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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 235 records · Page 13

Autonomous hybrid optimization of a SiO 2 plasma etching mechanism

Computational modeling of plasma etching processes at the feature scale relevant to the fabrication of nanometer semiconductor devices is critically dependent on the reaction mechanism representing the physical processes occurring between plasma produced reactant fluxes and the surface, reaction probabilities, yields, rate coefficients, and threshold energies that characterize these processes. The increasing complexity of the structures being fabricated, new materials, and novel gas mixtures increase the complexity of the reaction mechanism used in feature scale models and increase the difficulty in developing the fundamental data required for the mechanism. This challenge is further exacerbated by the fact that acquiring these fundamental data through more complex computational models or experiments is often limited by cost, technical complexity, or inadequate models. In this paper, we discuss a method to automate the selection of fundamental data in a reduced reaction mechanism for feature scale plasma etching of SiO 2 using a fluorocarbon gas mixture by matching predictions of etch profiles to experimental data using a gradient descent (GD)/Nelder–Mead (NM) method hybrid optimization scheme. These methods produce a reaction mechanism that replicates the experimental training data as well as experimental data using related but different etch processes.

36 MATERIALS SCIENCE↗

DOE Voluntary Partnership Program with Utilities and Local Governments Supports the Design of New Data Access Solutions

The Better Buildings Energy Data Accelerator (BBEDA) is a unique effort that has supported 22 pairs of local governments and their utility companies to help building owners gain access to their whole-building energy data. Municipal and Utility BBEDA Partners committed to develop streamlined and easy-to-use solutions to provide whole-building energy data, especially for multitenant commercial buildings, by the end of 2015. As a result, building owners would be able to make data-driven decisions about their buildings by utilizing readily available energy consumption data for entire buildings. Traditionally, data access was difficult to implement due to technical barriers and the lack of clear value propositions for the utilities. During the past two years, BBEDA has taken a hands-on approach to overcome these barriers by offering a platform for the partners to discuss their challenges and solutions. Customized support was also provided to Partners building their local strategies. Based on the lessons learned from the partners, BBEDA developed a final toolkit with guiding documents that addressed key barriers and served as a resource for the other cities and utilities attempting to establish whole-building data access, including an exploration of opportunities to apply the whole-building data to various aspects of utility demand-side management (DSM) programs. BBEDA has been a catalyst for market transformation by addressing the upstream (to efficiency implementation) barrier of data access, demonstrated through the success of the BBEDA partners to address policy, engagement, and technical hurdles and arrive at replicable solutions to make data access a standard practice nationwide. As a result of best practices identified by the BBEDA, 18 utilities serving more than 2.6 million commercial customers nationwide will provide whole-building energy data access to building owners by 2017. This historic expansion of data accessibility will increase building energy benchmarking, the first step many building owners take to improve the energy efficiency of their buildings.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Virtual Log-Structured Storage for High-Performance Streaming

Over the past decade, given the higher number of data sources (e.g., Cloud applications, Internet of things) and critical business demands, Big Data transitioned from batch-oriented to real-time analytics. Stream storage systems, such as Apache Kafka, are well known for their increasing role in real-time Big Data analytics. For scalable stream data ingestion and processing, they logically split a data stream topic into multiple partitions. Stream storage systems keep multiple data stream copies to protect against data loss while implementing a stream partition as a replicated log. This architectural choice enables simplified development while trading cluster size with performance and the number of streams optimally managed. This paper introduces a shared virtual log-structured storage approach for improving the cluster throughput when multiple producers and consumers write and consume in parallel data streams. Stream partitions are associated with shared replicated virtual logs transparently to the user, effectively separating the implementation of stream partitioning (and data ordering) from data replication (and durability). We implement the virtual log technique in the KerA stream storage system. When comparing with Apache Kafka, KerA improves the cluster ingestion throughput by up to 4x when multiple producers write over hundreds of data streams.

consistent stream ordering↗

Parser for Sabin-to-Mahoney Transition Model of Quasispecies Replication

This code is a data parse for preparing output from the Qspp agent-based stochastic simulation model for plotting in Excel. This code is specific to a set of simulations that were run for the purpose of preparing data for a publication. It is necessary to make this code open-source in order to publish the model code (Qspp), which has already been released. There is a necessity of assuring that results from using Qspp for a publication

