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At least 631 records · Page 35

Assembly of ordered DNA-curli fibril complexes during Salmonella biofilm formation correlates with strengths of the type I interferon and autoimmune responses

Deposition of human amyloids is associated with complex human diseases such as Alzheimer’s and Parkinson’s. Amyloid proteins are also produced by bacteria. The bacterial amyloid curli, found in the extracellular matrix of both commensal and pathogenic enteric bacterial biofilms, forms complexes with extracellular DNA, and recognition of these complexes by the host immune system may initiate an autoimmune response. Here, we isolated early intermediate, intermediate, and mature curli fibrils that form throughout the biofilm development and investigated the structural and pathogenic properties of each. Early intermediate aggregates were smaller than intermediate and mature curli fibrils, and circular dichroism, tryptophan, and thioflavin T analyses confirmed the establishment of a beta-sheet secondary structure as the curli conformations matured. Intermediate and mature curli fibrils were more immune stimulatory than early intermediate fibrils in vitro . The intermediate curli was cytotoxic to macrophages independent of Toll-like receptor 2. Mature curli fibrils had the highest DNA content and induced the highest levels of Isg15 expression and TNFα production in macrophages. In mice, mature curli fibrils induced the highest levels of anti-double-stranded DNA autoantibodies. The levels of autoantibodies were higher in autoimmune-prone NZBWxF/1 mice than wild-type C57BL/6 mice. Chronic exposure to all curli forms led to significant histopathological changes and synovial proliferation in the joints of autoimmune-prone mice; mature curli was the most detrimental. In conclusion, curli fibrils, generated during biofilm formation, cause pathogenic autoimmune responses that are stronger when curli complexes contain higher levels of DNA and in mice predisposed to autoimmunity.

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↗

Nutrient and stress tolerance traits linked to fungal responses to global change: Four case studies

In this case study analysis, we identified fungal traits that were associated with the responses of taxa to 4 global change factors: elevated CO2, warming and drying, increased precipitation, and nitrogen (N) enrichment. We developed a trait-based framework predicting that as global change increases limitation of a given nutrient, fungal taxa with traits that target that nutrient will represent a larger proportion of the community (and vice versa). In addition, we expected that warming and drying and N enrichment would generate environmental stress for fungi and may select for stress tolerance traits. We tested the framework by analyzing fungal community data from previously published field manipulations and linking taxa to functional gene traits from the MycoCosm Fungal Portal. Altogether, fungal genera tended to respond similarly to 3 elements of global change: increased precipitation, N enrichment, and warming and drying. The genera that proliferated under these changes also tended to possess functional genes for stress tolerance, which suggests that these global changes—even increases in precipitation—could have caused environmental stress that selected for certain taxa. In addition, these genera did not exhibit a strong capacity for C breakdown or P acquisition, so soil C turnover may slow down or remain unchanged following shifts in fungal community composition under global change. Since we did not find strong evidence that changes in nutrient limitation select for taxa with traits that target the more limiting nutrient, we revised our trait-based framework. The new framework sorts fungal taxa into Stress Tolerating versus C and P Targeting groups, with the global change elements of increased precipitation, warming and drying, and N enrichment selecting for the stress tolerators.

59 BASIC BIOLOGICAL SCIENCES↗

Spurious regulatory connections dictate the expression-fitness landscape of translation factors

During steady-state cell growth, individual enzymatic fluxes can be directly inferred from growth rate by mass conservation, but the inverse problem remains unsolved. Perturbing the flux and expression of a single enzyme could have pleiotropic effects that may or may not dominate the impact on cell fitness. Here, we quantitatively dissect the molecular and global responses to varied expression of translation termination factors (peptide release factors, RFs) in the bacterium Bacillus subtilis. While endogenous RF expression maximizes proliferation, deviations in expression lead to unexpected distal regulatory responses that dictate fitness reduction. Molecularly, RF depletion causes expression imbalance at specific operons, which activates master regulators and detrimentally overrides the transcriptome. Through these spurious connections, RF abundances are thus entrenched by focal points within the regulatory network, in one case located at a single stop codon. Such regulatory entrenchment suggests that predictive bottom-up models of expression-fitness landscapes will require near-exhaustive characterization of parts.

