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DOE OSTI2023

Phosphate Limitation Responses in Marine Green Algae Are Linked to Reprogramming of the tRNA Epitranscriptome and Codon Usage Bias

Marine algae are central to global carbon fixation, and their productivity is dictated largely by resource availability. Reduced nutrient availability is predicted for vast oceanic regions as an outcome of climate change; however, there is much to learn regarding response mechanisms of the tiny picoplankton that thrive in these environments, especially eukaryotic phytoplankton. Here, we investigate responses of the picoeukaryote Micromonas commoda, a green alga found throughout subtropical and tropical oceans. Under shifting phosphate availability scenarios, transcriptomic analyses revealed altered expression of transfer RNA modification enzymes and biased codon usage of transcripts more abundant during phosphate-limiting versus phosphate-replete conditions, consistent with the role of transfer RNA modifications in regulating codon recognition. To associate the observed shift in the expression of the transfer RNA modification enzyme complement with the transfer RNAs encoded by M. commoda, we also determined the transfer RNA repertoire of this alga revealing potential targets of the modification enzymes. Codon usage bias was particularly pronounced in transcripts encoding proteins with direct roles in managing phosphate limitation and photosystem-associated proteins that have ill-characterized putative functions in “light stress.” The observed codon usage bias corresponds to a proposed stress response mechanism in which the interplay between stress-induced changes in transfer RNA modifications and skewed codon usage in certain essential response genes drives preferential translation of the encoded proteins. Collectively, we expose a potential underlying mechanism for achieving growth under enhanced nutrient limitation that extends beyond the catalog of up- or downregulated protein-encoding genes to the cell biological controls that underpin acclimation to changing environmental conditions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Effect of Ladle Usage on Cleanliness of Bearing Steel

To investigate the effects of ladle usage on the inclusions and total oxygen contents of bearing steel, MgO refractory rods with different glazes were used to simulate different ladle usages. The results show that the effects of different ladle usages on the cleanliness of the steel differ from each other. The total oxygen content of steel increases with the decreasing glaze basicity. Ladle glaze having a lower basicity has a more negative impact on the cleanliness of steel in the subsequent production. Inclusions can be generated by the flush-off of ladle glaze, and the initial glaze is important in the evolution of inclusions in the subsequent heats. To avoid the negative effect of ladle usage and to improve the steel cleanliness as much as possible, specialized ladles were suggested for producing high-quality steel grades.

36 MATERIALS SCIENCE↗

DOE OSTI2014

Video game console usage and US national energy consumption: Results from a field-metering study

There has been an increased in attention placed on the energy consumption of miscellaneous electronic loads in buildings by energy analysts and policymakers in recent years. The share of electricity consumed by consumer electronics in US households has increased in the last decade. Many devices, however, lack robust energy use data, making energy consumption estimates difficult and uncertain. Video game consoles are high-performance machines present in approximately half of all households and can consume a considerable amount of power. The precise usage of game consoles has significant uncertainty, however, leading to a wide range of recent national energy consumption estimates. We present here an analysis based on field-metered usage data, collected as part of a larger field metering study in the USA. This larger study collected data from 880 households in 2012 on a variety of devices, including 113 game consoles (the majority of which are Generation 7 consoles). From our metering, we find that although some consoles are left on nearly 24 h/day, the overall average usage is lower than many other studies have assumed, leading to a US national energy consumption estimate of 7.1 TWh in 2012. Nevertheless, there is an opportunity to reduce energy use with proper game console power management, as a substantial amount of game console usage occurs with the television turned off. The emergence of Generation 8 consoles may increase national energy consumption.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2023

Cooking methods and kitchen ventilation availability, usage, perceived performance and potential in Canadian homes