Ecale Zhou, Carol↗

Parser for Sabin-to-Mahoney Transition Model of Quasispecies Replication

This code is a data parse for preparing output from the Qspp agent-based stochastic simulation model for plotting in Excel. This code is specific to a set of simulations that were run for the purpose of preparing data for a publication. It is necessary to make this code open-source in order to publish the model code (Qspp), which has already been released. There is a necessity of assuring that results from using Qspp for a publication

Ecale Zhou, Carol↗

A Fault-oblivious Extreme-scale Execution Environment

Exascale computing systems will provide a thousand-fold increase in parallelism and a proportional increase in failure rate relative to today's machines. Systems software for exascale machines must provide the infrastructure to support existing applications while simultaneously enabling efficient execution of new programming models that naturally express dynamic, adaptive, irregular computation; coupled simulations; and massive data analysis in a highly unreliable hardware environment with billions of threads of execution. We propose a new approach to the data and work distribution model provided by system software based on the unifying formalism of an abstract file system. The proposed hierarchical data model provides simple, familiar visibility and access to data structures through the file system hierarchy, while providing fault tolerance through selective redundancy. The hierarchical task model features work queues whose form and organization are represented as file system objects. Data and work are both first class entities. By exposing the relationships between data and work to the runtime system, information is available to optimize execution time and provide fault tolerance. The data distribution scheme provides replication (where desirable and possible) for fault tolerance and efficiency, and it is hierarchical to make it possible to take advantage of locality. The user, tools, and applications, including legacy applications, can interface with the data, work queues, and one another through the abstract file model. This runtime environment will provide multiple interfaces to support traditional Message Passing Interface applications, languages developed under DARPA's High Productivity Computing Systems program, as well as other, experimental programming models. We will validate our runtime system with pilot codes on existing platforms and will use simulation to validate for exascale-class platforms. In this final report, we summarize research results from the work done at the Ohio State University towards the larger goals of the project listed above.

97 MATHEMATICS AND COMPUTING↗

Omics-Lethal Human Viruses, West Nile Experiment WCN002

The purpose of this experiment was to evaluate the host response to wild-type West Nile virus (WNV NY99 clone 382) and mutant (WNVE218A) virus infection. Sample data was obtained from mouse cortical neuron tissue and processed for mRNA and miRNA expression analysis. This data set comprises two complete biological replicate experiments conducted in the same conditions and with data processed independently (WCN003). Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Transcriptomics dataset downloads have a direct relationship to a primary sample submission corresponding to a specific West Nile virus infection.

59 BASIC BIOLOGICAL SCIENCES↗

H4K20me0 marks post-replicative chromatin and recruits the TONSL₋MMS22L DNA repair complex

Here, we report that after DNA replication, chromosomal processes including DNA repair and transcription take place in the context of sister chromatids. While cell cycle regulation can guide these processes globally, mechanisms to distinguish pre- and post-replicative states locally remain unknown. In this paper we reveal that new histones incorporated during DNA replication provide a signature of post-replicative chromatin, read by the human TONSL–MMS22L 1, 2, 3, 4 homologous recombination complex. We identify the TONSL ankyrin repeat domain (ARD) as a reader of histone H4 tails unmethylated at K20 (H4K20me0), which are specific to new histones incorporated during DNA replication and mark post-replicative chromatin until the G2/M phase of the cell cycle. Accordingly, TONSL–MMS22L binds new histones H3–H4 both before and after incorporation into nucleosomes, remaining on replicated chromatin until late G2/M. H4K20me0 recognition is required for TONSL–MMS22L binding to chromatin and accumulation at challenged replication forks and DNA lesions. Consequently, TONSL ARD mutants are toxic, compromising genome stability, cell viability and resistance to replication stress. Finally, together, these data reveal a histone-reader-based mechanism for recognizing the post-replicative state, offering a new angle to understand DNA repair with the potential for targeted cancer therapy.

