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At least 541 records · Page 30

Prediction of non-intuitive metabolic targets with bayesian metabolic control analysis to improve 3-hydroxypropionic acid production in Aspergillus niger

Development of efficient bioconversion processes is limited by the ability to predictably improve metabolic flux. Here we deployed Bayesian Metabolic Control Analysis as a platform to integrate multi-omics data with metabolic modeling and evaluated its ability to predict genetic interventions that improve metabolic flux. Global Metabolomics and proteomics data was collected from 17 Aspergillus niger strains engineered to produce the platform biochemical 3-hydroxypropionic acid from which seven actional genetic interventions were predicted from significant flux control coefficients. Of the suggested genetic interventions, two were present within the intuitively designed strains used for training (malonic semialdehyde dehydrogenase and pyruvate carboxylase) while five predicted targets were present within non-intuitive areas of the metabolic network including 5-formyltetrahydrofolate deformylase and four mitochondrial enzymes, alcohol dehydrogenase, succinyl-CoA ligase, aspartate aminotransferase, and malate dehydrogenase. Six of the targets were validated in the highest performing 3-HP strain used for multi-omics data generation which contained a prior disruption of the highest scoring target malonic semialdehyde dehydrogenase. Predicted directional perturbation of five of the six tested targets significantly improved titer and rate of 3-HP production and two significantly improved yield. The greatest improvements were observed following disruption of the non-intuitive target succinyl-CoA ligase which increased titer by 39% and yield by 29% (to 20.4 g/L 3-HP and 0.31 g 3-HP/g glucose) over the strains used for training. This study demonstrates the utility of Bayesian Metabolic Control Analysis and highlights the ability to predict meaningful genetic targets in unexpected areas of metabolism to improve engineered strains for bioconversion.

3-hydroxypropionic acid↗

Automated Work Package: Initial Wireless Communication Platform Design, Development, and Evaluation

The Department of Energy's Light Water Reactor Sustainability Program is developing the scientific basis to ensure long-term reliability, productivity, safety, and security of the nuclear power industry in the United States. The Instrumentation, Information, and Control (II and C) pathway of the program aims to increase the role of advanced II and C technologies to achieve this objective. One of the pathway efforts at Idaho National Laboratory (INL) is to improve the work packages execution process by replacing the expensive, inefficient, bulky, complex, and error-prone paper-based work orders with automated work packages (AWPs). An AWP is an automated and dynamic presentation of the work package designed to guide the user through the work process. It is loaded on a mobile device, such as a tablet, and is capable of communicating with plant equipment and systems to acquire plant and procedure states. The AWP replaces those functions where a computer is more efficient and reliable than a human. To enable the automatic acquisition of plant data, it is necessary to design and develop a prototype platform for data exchange between the field instruments and the AWP mobile devices. The development of the platform aims to reveal issues and solutions generalizable to large-scale implementation of a similar system. Topics such as bandwidth, robustness, response time, interference, and security are usually associated with wireless communication. These concerns, along with other requirements, are listed in an earlier INL report. Specifically, the targeted issues and performance aspects in this work are relevant to the communication infrastructure from the perspective of promptness, robustness, expandability, and interoperability with different technologies. The development of a prompt system entailed significant performance optimization, including the use of parallel processing, parallel communication, modularity, noise filtering, and frequency tuning. A robust system was achieved by enforcing a persistent continuous data exchange that automatically detects and conveys a failure of any link or component in any part of the system, and that automatically restores the communication once the link or component is restored. An expandable topology was enabled by modularity and load sharing. The number of servers, mobile devices, and field instruments is not limited from a system structure point of view. The system interoperability was achieved by enforcing the independence of the field communication application from the mobile device application. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Evaluation and Intercomparison of Small Uncrewed Aircraft Systems Used for Atmospheric Research

Abstract Small uncrewed aircraft systems (sUAS) are regularly being used to conduct atmospheric research and are starting to be used as a data source for informing weather models through data assimilation. However, only a limited number of studies have been conducted to evaluate the performance of these systems and assess their ability to replicate measurements from more traditional sensors such as radiosondes and towers. In the current work, we use data collected in central Oklahoma over a 2-week period to offer insight into the performance of five different sUAS platforms and associated sensors in measuring key weather data. This includes data from three rotary-wing and two fixed-wing sUAS and included two commercially available systems and three university-developed research systems. Flight data were compared to regular radiosondes launched at the flight location, tower observations, and intercompared with data from other sUAS platforms. All platforms were shown to measure atmospheric state with reasonable accuracy, though there were some consistent biases detected for individual platforms. This information can be used to inform future studies using these platforms and is currently being used to provide estimated error covariances as required in support of assimilation of sUAS data into weather forecasting systems.