Cooking is a substantial contributor to air pollutant exposures in many residences. Effective use of kitchen ventilation can mitigate exposure; however, information on its availability, usage, and potential to increase its use across the population has been limited. This study aimed to obtain nationally representative information on cooking methods, kitchen ventilation availability and usage, and the potential for education to increase effective usage. An online survey was sent to a representative sample of Canadian homes to collect data on cooking methods, the presence and use of mechanical kitchen ventilation devices, perceived device performance, and willingness to implement mitigation strategies. Responses were weighted to match key demographic factors and analyzed using non-parametric statistics. Among the 4500 respondents, 90% had mechanical ventilation devices over the cooktop (66% of which were vented to the outside), and 30% reported regularly using their devices. Devices were used most often for deep-frying, followed by stir-frying, sautéing or pan-frying, indoor grilling, boiling or steaming. Almost half reported rarely or never using their ventilation devices during baking or oven self-cleaning. Only 10% were fully satisfied with their devices. More frequent use was associated with the device being vented to the outdoors, having more than two speed settings, quiet operation if only one speed, covering over half of the cooktop, and higher perceived effectiveness. After being informed of the benefits of kitchen ventilation, 64% indicated they would consider using their devices more often, preferentially using back burners with ventilation, and/or using higher ventilation device settings when needed. This study provides population-representative data on the most used cooking methods, kitchen ventilation availability and usage, and influencing factors in Canadian homes. Such data are needed for exposure assessments and evaluating the potential to mitigate cooking-related pollutant exposures via more effective use of kitchen ventilation. The data can be reasonably extrapolated to the United States, given the similarities in residential construction practices and cultural norms between the two countries.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2021

Genome-wide role of codon usage on transcription and identification of potential regulators

Significance Codon usage bias, the preference for certain synonymous codons, is a feature of all genomes and plays an important role in determining gene expression levels. Surprisingly, in addition to its role in mRNA translation, codon usage was recently shown to regulate gene expression at the transcriptional level. In this study, our results suggest that codon usage influences transcription genome-wide independently of its effect on translation. By carrying out a large-scale genetic screen, we identified 18 factors participating in multiple transcriptional regulatory mechanisms involved in the codon usage-mediated transcriptional effects. Together, our study establishes a foundation for future mechanistic understanding of this gene regulatory phenomenon.

Zhao, Fangzhou↗

DOE OSTI2018

Structural Comparison of Human Anti-HIV-1 gp120 V3 Monoclonal Antibodies of the Same Gene Usage Induced by Vaccination and Chronic Infection

ABSTRACT Elucidating the structural basis of antibody (Ab) gene usage and affinity maturation of vaccine-induced Abs can inform the design of immunogens for inducing desired Ab responses in HIV vaccine development. Analyses of monoclonal Abs (MAbs) encoded by the same immunoglobulin genes at different stages of maturation can help to elucidate the maturation process. We have analyzed four human anti-V3 MAbs with the same VH1-3*01 and VL3-10*01 gene usage. Two MAbs, TA6 and TA7, were developed from a vaccinee in the HIV vaccine phase I trial DP6-001 with a polyvalent DNA prime/protein boost regimen, and two others, 311-11D and 1334, were developed from HIV-infected patients. The somatic hypermutation (SHM) rates in VH of vaccine-induced MAbs are lower than in chronic HIV infection-induced MAbs, while those in VL are comparable. Crystal structures of the antigen-binding fragments (Fabs) in complex with V3 peptides show that these MAbs bind the V3 epitope with a new cradle-binding mode and that the V3 β-hairpin lies along the antigen-binding groove, which consists of residues from both heavy and light chains. Residues conserved from the germ line sequences form specific binding pockets accommodating conserved structural elements of the V3 crown hairpin, predetermining the Ab gene selection, while somatically mutated residues create additional hydrogen bonds, electrostatic interactions, and van der Waals contacts, correlating with an increased binding affinity. Our data provide a unique example of germ line sequences determining the primordial antigen-binding sites and SHMs correlating with affinity maturation of Abs induced by vaccine and natural HIV infection. IMPORTANCE Understanding the structural basis of gene usage and affinity maturation for anti-HIV-1 antibodies may help vaccine design and development. Antibodies targeting the highly immunogenic third variable loop (V3) of HIV-1 gp120 provide a unique opportunity for detailed structural investigations. By comparing the sequences and structures of four anti-V3 MAbs at different stages of affinity maturation but of the same V gene usage, two induced by vaccination and another two by chronic infection, we provide a fine example of how germ line sequence determines the essential elements for epitope recognition and how affinity maturation improves the antibody's recognition of its epitope.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Data-driven analysis to understand GPU hardware resource usage of optimizations