Histone post-translational modifications↗

Both RIG-I and MDA5 detect alphavirus replication in concentration-dependent mode

Alphaviruses are a family of positive-strand RNA viruses that circulate on all continents between mosquito vectors and vertebrate hosts. Despite a significant public health threat, their biology is not sufficiently investigated, and the mechanisms of alphavirus replication and virus–host interaction are insufficiently understood. In this study, we have applied a variety of experimental systems to further understand the mechanism by which infected cells detect replicating alphaviruses. Our new data strongly suggest that activation of the antiviral response by alphavirus-infected cells is determined by the integrity of viral genes encoding proteins with nuclear functions, and by the presence of two cellular pattern recognition receptors (PRRs), RIG-I and MDA5. No type I IFN response is induced in their absence. The presence of either of these PRRs is sufficient for detecting virus replication. However, type I IFN activation in response to pathogenic alphaviruses depends on the basal levels of RIG-I or MDA5. - Highlights: • Both RIG-I and MDA5 detect alphavirus replication. • Alphavirus-induced transcriptional shutoff affects type I IFN induction. • Sensing of alphavirus replication by RIG-I and MDA5 depends on their concentrations. • High basal level of RIG-I and MDA5 allows IFN induction by pathogenic alphaviruses. • This dependence determines the discrepancy between the in vivo and in vitro data.

60 APPLIED LIFE SCIENCES↗

Galaxy–galaxy lensing with the DES-CMASS catalogue: measurement and constraints on the galaxy-matter cross-correlation

ABSTRACT The DMASS sample is a photometric sample from the DES Year 1 data set designed to replicate the properties of the CMASS sample from BOSS, in support of a joint analysis of DES and BOSS beyond the small overlapping area. In this paper, we present the measurement of galaxy–galaxy lensing using the DMASS sample as gravitational lenses in the DES Y1 imaging data. We test a number of potential systematics that can bias the galaxy–galaxy lensing signal, including those from shear estimation, photometric redshifts, and observing conditions. After careful systematic tests, we obtain a highly significant detection of the galaxy–galaxy lensing signal, with total S/N = 25.7. With the measured signal, we assess the feasibility of using DMASS as gravitational lenses equivalent to CMASS, by estimating the galaxy-matter cross-correlation coefficient rcc. By jointly fitting the galaxy–galaxy lensing measurement with the galaxy clustering measurement from CMASS, we obtain $r_{\rm cc}=1.09^{+0.12}_{-0.11}$ for the scale cut of $4 \, h^{-1}{\rm \,\,Mpc}$ and $r_{\rm cc}=1.06^{+0.13}_{-0.12}$ for $12 \, h^{-1}{\rm \,\,Mpc}$ in fixed cosmology. By adding the angular galaxy clustering of DMASS, we obtain rcc = 1.06 ± 0.10 for the scale cut of $4 \, h^{-1}{\rm \,\,Mpc}$ and rcc = 1.03 ± 0.11 for $12 \, h^{-1}{\rm \,\,Mpc}$. The resulting values of rcc indicate that the lensing signal of DMASS is statistically consistent with the one that would have been measured if CMASS had populated the DES region within the given statistical uncertainty. The measurement of galaxy–galaxy lensing presented in this paper will serve as part of the data vector for the forthcoming cosmology analysis in preparation.

79 ASTRONOMY AND ASTROPHYSICS↗

A metagenomic survey of forest soil microbial communities more than a decade after timber harvesting

The scarcity of long-term data on soil microbial communities in the decades following timber harvesting limits current understanding of the ecological problems associated with maintaining the productivity of managed forests. The high complexity of soil communities and the heterogeneity of forest and soil necessitates a comprehensive approach to understand the role of microbial processes in managed forest ecosystems. Here, we describe a curated collection of well replicated, multi-faceted data from eighteen reforested sites in six different North American ecozones within the Long-term Soil Productivity (LTSP) Study, without detailed analysis of results or discussion. The experiments were designed to contrast microbial community composition and function among forest soils from harvested treatment plots with varying intensities of organic matter removal. The collection includes 724 bacterial (16S) and 658 fungal (ITS2) amplicon libraries, 133 shotgun metagenomic libraries as well as stable isotope probing amplicon libraries capturing the effects of harvesting on hemicellulolytic and cellulolytic populations. This collection serves as a foundation for the LTSP Study and other studies of the ecology of forest soil and forest disturbance.