54 ENVIRONMENTAL SCIENCES↗

WindView [SWR-18-51]

The National Laboratory of the Rockies (NLR) FKA: National Renewable Energy Laboratory (NREL) and Argonne National Laboratory (ANL) developed an open-source situational awareness and decision support platform called WindView that provides grid operators with knowledge on the state and performance of wind power on their system. University Texas Dallas is contracted by NLR to create a wind power forecaster that will be integrated into WindView. WindView does not provide any data, it is a visualization platform which requires the user to provide their own data. During the three year project, there has been collaboration with industry through technical review committees and specifically the Western Area Power Authority's, WAPA's Energy Training Power Center, EPTC to develop a production-level version of WindView which will work for industry.

Gamble, Christine↗

Near Surface Leakage Monitoring for the Verification and Accounting of Geologic Carbon Sequestration Using a Field Ready 14 C Isotopic Analyzer

Results for the development of a field ready multi-isotopic analyzer for 12 CO 2 , 13 CO 2 and 14 CO 2 and applications for carbon capture and storage (CCS) containment performance are described. A design goal of the field platform was to provide isotopic data with a high data rate, a standardized reference baseline and acceptable precision (e.g., ~ ±50 per mil D 14 CO 2 ) for detection and quantification of fossil-fuel CO 2 CCS leakage scenarios. The instrument platform was not designed to replace high precision accelerator mass spectrometry. An additional goal was to combine project scale isotopic data and associated fluxes with unique financial instruments linking CCS containment performance to a publicly traded security providing project revenue to stakeholders. While the primary goals of the project were attained additional work is needed for the instrument platform and deployment within a full scale CCS site that was not available during the project timeframe.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Measuring success for a future vision: Defining impact in science gateways/virtual research environments

Scholars worldwide leverage science gateways/virtual research environments (VREs) for a wide variety of research and education endeavors spanning diverse scientific fields. Evaluating the value of a given science gateway/VRE to its constituent community is critical in obtaining the financial and human resources necessary to sustain operations and increase adoption in the user community. In this article, we feature a variety of exemplar science gateways/VREs and detail how they define impact in terms of, for example, their purpose, operation principles, and size of user base. Further, the exemplars recognize that their science gateways/VREs will continuously evolve with technological advancements and standards in cloud computing platforms, web service architectures, data management tools and cybersecurity. We also present a number of technology advances that could be incorporated in next-generation science gateways/VREs to enhance their scope and scale of their operations for greater success/impact. The exemplars are selected from owners of science gateways in the Science Gateways Community Institute (SGCI) clientele in the United States, and from the owners of VREs in the International Virtual Research Environment Interest Group (VRE-IG) of the Research Data Alliance. Thus, community-driven best practices and technology advances are compiled from diverse expert groups with an international perspective to envisage futuristic science gateway/VRE innovations.

97 MATHEMATICS AND COMPUTING↗

Assessment of online public opinions on large infrastructure projects: A case study of the Three Gorges Project in China

Public opinion becomes increasingly salient in the ex post evaluation stage of large infrastructure projects which have significant impacts to the environment and the society. However, traditional survey methods are inefficient in collection and assessment of the public opinion due to its large quantity and diversity. Recently, Social media platforms provide a rich data source for monitoring and assessing the public opinion on controversial infrastructure projects. This paper proposes an assessment framework to transform unstructured online public opinions on large infrastructure projects into sentimental and topical indicators for enhancing practices of ex post evaluation and public participation. The framework uses web crawlers to collect online comments related to a large infrastructure project and employs two natural language processing technologies, including sentiment analysis and topic modeling, with spatio-temporal analysis, to transform these comments into indicators for assessing online public opinion on the project. Based on the framework, we investigate the online public opinion of the Three Gorges Project on China's largest microblogging site, namely, Weibo. Assessment results present spatial-temporal distributions of post intensity and sentiment polarity, reveals major topics with different sentiments and summarizes managerial implications, for ex post evaluation of the world's largest hydropower project. The proposed assessment framework is expected to be widely applied as a methodological strategy to assess public opinion in the ex post evaluation stage of large infrastructure projects. - Highlights: • We developed a framework to assess online public opinion on large infrastructure projects with environmental impacts. • Indicators were built to assess post intensity, sentiment polarity and major topics of the public opinion. • We took the Three Gorges Project (TGP) as an example to demonstrate the effectiveness proposed framework. • We revealed spatial-temporal patterns of post intensity and sentiment polarity on the TGP. • We drew implications for a more in-depth understanding of the public opinion on large infrastructure projects.

