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At least 235 records · Page 13

Translational Systems Pharmacology‐Based Predictive Assessment of Drug‐Induced Cardiomyopathy

Drug‐induced cardiomyopathy contributes to drug attrition. We compared two pipelines of predictive modeling: (1) applying elastic net (EN) to differentially expressed genes (DEGs) of drugs; (2) applying integer linear programming (ILP) to construct each drug's signaling pathway starting from its targets to downstream proteins, to transcription factors, and to its DEGs in human cardiomyocytes, and then subjecting the genes/proteins in the drugs' signaling networks to EN regression. We classified 31 drugs with availability of DEGs into 13 toxic and 18 nontoxic drugs based on a clinical cardiomyopathy incidence cutoff of 0.1%. The ILP‐augmented modeling increased prediction accuracy from 79% to 88% (sensitivity: 88%; specificity: 89%) under leave‐one‐out cross validation. The ILP‐constructed signaling networks of drugs were better predictors than DEGs. Per literature, the microRNAs that reportedly regulate expression of our six top predictors are of diagnostic value for natural heart failure or doxorubicin‐induced cardiomyopathy. This translational predictive modeling might uncover potential biomarkers.

59 BASIC BIOLOGICAL SCIENCES↗

Policy impact on economic and environmental sustainability of anaerobic digestion: Industrial case study Insights

This paper thoroughly examines how policy incentives impact the economic and environmental sustainability of anaerobic digestion (AD) systems. It uses techno-economic and life cycle analyses, along with real industry data, to explore the entire AD process—from feedstock acceptance to digestate disposal. It evaluates the effects of various U.S. policy crediting programs on the economic viability of different AD pathways for treating sewage sludge and food waste. Furthermore, tipping fees are identified as the primary driver of profitability, while policy credits play a crucial role in enhancing economic feasibility, particularly for renewable natural gas production. However, future regulatory changes could reshape this economic landscape. All AD pathways are found to significantly reduce greenhouse gas emissions, though economic outcomes are highly sensitive to digestate disposal costs and feedstock tipping fees. Co-digestion with food waste is proposed as a strategy to reduce dependence on policy credits and improve long-term economic stability.

Anaerobic Digestion↗

Kinetics and mechanism of light-induced phase separation in a mixed-halide perovskite

Halide ion phase separation is a barrier to the application of mixed-halide perovskites, whereby the presence of large populations of photo-generated or injected carriers causes undesirable changes in the local band gap. Here, we investigate the mechanism of phase separation in CsPbI x Br 3-x perovskite single crystals driven by light. The phase separation process and its dynamics are visualized at the nanometer scale at cryogenic temperatures using in-situ scanning transmission electron microscopy and cathodoluminescence. Combined with phase field modeling that accounts for the coupling between electronic and chemical driving forces, our observations point to a spinodal decomposition mechanism in which both the amplitude of composition fluctuation and the characteristic length scale grow non-linearly with time. Our findings provide microscopic insights that can assist in further engineering mixed-halide perovskites either for stability or for intentional programming of the local halide ion composition, opening pathways to a wide range of applications.

36 MATERIALS SCIENCE↗

Rational Modulation of Plant Root Development Using Engineered Cytokinin Regulators

Achieving precise control over quantitative developmental phenotypes is a key objective in plant biology. Recent advances in synthetic biology have enabled tools to reprogram entire developmental pathways; however, the complexity of designing synthetic genetic programs and the inherent interactions between various signaling processes remains a critical challenge. Here, we leverage Type-B response regulators to modulate the expression of genes involved in cytokinin-dependent growth and development processes. We rationally engineered these regulators to modulate their transcriptional activity (i.e., repression or activation) and potency while reducing their sensitivity to cytokinin. By localizing the expression of these engineered transcription factors using tissue-specific promoters, we can predictably tune cytokinin-regulated traits. As a proof of principle, we deployed this synthetic system in Arabidopsis thaliana to either decrease or increase the number of lateral roots. The simplicity and modularity of our approach makes it an ideal system for controlling other developmental phenotypes of agronomic interest in plants.

Cell signaling↗

Path Finder

PathFinder is a graph search program, traversing a directed cyclic graph to find pathways between labeled nodes. Searches for paths through ordered sequences of labels are termed signatures. Determining the presence of signatures within one or more graphs is the primary function of Path Finder. Path Finder can work in either batch mode or interactively with an analyst. Results are limited to Path Finder whether or not a given signature is present in the graph(s).