59 BASIC BIOLOGICAL SCIENCES↗

Towards a Stronger Foundation: Digitizing Commercial Buildings with Brick to Enable Portable Advanced Applications

Most large commercial buildings have digital controls for their heating, ventilation, and air-conditioning (HVAC) and lighting systems with the potential to implement advanced control strategies and data analytics. However, advanced control strategies and data analytics are rarely deployed at scale due to non-standard naming conventions and heterogenous building configurations. Semantic metadata standards, like Brick, show promise to proliferate these applications across many buildings, but they have not been widely adopted by industry due to barriers such as perceived risk and unfamiliarity with the technology. This paper describes the workflow we established and evaluated while using it to develop over ten Brick models of existing buildings. Through this process, we observed that digitizing existing commercial buildings is a cost and labor-intensive effort in which understanding the buildings’ data streams is the major bottleneck. Yet, we conclude this investment is worthwhile since various use case applications such as fault detection and diagnostics, thermal comfort analysis, and HVAC control optimization can utilize the same Brick model. The paper also explores the challenges and lessons learned we encountered while creating these data models, such as: 1) difficulties in finding metadata descriptions and relationships for existing buildings; 2) handling missing concepts in the schema needed to model a building; 3) lack of guidance on how to structure the data model or how much detail to include; 4) unfamiliarity with technologies, which makes the learning curve steep for applications developers. Finally, we also describe future directions for semantic metadata research and development to make such transformative technologies more accessible to practitioners.

Roa, Carlos Duarte↗

Open-Source High-Fidelity Aggregate Composite Load Models of Emerging Load Behaviors for Large-Sale Analysis

The goal of this project is to accurately model the dynamic loads for power system planning and operation and to address the challenges inherent in such modeling. Existing load models are inadequate to handle the increasing proliferation of residential air conditioner loads and distributed energy resources, the emerging trends of price-responsive demand, and the growing importance of protective devices in equipment and buildings. A need has emerged to develop a fundamentally new class of load models and next-generation data tools. This work proposes to develop a set of regional–level, scalable open source load models and tools, including large-scale aggregate load protection, concept of price responsive demand, advanced load composition data, next-generation load model data tools, and advanced composite load model calibration and validation frameworks to address new challenges in the representation of next-generation load models.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Coupling between interfacial charge and mechanical deformation at high temperatures in ceramics. Final report

Basic research, under this project, has led to new fundamental discoveries in the effect of electric field (and temperature) on diffusion kinetics, electroluminescence and electronic conductivity in ceramic materials. For example, yttria stabilized zirconia sinters in just seconds well below 1000°C, while, at the same time, exhibiting a highly non-linear rise in conductivity, and intense electroluminescence. The phenomenon has been shown to occur in nearly all ceramics whether they are ionic or electronic conductors, or insulators. The rise in conductivity leads to Joule heating but in-situ measurements with a platinum standard at APS and Brookhaven (NSLS-II) have shown that the temperatures are much below what would have been needed to sinter in a few seconds. We have explored the hypothesis that huge concentrations of Frenkel pairs of vacancies and interstitials are produced. While these point defects accelerate sintering (by the interstitials being transported to the pores and the vacancies to the grain boundaries), they may also produce electron-hole pairs which can impart high electrical conductivity or recombine to emit photons. Many measurements, including in-situ measurements of lattice expansion are consistent with this hypothesis. However, the energy barrier for generating Frenkels in zirconia for example is much larger than can be expected at temperature and electrical fields in these experiments. Most recent work suggests that short wavelength phonons play a critical role in the genesis of the “flash” phenomenon. For example, the Debye temperature has been shown to be the lower bound for initiating flash. Molecular dynamics simulations have shown that large concentrations of Frenkel pairs can form under the proliferation of “optical” phonons at the edge of the Brillouin zone, that is with a wavelength at or below the lattice parameter. This project has led to the development of new experimental techniques as well as a software hardware interface for process and control and data analysis in real time, with a time scale of less than one second. This approach spells a new paradigm in materials science research. It potential impact on high rate manufacturing is self evident.