54 ENVIRONMENTAL SCIENCES↗

Fast neutron background characterization with the Radiological Multi-sensor Analysis Platform (RadMAP)

In an effort to characterize the fast neutron radiation background, 16 EJ-309 liquid scintillator cells were installed in the Radiological Multi-sensor Analysis Platform (RadMAP) to collect data in the San Francisco Bay Area. Each fast neutron event was associated with specific weather metrics (pressure, temperature, absolute humidity) and GPS coordinates. Furthermore, the expected exponential dependence of the fast neutron count rate on atmospheric pressure was demonstrated and event rates were subsequently adjusted given the measured pressure at the time of detection. Pressure adjusted data was also used to investigate the influence of other environmental conditions on the neutron background rate. Using National Oceanic and Atmospheric Administration (NOAA) coastal area lidar data, an algorithm was implemented to approximate sky-view factors (the total fraction of visible sky) for points along RadMAPs route. In the three areas we analyzed, San Francisco, Downtown Oakland, and Berkeley, all demonstrated a suppression in the background rate of over 50% for the range of sky-view factors measured. This effect, which is due to the shielding of cosmic-ray produced neutrons by surrounding buildings, was comparable to the pressure influence which yielded a 32% suppression in the count rate over the range of pressures measured.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

A Blockchain-Enabled Sustainable Safety Management Framework for Connected Vehicles

The notion of an intelligent transportation system (ITS) aims to boost the performance of transportation networks, which has gained more and more traction in both academic and commercial circles. ITS is a constantly evolving vision that combines cutting-edge transportation approaches with new information, communication, computers, and other technology. ITS should discover consequence routes to enhance the sustainability, safety, and trustworthiness of the entire transportation system utilizing emerging technologies. In this paper, a sustainable safety management framework for connected vehicles is proposed by integrating blockchain. It introduces smart transportation equipment called an AI-enabled vehicle smart device (AVSD) for vehicular communications. AVSD can reduce energy consumption by decreasing the computational costs in vehicular communications. Smart contracts are used to identify vehicles automatically and establish secure communication among vehicles and emergency service stations (ESSs) like hospitals, police stations, and fire stations. The experiment results show that the proposed framework provides a communication environment for sustainable safety and security using the introduced smart transportation device. In conclusion, the proposed blockchain-enabled sustainable safety management framework has the potential to improve safety and sustainability in the transportation industry by creating a secure, decentralized, and transparent platform for managing safety data and promoting safe and sustainable driving behaviors.

42 ENGINEERING↗

Intersection of Hydrologic Change and Hydropower in the United States: Needs for Future Research and Practice

Hydropower is crucial for electric‐grid stability in the context of variable renewables but faces threats from changing hydrology. Here, we summarize the state of the science at the intersection of hydropower operations and planning, hydrologic science, and climate. We focus on the United States, outlining research, development, and training needs. Key knowledge gaps include the risk that intensification of compound extreme events poses to future generation, as well as uncertainties surrounding greenhouse gas emissions from hydropower reservoirs with relevance to hydropower's role in energy decarbonization. Quantifying such impacts and reducing uncertainty are critical where possible, but remaining irreducible or deep uncertainty will require new approaches. Future monitoring and modeling methods must provide a better understanding of the complexity inherent in large watersheds that is critical to managing both hydropower and watersheds in the context of hydrologic change. Yet, research and development will have little impact if they do not inform practice. Standardization and consolidation of platforms are essential for data, modeling, and tool translation to local scales and small operators. An enhanced industry‐academia dialog is pivotal for fostering a robust pipeline of hydropower professionals. Collaboration among researchers, policymakers, authorities, and industry stakeholders emerges as a recurring theme, highlighting the imperative for collective efforts.

13 HYDRO ENERGY↗

Cabana

Physics simulations that use particles in their algorithms are ubiquitous on modern high performance computers. Cabana is a C++ library for developing particle-based simulations on heterogeneous high performance computing platforms. Cabana provides general data structures and algorithms for common particle operations in a way that is both performant and portable on HPC systems. This includes particle data structure allocatable and configurable on GPU and CPU architectures, and threaded and distributed algorithms for sorting particles, halo exchanges, neighbor list generation, and other basic particle operations.