Rigdon, JamesBrian↗

Novel Biological Conversion of Hydrogen and Carbon Dioxide Directly into Biodiesel

OPX Biotechnologies, Inc. (OPX), the National Renewable Energy Laboratory (NREL), and Johnson Matthey will develop and optimize a novel, engineered microorganism that directly produces biodiesel from renewable hydrogen (H 2 ) and carbon dioxide (CO 2 ). The proposed process will fix CO 2 utilizing H 2 to generate an infrastructure-compatible, energy-dense fuel at costs of less than $2.50 per gallon, with water being produced as the primary byproduct. NREL will perform metabolic engineering on the bacterium Cupriavidus necator (formerly Ralstonia eutropha) and a techno-economic analysis to guide future scale-up work. H 2 and CO 2 uptakes rates will be genetically increased, production of free fatty acids will be enhanced and their degradation pathway blocked in order to meet the ultimate program goals.

08 HYDROGEN↗

RELAP-7 Development Updates

RELAP-7 is a nuclear systems safety analysis code being developed at the Idaho National Laboratory, and is the next generation tool in the RELAP reactor safety/systems analysis application series. RELAP-7 development began in 2011 to support the Risk Informed Safety Margins Characterization (RISMC) Pathway of the Light Water Reactor Sustainability (LWRS) program. The overall design goal of RELAP-7 is to take advantage of the previous thirty years of advancements in computer architecture, software design, numerical methods, and physical models in order to provide capabilities needed for the RISMC methodology and to support nuclear power safety analysis. The code is being developed based on Idaho National Laboratory’s modern scientific software development framework – MOOSE (the Multi-Physics Object-Oriented Simulation Environment). The initial development goal of the RELAP-7 approach focused primarily on the development of an implicit algorithm capable of strong (nonlinear) coupling of the dependent hydrodynamic variables contained in the 1-D/2-D flow models with the various 0-D system reactor components that compose various boiling water reactor (BWR) and pressurized water reactor nuclear power plants (NPPs). During Fiscal Year (FY) 2015, the RELAP-7 code has been further improved with expanded capability to support boiling water reactor (BWR) and pressurized water reactor NPPs analysis. The accumulator model has been developed. The code has also been coupled with other MOOSE-based applications such as neutronics code RattleSnake and fuel performance code BISON to perform multiphysics analysis. A major design requirement for the implicit algorithm in RELAP-7 is that it is capable of second-order discretization accuracy in both space and time, which eliminates the traditional first-order approximation errors. The second-order temporal is achieved by a second-order backward temporal difference, and the one-dimensional second-order accurate spatial discretization is achieved with the Galerkin approximation of Lagrange finite elements. During FY-2015, we have done numerical verification work to verify that the RELAP-7 code indeed achieves 2nd-order accuracy in both time and space for single phase models at the system level.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

RELAP-7 Pressurizer Component Development Updates

RELAP-7 is a nuclear systems safety analysis code being developed at the Idaho National Laboratory (INL). RELAP-7 development began in 2011 to support the Risk Informed Safety Margins Characterization (RISMC) Pathway of the Light Water Reactor Sustainability (LWRS) program. The overall design goal of RELAP-7 is to take advantage of the previous thirty years of advancements in computer architecture, software design, numerical methods, and physical models in order to provide capabilities needed for the RISMC methodology and to support nuclear power safety analysis. The code is being developed based on Idaho National Laboratory’s modern scientific software development framework – MOOSE (the Multi-Physics Object-Oriented Simulation Environment). The initial development goal of the RELAP-7 approach focused primarily on the development of an implicit algorithm capable of strong (nonlinear) coupling of the dependent hydrodynamic variables contained in the 1-D/2-D flow models with the various 0-D system reactor components that compose various boiling water reactor (BWR) and pressurized water reactor nuclear power plants (NPPs). As part of the efforts to expand the capability for PWR simulation, an equilibrium single-region pressurizer model has been implemented in RELAP-7. The pressurizer component can simulate pressure and water level change through insurge, spray, and heating processes. Two simple tests – one for insurge process and another for outsurge process – have been reported to demonstrate and verify the functions of the pressurizer model. The typical single-phase PWR system model presented in the first RELAP-7 milestone report has been updated, as part of system level test for the new pressurizer model. The updated PWR system model with the pressurizer component can be used for more realistic transient simulations. The addition of the equilibrium single-region pressurizer model represents the first step of developing a suite of pressurizer models with different levels of fidelities. Non-equilibrium two-region two-zone model and non-equilibrium five-region three zone model will be implemented in the near future. Cross comparison and validation will be pursued when higher fidelity pressurizer models are completed.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Linking Strategic Astrophysics Missions, Technology Gaps, and Technology Maturation Investments