36 MATERIALS SCIENCE↗

Global Security: 5-10 Year Strategy [Slides]

Global Security delivers innovative engineering solutions to protect the nation from strategic threats home and abroad. Global Security programs focus on developing and implementing technical solutions to address global security challenges through three enduring missions: Global Monitoring, Preventing Proliferation, and Nuclear Weapon Security.

42 ENGINEERING↗

Integrating Data Sources for Improved Safeguards and Accountancy of Electrochemical Fuel Reprocessing Systems. Final Report

Electrochemical reprocessing (also commonly known as “pyroprocessing”) of used nuclear fuel is an alternative to aqueous reprocessing that confers a number of advantages, including the ability to process more recently-discharged fuel, smaller resultant waste volumes, and the lack of isolation of plutonium in the product stream. While electrochemical reprocessing systems have seen a significant research and development effort, nuclear safeguards and security of these systems remains under-developed, particularly given the significant differences in operating environment and process flowsheet compared with established aqueous methods. Objective 4 of DOE’s nuclear energy research and development activities in Nuclear Energy Research and Development Roadmap is: “Understand and minimize the risks of nuclear proliferation and terrorism.” Material Control & Accountancy (MC&A) programs at nuclear processing plants deter and detect theft and diversion of nuclear material by both outside and inside adversaries. Empirical modeling and data analytics of online measurements and state indicators can improve the timeliness of detection and reduce the uncertainty in accountancy measures. To support the development and demonstration of such methods, data are needed that capture expected measurement values collected throughout electrochemical reprocessing facilities. A review of the available literature of current research in measurements for electrochemical reprocessing systems identified twenty-two candidate measurement methodologies, which characterize fuel/salt composition, concentrations of various isotopes and elements, and operational parameters throughout the reprocessing facility. Four primary measurement methodologies have been simulated based on either physical simulations or empirical correlations: gamma emissions, neutron emissions, hybrid k-edge densitometry (HKED), and cyclic voltammetry. Initial investigation into the use of these measures for process monitoring and detection suggests the approach is viable and worthy of further investigation. This report summarizes efforts to generate signatures of key measurements during operation of electrochemical reprocessing facilities and initial investigation of data analytics to support process monitoring, diversion detection, and accountancy.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

NNSA GenScen 2.1 Methodology

Nuclear weapons stockpile planning is a complex process. The Non-Proliferation Treaty,' New START Treaty,2 DOE/NNSA, STRATCOM, Navy, Air Force, and Executive-Branch all have objectives that drive requirements for the types and quantities of nuclear weapons, which in turn drive how nuclear weapons are designed, manufactured, tested, maintained, deployed, transported, stored, retired, and ultimately dismantled. An estimated 200 distinct individuals contribute to the development, completion, and approval of this plan. And once that plan is completed, herein called the N NSA Program of Record (POR), ensuring that the plan is feasible — that the stockpile work can get done — ensures that the Nuclear Security Enterprise (NSE) can deliver the intended nuclear force posture.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

NA-22 Write for Consortium Efforts

We are asked to look into the improvements for the measurement of Pu of a variety of material types (MT): MT41 (Pu-242, 20 – 60% enriched), MT42 (Pu-242 > 60% enrichment), and MT-82 (Np-237). Many of these are legacy items that were packaged years ago (Fig 1&2), and when the items are re-packaged for long-term storage, they must be re-measured using either NDA (nondestructive analysis methods or radiochemical methods. It is of interest to improve the NDA and radiochemistry to reduce the un-certainty in the measurements, as in the case of larger items (250 g to 2 kg items) the uncertainty in measurements makes it difficult to certify the mass of the material down to the 0.5 g accountability requirement per DOE orders by only doing NDA measurement. It would be of interest to look into methods to improve the detection of these materials, which would not only benefit the weapon manufacturing community, but also has the ability to significantly improve the non-proliferation community.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Fast Data Processing for Hyperspectral Sensors on Small Platforms