With heterogeneous systems, the number of GPUs per chip increases to provide computational capabilities for solving science at a nanoscopic scale. However, low utilization for single GPUs defies the need to invest more money in expensive accelerators. Although related work develops optimizations to improve application performance, none studies how these optimizations impact hardware resource usage or average GPU utilization. Here, this paper takes a data-driven analysis approach in addressing this gap by (1) characterizing how hardware resource usage affects device utilization, execution time, or both, (2) presenting a multiobjective metric to identify important application-device interactions that can be optimized to improve device utilization and application performance jointly, (3) studying hardware resource usage behaviors of several optimizations for a benchmark application, and finally (4) identifying optimization opportunities for several scientific proxy applications based on their hardware resource usage behaviors. Furthermore, we demonstrate the applicability of our methodology by applying the identified optimizations to a proxy application, which improves the execution time, device utilization, and power consumption by up to 29.6%, 5.3% and 26.5% respectively.

Computer science↗

DOE OSTI2021

Signatures of optimal codon usage in metabolic genes inform budding yeast ecology

Reverse ecology is the inference of ecological information from patterns of genomic variation. One rich, heretofore underutilized, source of ecologically relevant genomic information is codon optimality or adaptation. Bias toward codons that match the tRNA pool is robustly associated with high gene expression in diverse organisms, suggesting that codon optimization could be used in a reverse ecology framework to identify highly expressed, ecologically relevant genes. To test this hypothesis, we examined the relationship between optimal codon usage in the classic galactose metabolism ( GAL ) pathway and known ecological niches for 329 species of budding yeasts, a diverse subphylum of fungi. We find that optimal codon usage in the GAL pathway is positively correlated with quantitative growth on galactose, suggesting that GAL codon optimization reflects increased capacity to grow on galactose. Optimal codon usage in the GAL pathway is also positively correlated with human-associated ecological niches in yeasts of the CUG-Ser1 clade and with dairy-associated ecological niches in the family Saccharomycetaceae. For example, optimal codon usage of GAL genes is greater than 85% of all genes in the genome of the major human pathogen Candida albicans (CUG-Ser1 clade) and greater than 75% of genes in the genome of the dairy yeast Kluyveromyces lactis (family Saccharomycetaceae). We further find a correlation between optimization in the GAL actose pathway genes and several genes associated with nutrient sensing and metabolism. This work suggests that codon optimization harbors information about the metabolic ecology of microbial eukaryotes. This information may be particularly useful for studying fungal dark matter—species that have yet to be cultured in the lab or have only been identified by genomic material.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Hourly natural gas usage surrounding NIST NEB and NWB GHG monitoring stations in 2023

This dataset includes hourly natural gas usage surrounding two National Institute of Standards and Technology (NIST) greenhouse gas (GHG) monitoring stations, Northwest Baltimore (NWB; 39.3445°N, 76.6851°W) and Northeast Baltimore (NEB; 39.3154°N, 76.5830°W), for the year 2023 in units of therms. The gas usage was provided by the local gas distribution company and includes hourly data averaged across groups of 15 or more addresses to maintain anonymity. The hourly data was averaged spatially within a radius of 1 km from each monitoring station, including all groups containing data from any address within 1km of the monitoring station. This dataset only includes gas usage from service points equipped with advanced metering infrastructure (AMI). Between the two monitoring sites, this dataset includes usage from a total of 3649 service points, which we estimate is at least 44% of the service points in the domain.

Kenion, Helen C. R. [School of Environment and Sus↗

DOE OSTI2017

System and methods of resource usage using an interoperable management framework

Generic rights expression language allowing interoperability across different computing environments including resource usage of different applications. A formal framework for usage management provides scaffolding upon which interoperable usage management systems can be built. Certain features of the framework are standardized, such as the operational semantics, including areas free of standards that necessitate choice and innovation to achieve a balance of flexibility and usability for interoperability in usage management systems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Accounting for multi-dimensional dependencies among decision-makers within a generalized model framework: An application to understanding shared mobility service usage levels