The National Aeronautics and Space Administration’s (NASA) Astrophysics Division (APD) funds the development of cutting-edge technologies through multiple programs to enable its strategic missions to achieve ambitious and groundbreaking science goals. These technology development efforts are managed by the Cosmic Origins (COR), Exoplanet Exploration (ExE), and Physics of the Cosmos (PhysCOS) programs. The 2020 Astronomy and Astrophysics Decadal Survey, “Pathways to Discovery in Astronomy and Astrophysics for the 2020s,” (Astro2020) recommended a pan-chromatic set of missions, including three Great Observatories (GO) and three Probe-class missions that could collect unprecedented data over the coming decades. We show the correlation between these strategic missions and the current Astrophysics technology gaps, as well as recent and current technology maturation projects funded to help close these technology gaps. We also cover how these investments advanced their Technology Readiness Levels (TRLs) [1] and where they have been infused into missions and projects.

SAT↗

Path Finder

PathFinder is a graph search program, traversing a directed cyclic graph to find pathways between labeled nodes. Searches for paths through ordered sequences of labels are termed signatures. Determining the presence of signatures within one or more graphs is the primary function of Path Finder. Path Finder can work in either batch mode or interactively with an analyst. Results are limited to Path Finder whether or not a given signature is present in the graph(s).

Rigdon, J. Brian↗

Assessing Solar Cybersecurity: Questions for States to Ask Electric Utilities

To help State Energy Officials and Public Utility Commissions engaging investor-and consumer-owned utilities and the solar industry in topical discussions about their cybersecurity practices and priorities in general, and for interconnected solar systems, specifically, this report outlines discussions prompts for these discussions. By using the questions in this tool states can explore aspects of utilities’ cybersecurity risk management programs that target solar devices, systems, and communication pathways. Such discussions help states identify cybersecurity gaps and assist in emergency response planning, as well as general risk awareness.

14 SOLAR ENERGY↗

Development of Analysis Methods that Integrate Numeric and Textual Equipment Reliability Data

Within the Light Water Reactor Sustainability (LWRS) program, the Risk-Informed Systems Analysis (RISA) Pathway is performing collaborative research on the development and deployment of technologies designed to assist operating nuclear power plants (NPPs) to reduce operating costs improve plant reliability and availability. One of the RISA research areas is focusing on the development of methods and tools designed to optimize plant operations (e.g., maintenance/replacement schedules, optimal maintenance postures for plant structures, systems, and components [SSCs]) in a manner that is more cost effective than current approaches and makes better use of available SSC health data. The Risk-Informed Asset Management (RIAM) project targets this research area by creating a direct bridge between component equipment reliability (ER) data and system engineer decision making regarding maintenance activity scheduling and component aging management. In this respect, one challenge that NPP system engineers are facing is that the amount of ER data being continuously generated is not only extremely large in size, but it comes in different forms: textual (e.g., condition or maintenance reports) and numeric (e.g., generated by monitoring systems). All these data elements provide them with valuable insights and information regarding: 1) the discovery of anomalous behaviors or degradation trends, 2) the identification of the possible causes behind such behaviors/trends, and 3) the prediction of their direct consequences. However, several challenges have proved to be roadblocks to this process. While some of these challenges are technical in nature (i.e., data are often distributed over several physical servers/databases), others are conceptual in nature: data elements come in different formats (e.g., numeric or textual), and measured values have different scales (e.g., vibration spectra and oil temperature). The activities performed by the RIAM project during FY23 directly tackles the need to simultaneously integrate the analysis of ER data in all its forms, numeric and textual. Note that such task has never been performed before due to the complexity of the systems under consideration but, most importantly, because of the technical challenges behind the harmonization of ER data formats and the lack of adequate computational methods to analyze them. Our approach borrows ideas and concepts from the medical field where integration of several data sources is vital to assist medical practitioners to perform correct diagnosis and indicate optimal treatments. In our view a NPP asset is equivalent to a patient in a medical context. The main difference is the complexity of a human body is a magnitude more complex when compared to typical assets commonly present in NPPs (e.g., centrifugal pumps, or motor operated valves). This simplifies our first requirement when analyzing heterogenous ER data formats: to put data into “context”. Context is here intended as the additional piece of information that is needed by ER data analysis tools to understand what these data elements are referring to, i.e., which king of knowledge they are generating. In our context, this knowledge can be translated into models that capture the form and functional architecture of assets/systems, their dependencies, and how they interact. These models actually emulate the knowledge that that NPP system engineers possess about assets and systems; this is their key of success when analyzing ER data, their challenge is ability to handle large amount of data. Here, we employ model-based system engineering (MBSE) models of systems and assets to represent and capture their architecture and functional, i.e. cause-effect, relations. Then, ER data elements are processed by identifying first of all which elements of the developed MBSE elements they are referring to. For numeric ER data this task is fairly easy since it is possible to precisely pinpoint what MBSE elements the corresponding sensor are observing (e.g., bearing temperature of a centrifugal pump). Task is much harder for textual data since the information contained in issue or maintenance reports needs to “be understood” by a computational tool. Here we called this process as “knowledge extraction”. Once again, we borrow the experience in the medical field where methods to extract knowledge from textual data have been developed in the past decade. The missing element for us is the availability of a complete dictionary of NPP related concepts (in addition to the MBSE models presented earlier) that can put “text into context”. In FY23, such dictionary has been developed along with all the computational elements required for knowledge extraction. Lastly, once numeric and textual ER data elements have been processed and “understood”, then the last step is the discovery of possible cause-effect relations among them. This is performed by observing if a logical connection through the MBSE models exists, and if the