Hyperspectral imaging is a very promising technology for nuclear proliferation detection. However, due to size and weight restrictions, small hyperspectral platforms such as satellites and small drones lack the on-board computing resources for accurate, real-time analysis of the enormous flow of data that a continuously operating hyperspectral sensor generates. This severely limits satellite systems, which can collect far more data than what they can telemeter, and hinders the ability of all platforms to adapt their missions on the fly in response to observations. This program addresses the hyperspectral data processing challenge through development of new, fast and accurate algorithms that produce data products in real time. The algorithms circumvent the major computational bottlenecks in existing processing streams, and would be incorporated in lightweight, power-efficient single-board computer systems. The toolkit of fast algorithms will be immediately useful in current and future hyperspectral systems being built by the Government and by private industry, including drone-based systems and satellite constellations that acquire timely global imagery.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Sandia Nuclear Cartridge Concept

Nuclear power offers the promise of long-term electrical power for remote areas. Recent advances in passive safety and long-life cores make a reactor that can be operated autonomously for 20 years or more a real possibility. This white paper discusses a reactor concept that offers the potential for further development, resulting in a permanently hermetically-sealed "nuclear cartridge." The term "nuclear cartridge" is meant to imply a nuclear energy source that can be inserted into a site and operated autonomously until its energy has been depleted, then withdrawn and replaced by another cartridge. The concept can be scaled for various sizes, ranging from about 1 megawatt-electric (MWe) to about 100 MWe. The paper also discusses the concept of Integrated Safety, Operations, Security, and Safeguards (ISOSS) by design as it applies to this reactor design. Finally, a discussion of smart grids and how they can benefit the transfer of power to the end user is included. The Nuclear Cartridge concept has been developed with the following characteristics in mind: highly reliable autonomous operation coupled with international monitoring, requiring minimal on-site operations personnel; walkaway passively safe design; cartridge replacement cycle on the order of 20 years; load following capability; physical security by design requiring minimal security personnel during operations; and proliferation resistance by design. As illustrated in figure 1, integrating the reactor with advanced power conversion, smart grids, and other sources of energy results in a resilient and sustainable energy source.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Platform for efficient large-scale storage and analysis of multi-omics data in plant and microbial systems (Final Technical Report)

Genomic variation at the sequence level fundamentally affects the phenotypic state of all organisms at all stages of development, while dynamic processes such as changes in the epigenome (e.g. DNA methylation state) and transcriptome regulate the specific phenotype expressed at any given state of development based upon that genomic variation. In plants, DNA methylation is a particularly important mechanism for both regulating transcriptomic expression and for management of genomic variations that could be deleterious to the organism due to the presence of active retrotransposons in plant genomes. While DNA methylation is heritable, it is also dynamic through a given plant’s development and life cycle, particularly during the development from seed to mature specimen suggesting variations in DNA methylation could be critical regulators of biologically and commercially important phenotypes such as time to flowering; in addition, plant DNA methylation is more complex than that of animals, with methylation of CHG and CHH trinucleotides evident in addition to the better-known CG methylation. The complexity of plant DNA methylation and its interplay with genomic sequence variation, transcriptomics and other epigenomic factors demand a storage and analysis framework that can cope with the complexity both within a single specimen and with analyses that span many individuals and even many species, such as attempts to extend models from model organisms to commercially relevant species. In addition to complexity, the rapid development and proliferation of sequencing technology has led to an explosion of data volume that conventional storage and analysis solutions will likely be unable to cope with in the long run. We proposed to study these with suitable distributed storage and computation and therefore for the application of cloud computing to biological analyses; integrate with existing data sources and compatible with virtually any interface use case, from fully automated shell scripts to notebooks and do all these at scale in this STTR grant.

60 APPLIED LIFE SCIENCES↗

The Automated Mobility District Implementation Catalog: Insights from Ten Early-Stage Deployments

Major disruptive technologies are set to redefine the way in which people view travel, particularly in dense urban areas. Already, ride-hailing services have redefined mobility expectations of a new generation of urban dwellers in some places around the country. Over the next few decades, the proliferation of autonomous vehicles, which are generally referred to in the industry as “automated vehicles (AVs),” will be enhanced by the next generation of shared mobility. This combination of AV operations with on-demand service will provide convenience of mobility similar to that being exhibited in today’s transportation networking companies (TNCs). Shared, automated, public mobility resulting from the cross-hybridization of AVs with on-demand mobility service will bring economic and system efficiencies. Economic efficiencies may be realized by less vehicle ownership and more vehicle “usership.” Many companies are already exploring avenues for shared automated mobility through fleet operations as the wave of the future.