Activity-travel choices of individuals are influenced by spatial dependency effects. As individuals interact and exchange information with, or observe the behaviors of, those in close proximity of themselves, they are likely to shape their behavioral choices accordingly. For this reason, econometric choice models that account for spatial dependency effects have been developed and applied in a number of fields, including transportation. However, spatial dependence models to date have largely defined the strength of association across behavioral units based on spatial or geographic proximity. In the current context of social media platforms and ubiquitous internet and mobile connectivity, the strength of associations among individuals is no longer solely dependent on spatial proximity. Rather, the strength of associations among individuals may be based on shared attitudes and preferences as well. In other words, behavioral choice models may benefit from defining dependency effects based on attitudinal constructs in addition to geographical constructs. In this paper, frequency of usage of car-sharing and ride-hailing services is modeled using a generalized heterogeneous data model (GHDM) framework that incorporates multi-dimensional dependencies among decision-makers. The model system is estimated on the 2014-2015 Puget Sound Regional Travel Study survey sample, with proximity in latent attitudinal constructs defined by a number of personality trait variables. Model estimation results show that social dependency effects arising from similarities in attitudes and preferences are significant in explaining shared mobility service usage. Ignoring such effects may lead to erroneous estimates of the adoption and usage of future transportation technologies and mobility services.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2020

Investigating the interconnectedness of active transportation and public transit usage as a primer for Mobility-as-a-Service adoption and deployment

With the advent of Mobility-as-a-Service packages to reduce car usage and (by extension) greenhouse gas emissions, it is crucial that researchers and practitioners consider mutual determinants and outcomes that link the adoption of multiple alternative modes. This study therefore investigates the joint usage of active travel (walking, cycling, bike-sharing) and public transit (bus, rail) modes with respect to personal and situational contexts. Online survey data (n = 826) were collected across six Midwestern U.S. states using Amazon MTurk. Respondents indicated their average weekly usage of eight travel modes across three trip purposes so that multimodality could be assessed. Several psychological constructs were extracted via (a) the stages of change framework, used to indicate willingness to adopt new behavior, and (b) confirmatory factor analysis conducted on Likert scales rooted in theories of community, identity, norms, personality, and well-being. A multiple-indicators multiple-causes structural equation model is then employed to investigate the process of adopting a modality style that incorporates active and transit modes. The model confirms that compatible physical and social contexts, as well as navigational skills and openness to learning, are key primers of multimodalism. However, a path juncture stemming from neighborhood support for mobility innovation illustrates a potential polarity in outcomes between individuals and communities. In addition, the stage of active mobility adoption is linked to identity and norm activation, offering further guidance on what influences readiness for change. The seamless integration of mobility services is critical to matching the convenience and comfort of the private vehicle; understanding potential pathways to sustainable mobility, though, requires analyses and interventions that are driven by well-being outcomes and grounded in rigorous psychological frameworks. Here, the research findings offer practical guidance for identifying intervention opportunities to be linked with MaaS enrollment while demonstrating the need to illuminate how mobility might relate to social cohesion, identity expression, and various sources of satisfaction.

42 ENGINEERING↗

DOE OSTI2013

Mining Software Usage with the Automatic Library Tracking Database (ALTD)

Tracking software usage is important for HPC centers, computer vendors, code developers and funding agencies to provide more efficient and targeted software support, and to forecast needs and guide HPC software effort towards the Exascale era. However, accurately tracking software usage on HPC systems has been a challenging task. In this paper, we present a tool called Automatic Library Tracking Database (ALTD) that has been developed and put in production on several Cray systems. The ALTD infrastructure prototype automatically and transparently stores information about libraries linked into an application at compilation time and also the executables launched in a batch job. We will illustrate the usage of libraries, compilers and third party software applications on a system managed by the National Institute for Computational Sciences.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Opportunistic Resource Usage in CMS

CMS is using a tiered setup of dedicated computing resources provided by sites distributed over the world and organized in WLCG. These sites pledge resources to CMS and are preparing them especially for CMS to run the experiment's applications. But there are more resources available opportunistically both on the GRID and in local university and research clusters which can be used for CMS applications. We will present CMS' strategy to use opportunistic resources and prepare them dynamically to run CMS applications. CMS is able to run its applications on resources that can be reached through the GRID, through EC2 compliant cloud interfaces. Even resources that can be used through ssh login nodes can be harnessed. All of these usage modes are integrated transparently into the GlideIn WMS submission infrastructure, which is the basis of CMS' opportunistic resource usage strategy. Technologies like Parrot to mount the software distribution via CVMFS and xrootd for access to data and simulation samples via the WAN are used and will be described. We will summarize the experience with opportunistic resource usage and give an outlook for the restart of LHC data taking in 2015.