97 MATHEMATICS AND COMPUTING↗

Demystifying Solar in WAP

Over the last two years, the National Renewable Energy Laboratory has identified the pathways for implementing solar in the Weatherization Assistance Program and Low Income Home Energy Assistance Program and practices for successful implementation. Learn about successful implementation models from around the network and the new resources that can give you a head start in planning solar into your program, including a demonstration of tools to help evaluate solar potential and cost-effectiveness at the household level, as well as a new tool from the U.S. Department of Energy National Community Solar Partnership to help connect households receiving LIHEAP assistance to community solar subscriptions that guarantee energy bill savings.

ENERGY PLANNING, POLICY, AND ECONOMY,SOLAR ENERGY↗

Systems-Level Modeling for CRISPR-Based Metabolic Engineering

The CRISPR-Cas system has enabled the development of sophisticated, multigene metabolic engineering programs through the use of guide RNA-directed activation or repression of target genes. To optimize biosynthetic pathways in microbial systems, we need improved models to inform design and implementation of transcriptional programs. Recent progress has resulted in new modeling approaches for identifying gene targets and predicting the efficacy of guide RNA targeting. Genome-scale and flux balance models have successfully been applied to identify targets for improving biosynthetic production yields using combinatorial CRISPR-interference (CRISPRi) programs. Here, the advent of new approaches for tunable and dynamic CRISPR activation (CRISPRa) promises to further advance these engineering capabilities. Once appropriate targets are identified, guide RNA prediction models can lead to increased efficacy in gene targeting. Developing improved models and incorporating approaches from machine learning may be able to overcome current limitations and greatly expand the capabilities of CRISPR-Cas9 tools for metabolic engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Cyber security evaluation of II&C technologies

The Light Water Reactor Sustainability (LWRS) Program is a research and development program sponsored by the Department of Energy, which is conducted in close collaboration with industry to provide the technical foundations for licensing and managing the long-term, safe and economical operation of current nuclear power plants The LWRS Program serves to help the US nuclear industry adopt new technologies and engineering solutions that facilitate the continued safe operation of the plants and extension of the current operating licenses. Within the LWRS Program, the Advanced Instrumentation, Information, and Control (II&C) Systems Technologies Pathway conducts targeted research and development (R&D) to address aging and reliability concerns with the legacy instrumentation and control and related information systems of the U.S. operating light water reactor (LWR) fleet. The II&C Pathway is conducted by Idaho National Laboratory (INL). Cyber security is a common concern among nuclear utilities and other nuclear industry stakeholders regarding the digital technologies that are being developed under this program. This concern extends to the point of calling into question whether these types of technologies could ever be deployed in nuclear plants given the possibility that the information in them can be compromised and the technologies themselves can potentially be exploited to serve as attack vectors for adversaries. To this end, a cyber security evaluation has been conducted of these technologies to determine whether they constitute a threat beyond what the nuclear plants already manage within their regulatory-required cyber security programs. Specifically, the evaluation is based on NEI 08-09, which is the industry’s template for cyber security programs and evaluations, accepted by the Nuclear Regulatory Commission (NRC) as responsive to the requirements of the nuclear power plant cyber security regulation found in 10 CFR 73.54. The evaluation was conducted by a cyber security team with expertise in nuclear utility cyber security programs and experience in conducting these evaluations. The evaluation has determined that, for the most part, cyber security will not be a limiting factor in the application of these technologies to nuclear power plant applications.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Light Water Reactor Sustainability Program: Digital Technology Business Case Methodology Guide