33 ADVANCED PROPULSION SYSTEMS↗

Impact of MURR LEU Conversion on Beryllium Reflector Lifetime

The U.S. National Nuclear Security Administration (NNSA) Office of Material Management and Minimization (M 3 ) has developed and is pursuing an integrated approach to address the persistent threat posed by unintentional proliferation of nuclear materials. The NNSA M 3 approach reduces the risk of highly enriched uranium (HEU) and plutonium falling into the hands of non-state actors by minimizing the use of and, when possible, eliminating weapons-usable nuclear material around the world. In this geopolitical context, most research and test reactors, both domestic and international, have completed or started a program of conversion from the use of HEU to low-enriched uranium (LEU) as fuel.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

How Low Can You Go? Using Synthetic 3D Imagery to Drastically Reduce Real-World Training Data for Object Detection

Deep convolutional neural networks (DCNNs) currently provide state-of-the-art performance on image classification and object detection tasks, and there are many global security mission areas where such models could be extremely useful. Crucially, the success of these models is driven in large part by the widespread availability of high-quality open source data sets such as Image Net, Common Objects in Context (COCO), and KITTI, which contain millions of images with thousands of unique labels. However, global security relevant objects-of-interest can be difficult to obtain: relevant events are low frequency and high consequence; the content of relevant images is sensitive; and adversaries and proliferators seek to obscure their activities. For these cases where exemplar data is hard to come-by, even fine-tuning an existing model with available data can be effectively impossible. Recent work demonstrated that models can be trained using a combination of real-world and synthetic images generated from 3D representations; that such models can exceed the performance of models trained using real-world data alone; and that the generated images need not be perfectly realistic (Tremblay, et al., 2018). However, this approach still required hundreds to thousands of real-world images for training and fine tuning, which for sparse, global security-relevant datasets can be an unrealistic hurdle. In this research, we validate the performance and behavior of DCNN models as we drive the number of real-world images used for training object detection tasks down to a minimal set. We perform multiple experiments to identify the best approach to train DCNNs from an extremely small set of real-world images. In doing so, we: Develop state-of-the-art, parameterized 3D models based on real-world images and sample from their parameters to increase the variance in synthetic image training data; Use machine learning explainability techniques to highlight and correct through targeted training the biases that result from training using completely synthetic images; and Validate our results by comparing the performance of the models trained on synthetic data to one another, and to a control model created by fine-tuning an existing ImageNet-trained model with a limited number (hundreds) of real-world images.

97 MATHEMATICS AND COMPUTING↗

The future of the NPT: REVCON and beyond

The Treaty on the Nonproliferation of Nuclear Weapons (NPT), with its quinquennial review conferences (RevCons), has become the foundation of the international nonproliferation regime over the course of its 50-year history. With more states parties than any other arms control agreement (currently 191), the Treaty provides a legally binding framework for all states parties, constraining proliferation of nuclear weapons and committing the five recognized states who possess nuclear weapons to work toward disarmament. The NPT has enjoyed wide success in constraining the spread of nuclear weapons. Only one state party has left the agreement and gone on to acquire these weapons, and the overall track record of compliance with IAEA safeguards has been robust. However, for all its effectiveness in the area of nonproliferation, its achievements on the disarmament front have been relatively unimpressive. While the NWS – most notably the United States and the Soviet Union/Russia – have decreased the overall size of their nuclear arsenals significantly since 1970, these arsenals have remained an important feature of NWS security policies. The limited progress towards disarmament has created friction between the NNWS and NWS and has been the source of mounting tension within the NPT regime. The 2020 RevCon, the 50th anniversary of the NPT and 25th anniversary of its indefinite extension, faces a range of contentious challenges, old and new, which call into question the Treaty’s future viability.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