Slattery, StuartR↗

Hydrogen Permeation Analysis Tool

There is a rising need for the measurement and understanding of hydrogen transport properties in materials for the energy and transportation industries. The Hydrogen Permeation Analysis Tool (HyPAT) provides a user friendly interface for batch analysis of dynamic hydrogen permeation data to calculate the transport properties permeability, solubility, and diffusivity. A built in literature database provides an easy comparison to known values. A common method for measuring these hydrogen transport properties is dynamic pressure rise permeation experiments, for example, those done in the Static Gas Absorption and Permeation (SGAP) experiment at INL. Most laboratories develop individual, in-house codes for data analysis. HyPAT provides a platform that can be adopted by other user groups for such experimental analysis and significantly reduce personnel time spent performing data analysis.

Fuerst, ThomasF↗

Long-read sequencing transcriptome quantification with lr-kallisto

RNA abundance quantification has become routine and affordable thanks to high-throughput “short-read” technologies that provide accurate molecule counts at the gene level. Similarly accurate and affordable quantification of definitive full-length, transcript isoforms has remained a stubborn challenge, despite its obvious biological significance across a wide range of problems. “Long-read” sequencing platforms now produce data-types that can, in principle, drive routine definitive isoform quantification. However some particulars of contemporary long-read datatypes, together with isoform complexity and genetic variation, present bioinformatic challenges. We show here, using ONT data, that fast and accurate quantification of long-read data is possible and that it is improved by exome capture. To perform quantifications we developed lr-kallisto, which adapts the kallisto bulk and single-cell RNA-seq quantification methods for long-read technologies.

Loving, Rebekah K. (ORCID:0000000187250376)↗

Draft genome of multiple resistance donor plant Sinapis alba: An insight into SSRs, annotations and phylogenetics

Sinapis alba is a wild member of the Brassicaceae family reported to possess genetic resistance against major biotic and abiotic stresses of oilseed brassicas. However, the resistance nature of S. alba was not exploited generously due to the unavailability of usable genome sequences in public databases. Therefore, the present study was conducted to assemble the first draft genome from raw whole genome shotgun sequences with annotation and develop simple sequence repeat markers for molecular genetics and marker-assisted breeding. Results The raw genome sequences had 96x coverage on the Illumina platform with 170 Gbp data. The developed assembly by SOAPdenovo2 has ~459 Mbp genome size covered in 403,423 contigs with an average size of 1138.04 bp. The assembly was BLASTX with Arabidopsis thaliana which showed 32.9% positive hits between both plants. The top hit species distribution analysis showed the highest similarity with A. thaliana. A total of 809,597 GO level annotations were recorded after BLASTX results, and 34,012 sequences were annotated with different enzyme codes grouped under seven classes. The gene prediction tool AUGUSTUS identified 113,107 probable genes with an average size of 684 bp. The biochemical pathway annotation assigned 16,119 potential genes to 152 KEGG maps and 1751 enzyme codes. The development of potential SSRs from the de-novo assembly yielded 70731 unique primer pairs. Out of 159 randomly selected SSR markers for validation, 149 successfully amplified in S. alba. However, 10 SSR markers did not amplify during the validation experiment. Conclusion The annotated genome assembly with a large number of SSRs was developed in the present study. To the best of our knowledge, this is the first report of S. alba genome assembly development, annotation, and SSRs mining to date. The data presented here will be a very important resource for future crop improvement programs, especially for resistant breeding.

59 BASIC BIOLOGICAL SCIENCES↗

Design of the Energy Partitioning Energy Coupling (EPEC) NIF Experiment

Using scaled experiments performed at the National Ignition Facility (NIF), the Energy Partitioning Energy Coupling (EPEC) experimental platform will provide benchmark data from scaled high energy density (HED) environments to validate codes for prompt yield determination following a near surface explosion. A set of numerical codes has been used to design the experiment and predict the experimental results. Preliminary NIF shots assessing performance of the EPEC energy source (a halfraum) have been carried out. Modeling of the EPEC experiments is discussed, with comparisons to results from the source shots.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Phase II Nevada Water Resources Data, Modeling, and Visualization (DMV) Center (Final Report)