The Department of Energy’s (DOE’s) Light Water Reactor Sustainability Program aims to develop and deploy technologies that will make the existing U.S. nuclear fleet more efficient and competitive. The program has developed a standard methodology for determining the impact of new technologies in order to assist nuclear power plant (NPP) operators in building sound business cases. The Advanced Instrumentation, Information, and Control (II&C) Systems Technologies Pathway is part of the DOE’s Light Water Reactor Sustainability (LWRS) Program. It conducts targeted research and development (R&D) to address aging and reliability concerns with the legacy instrumentation and control and related information systems of the U.S. operating light water reactor (LWR) fleet. This work involves two major goals: (1) to ensure that legacy analog II&C systems are not life-limiting issues for the LWR fleet and (2) to implement digital II&C technology in a manner that enables broad innovation and business improvement in the NPP operating model. Resolving long-term operational concerns with the II&C systems contributes to the long-term sustainability of the LWR fleet, which is vital to the nation’s energy and environmental security. The II&C Pathway is conducting a series of pilot projects that enable the development and deployment of new II&C technologies in existing nuclear plants. Through the LWRS program, individual utilities and plants are able to participate in these projects or otherwise leverage the results of projects conducted at demonstration plants. Performance advantages of the new pilot project technologies are widely acknowledged, but it has proven difficult for utilities to derive business cases for justifying investment in these new capabilities. Lack of a business case is often cited by utilities as a barrier to pursuing wide-scale application of digital technologies to nuclear plant work activities. The decision to move forward with funding usually hinges on demonstrating actual cost reductions that can be credited to budgets and thereby truly reduce O&M or capital costs. Technology enhancements, while enhancing work methods and making work more efficient, often fail to eliminate workload such that it changes overall staffing and material cost requirements. It is critical to demonstrate cost reductions or impacts on non-cost performance objectives in order for the business case to justify investment by nuclear operators. The Business Case Methodology (BCM) addresses the “benefit” side of the analysis—as opposed to the cost side—and how the organization evaluates discretionary projects (net present value (NPV), accounting effects of taxes, discount rates, etc.). The cost and analysis side is not particularly difficult for the organization and can usually be determined with a fair amount of precision (not withstanding implementation project cost overruns). It is in determining the "benefits" side of the analysis that utilities have more difficulty in technology projects and that is the focus of this methodology.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Application of photosynthetic N2-fixing cyanobacteria to the CELSS program

Commercially available air lift fermentors were used to simultaneously monitor biomass production, N2-fixation, photosynthesis, respiration, and sensitivity to oxidative damage during growth under various nutritional and light regimes, to establish a data base for the integration of these organisms into a Closed Ecological Life Support System (CELSS) program. Certain cyanobacterial species have the unique ability to reduce atmospheric N2 to organic nitrogen. These organisms combine the ease of cultivation characteristics of prokaryotes with the fully developed photosynthetic apparatus of higher plants. This, along with their ability to adapt to changes in their environment by modulation of certain biochemical pathways, make them attractive candidates for incorporation into the CELSS program.

Packer, L.↗

Fragment-based screening of programmed death ligand 1 (PD-L1)

The PD-1 immune checkpoint pathway is a highly validated target for cancer immunotherapy. Despite the potential advantages of small molecule inhibitors over antibodies, the discovery of small molecule checkpoint inhibitors has lagged behind. To discover small molecule inhibitors of the PD-1 pathway, we have utilized a fragment-based approach. Small molecules were identified that bind to PD-L1 and crystal structures of these compounds bound to PD-L1 were obtained.

60 APPLIED LIFE SCIENCES↗