous cleavage would promote proliferation by generating short fragments that act as primers. Furthermore, we show that catalytic cleavage function can naturally emerge and proliferate in this system. Specifically, a cooperative catalytic network with four subpopulations of oligomers is selected by the evolution in competition with chains lacking catalytic activity. The cooperative system emerges through the functional differentiation of oligomers into catalysts and their substrates. The model is inspired by the structure of the hammerhead RNA enzyme as well as other DNA- and RNA-based enzymes with cleavage activity that readily emerge through natural or artificial selection. We identify the conditions necessary for the emergence of the cooperative catalytic network. In particular, we show that it requires the catalytic rate enhancement over the spontaneous cleavage rate to be at least 10 2 –10 3 , a factor consistent with the existing experiments. The evolutionary pressure leads to a further increase in catalytic efficiency. The presented mechanism provides an escape route from a relatively simple pairwise replication of oligomers toward a more complex behavior involving catalytic function. This provides a bridge between the information-first origin of life scenarios and the paradigm of autocatalytic sets and hypercycles, albeit based on cleavage rather than synthesis of reactants.

Tkachenko, Alexei V. (ORCID:000000031291243X)↗