Water is unquestionably a critical resource throughout the United States. In the semi-arid west -- an area stressed by increase in human population and sprawl of the built environment -- water is the most important limiting resource. Crucially, science must understand factors that affect availability and distribution of water. To sustain growing consumptive demand, science needs to translate understanding into reliable and robust predictions of availability under weather conditions that could be average but might be extreme. These predictions are needed to support current and long-term planning. Similar to the role of weather forecast and climate prediction, water prediction over short and long temporal scales can contribute to resource strategy, governmental policy and municipal infrastructure decisions, which are arguably tied to the natural variability and unnatural change to climate. Change in seasonal and annual temperature, precipitation, snowmelt, and runoff affect the distribution of water over large temporal and spatial scales, which impact the risk of flooding and the groundwater recharge. Anthropogenic influences and impacts increase the complexity and urgency of the challenge. The goal of this project has been to develop a decision support framework of data acquisition, digital modeling, and 3D visualization. This integrated framework consists of tools for compiling, discovering and projecting our understanding of processes that control the availability and distribution of water. The framework is intended to support the analysis of the complex interactions between processes that affect water supply, from controlled availability to either scarcity or deluge. The developed framework enables DRI to promote excellence in water resource management, particularly within the Lake Tahoe basin. In principle, this framework could be replicated for other watersheds throughout the United States. Phase II of this project builds upon the research conducted during Phase I, in which the hydrologic framework was investigated and the development initiated. Phase II concentrates on practical implementation of the earlier work but emphasizes applications to the hydrology of the Lake Tahoe basin. Phase 1 efforts have been refined and extended by creating a toolset for geographic information systems (GIS) that is usable for disparate types of geospatial and geo-referenced data. The toolset is intended to serve multiple users for a variety of applications. The web portal for internet access to hydrologic and remotely sensed product data, prototyped in Phase I, has been significantly enhanced. The portal provides high performance access to LANDSAT-derived data using techniques developed during the course of the project. The portal is interactive, and supports the geo-referenced display of hydrologic information derived from remotely sensed data, such as various vegetative indices used to calculate water consumption. The platform can serve both internal and external constituencies using inter-operating infrastructure that spans both sides of the DRI firewall. The platform is intended grow its supported data assets and to serve as a template for replication to other geographic areas. An unanticipated development during the project was the use of ArcGIS software on a new computer system, called the IBM PureSytems, and the parallel use of the systems for faster, more efficient image processing. Additional data, independent of the portal, was collected within the Sagehen basin and provides detailed information regarding the processes that control hydrologic responses within mountain watersheds. The newly collected data include elevation, evapotranspiration, energy balance and remotely sensed snow-pack data. A Lake Tahoe basin hydrologic model has been developed, in part to help predict the hydrologic impacts of climate change. The model couples both the surface and subsurface hydrology, with the two components having been independently calibrated. Results from the coupled simulations involving both surface water and groundwater processes show that it is possible to fairly accurately simulate lake effects and water budget variables over a wide range of dry and wet cycles in the historical record. The Lake Tahoe basin is representative of the hydrology, topography and climate throughout the Sierra Nevada Range, and the entire model development is prototypical of the efforts required to replicate the decision support framework to other locales. The Lake Tahoe model in particular, could allow water managers to evaluate more accurately components of the water budget (ET, runoff, groundwater, etc) and to answer important questions regarding water resources in northern Nevada. This report discusses the geographic scale and the hydrologic complexity of the calibrated model developed as part of this project, as well as simulation results for historical and future climate projects To enable human-driven data exploration and discovery, de novo software for a globalized rendering module that extends the capability of our evolving custom visualization engine from Phase I (called SMEngine) has been developed. The new rendering component, called Horizon, supports terrain rendering capable of displaying and interrogating both remotely sensed and modeled data. The development of Horizon necessitated adaptation of the visualization engine to allow extensible integration of components such as the global rendering module and support for associated features. The resulting software is general in its GIS capability, but a specific Lake Tahoe visualization application suitable for immersive decision support in the DRIVE6 virtual reality facility has been developed. During the development, various features to enhance the value of the visualization experience were explored, including the use of hyperspectral image overlays. An over-arching goal of the visualization aspect of the project has been to develop and demonstrate the CAVE (CAVE Automatic Virtual Environment) as a practical tool for hydrologic research.

54 ENVIRONMENTAL SCIENCES↗

An Extensible Sensing and Control Platform for Building Energy Management

The goal of this project is to develop Mortar.io, an open-source BAS platform designed to simplify data collection, archiving, event scheduling and coordination of cross-system interactions. Mortar.io is optimized for (1) robustness to network outages, (2) ease of installation using plug-and-play and (3) scalable support for small to large buildings and campuses.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