Kreuzer, Peter↗

DOE OSTI2016

Extracting Baseline Electricity Usage Using Gradient Tree Boosting

To understand how specific interventions affect a process observed over time, we need to control for the other factors that influence outcomes. Such a model that captures all factors other than the one of interest is generally known as a baseline. In our study of how different pricing schemes affect residential electricity consumption, the baseline would need to capture the impact of outdoor temperature along with many other factors. In this work, we examine a number of different data mining techniques and demonstrate Gradient Tree Boosting (GTB) to be an effective method to build the baseline. We train GTB on data prior to the introduction of new pricing schemes, and apply the known temperature following the introduction of new pricing schemes to predict electricity usage with the expected temperature correction. Our experiments and analyses show that the baseline models generated by GTB capture the core characteristics over the two years with the new pricing schemes. In contrast to the majority of regression based techniques which fail to capture the lag between the peak of daily temperature and the peak of electricity usage, the GTB generated baselines are able to correctly capture the delay between the temperature peak and the electricity peak. Furthermore, subtracting this temperature-adjusted baseline from the observed electricity usage, we find that the resulting values are more amenable to interpretation, which demonstrates that the temperature-adjusted baseline is indeed effective.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2014

Commercial Building Tenant Energy Usage Aggregation and Privacy

A growing number of building owners are benchmarking their building energy use. This requires the building owner to acquire monthly whole-building energy usage information, which can be challenging for buildings in which individual tenants have their own utility meters and accounts with the utility. Some utilities and utility regulators have turned to aggregation of customer energy use data (CEUD) as a way to give building owners whole-building energy usage data while protecting customer privacy. Meter profile aggregation adds a layer of protection that decreases the risk of revealing CEUD as the number of meters aggregated increases. The report statistically characterizes the similarity between individual energy usage patterns and whole-building totals at various levels of meter aggregation.

Data aggregation,. Aggregation threhold selection↗

DOE OSTI2017

Review of Bison Usage in VERA

Bison is being used in VERA in a variety of ways; this milestone will document an independent review of the current usage of Bison and provide guidance that will improve the accuracy, performance, and consistency in the ways that Bison is used. This task will entail running a suite of small, single and multi-cycle problems with VERA-CS, followed by Bison, and Tiamat (inline) and evaluating the usage. It will also entail performing several detailed ramp to full power solutions to compare the one-way coupled solver with the fully-coupled Tiamat. This will include at least one iteration with the PHI team to incorporate some of the feedback and improve the usage. This work will also be completed in conjunction with an FMC task to evaluate the ability of Bison to model load-follow in a PWR

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

NLR HPC Facility Power Usage Effectiveness (PUE) Data

Timeseries of Energy Systems Integration Facility (ESIF) Data Center Power Usage Effectiveness (PUE) Data provided in Parquet and compressed CSV formats Power Metrics Timeseries Fields: ts: Timestamp cooling_kw: Cooling (kilowatts) - Captures the power used by fans and pipe trace heaters associated with outdoor cooling equipment. The dedicated tower filter pump power is also captured as cooling load. energy_reuse: Energy Reuse Effectiveness hvac_kw: Heating, ventilation, and air conditioning (kilowatts) - Captures fan walls, fan coils that support the data center electrical rooms, and the make-up air unit. it_power_kw: IT equipment (kilowatts) - Captures power used by the IT equipment on the data center floor. plug_and_light_kw: Lights and utility plugs (kilowatts) - Captures power associated with the data center and dedicated mechanical room. The crank-case heater for the emergency standby generator is also captured as light and plug load. pue: Power Usage Effectiveness pump_kw: Pumps (kilowatts) - Captures power from pumps that move water in the data center Energy Recover Water loop and the Tower Water loops, and also captures power used by the boost pumps that circulate water through the fan walls. Note: The tower filter pump runs constantly to filter water from the data center cooling tower system, so 2.67 kilowatts are attributed to this pump and that is not reflected in this data field. day: Day of month Outside Weather Station Timeseries Fields: ts: Timestamp outside_air_humidity: Outside air humidity - Relative humidity percent outside_air_temp: Outside air temperature - Degrees Fahrenheit day: Day of month More detail: High-Performance Computing Data Center Power Usage Effectiveness

97 MATHEMATICS AND COMPUTING↗