54 ENVIRONMENTAL SCIENCES↗

Requirements for a global data infrastructure in support of CMIP6

The World Climate Research Programme (WCRP)'s Working Group on Climate Modelling (WGCM) Infrastructure Panel (WIP) was formed in 2014 in response to the explosive growth in size and complexity of Coupled Model Intercomparison Projects (CMIPs) between CMIP3 (2005–2006) and CMIP5 (2011–2012). This article presents the WIP recommendations for the global data infrastructure needed to support CMIP design, future growth, and evolution. Developed in close coordination with those who build and run the existing infrastructure (the Earth System Grid Federation; ESGF), the recommendations are based on several principles beginning with the need to separate requirements, implementation, and operations. Other important principles include the consideration of the diversity of community needs around data – a data ecosystem – the importance of provenance, the need for automation, and the obligation to measure costs and benefits. This paper concentrates on requirements, recognizing the diversity of communities involved (modelers, analysts, software developers, and downstream users). Such requirements include the need for scientific reproducibility and accountability alongside the need to record and track data usage. One key element is to generate a dataset-centric rather than system-centric focus, with an aim to making the infrastructure less prone to systemic failure. With these overarching principles and requirements, the WIP has produced a set of position papers, which are summarized in the latter pages of this document. They provide specifications for managing and delivering model output, including strategies for replication and versioning, licensing, data quality assurance, citation, long-term archiving, and dataset tracking. They also describe a new and more formal approach for specifying what data, and associated metadata, should be saved, which enables future data volumes to be estimated, particularly for well-defined projects such as CMIP6. The paper concludes with a future facing consideration of the global data infrastructure evolution that follows from the blurring of boundaries between climate and weather, and the changing nature of published scientific results in the digital age.

54 ENVIRONMENTAL SCIENCES↗

A Deep Learning Approach for TNC Trip Demand Prediction Considering Spatial-Temporal Features: Preprint

Ride-hailing or transportation network companies (TNCs), such as Uber, Lyft, DiDi Chuxing, or RideAustin, are emerging as a new and disruptive on-demand mobility service in recent years. However, the methods for developing predictive analytics to explore the nature and dynamics of TNCs across cities in the United States are still nascent due to the lack of publicly available data. Recently available public datasets on TNCs by RideAustin offer a unique opportunity to examine spatial, temporal, environmental, and special event factors associated with TNC trip demand. This study explores the use of a deep learning approach - Long Short-Term Memory (LSTM) - to predict TNC trip demand at the ZIP Code level using data from Austin, Texas. The analysis includes key predictive factors such as time of day, day of week, precipitation, and temperature, indicating their corresponding associations with TNC trip demand. Results from initial analysis show that LSTM is able to predict the TNC trip demand for the upcoming hour accurately. LSTM, when compared to other prediction methods, such as historical average and instantaneous trip demand, reduces the mean absolute error (MAE) of the model predictions by 37% and 24%, respectively. This novel method offers significant potential for scaling up and/or replicability across cities where data are available for understanding TNC trip demand to inform emerging mobility system operators. Predicting trip demand can help TNC drivers make informed decisions on how to be more efficient by maximizing passenger pickups and minimizing wait times and deadheading.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Pitfalls in Prediction Modeling for Normal Tissue Toxicity in Radiation Therapy: An Illustration With the Individual Radiation Sensitivity and Mammary Carcinoma Risk Factor Investigation Cohorts

Purpose: To identify the main causes underlying the failure of prediction models for radiation therapy toxicity to replicate. Methods and Materials: Data were used from two German cohorts, Individual Radiation Sensitivity (ISE) (n=418) and Mammary Carcinoma Risk Factor Investigation (MARIE) (n=409), of breast cancer patients with similar characteristics and radiation therapy treatments. The toxicity endpoint chosen was telangiectasia. The LASSO (least absolute shrinkage and selection operator) logistic regression method was used to build a predictive model for a dichotomized endpoint (Radiation Therapy Oncology Group/European Organization for the Research and Treatment of Cancer score 0, 1, or ≥2). Internal areas under the receiver operating characteristic curve (inAUCs) were calculated by a naïve approach whereby the training data (ISE) were also used for calculating the AUC. Cross-validation was also applied to calculate the AUC within the same cohort, a second type of inAUC. Internal AUCs from cross-validation were calculated within ISE and MARIE separately. Models trained on one dataset (ISE) were applied to a test dataset (MARIE) and AUCs calculated (exAUCs). Results: Internal AUCs from the naïve approach were generally larger than inAUCs from cross-validation owing to overfitting the training data. Internal AUCs from cross-validation were also generally larger than the exAUCs, reflecting heterogeneity in the predictors between cohorts. The best models with largest inAUCs from cross-validation within both cohorts had a number of common predictors: hypertension, normalized total boost, and presence of estrogen receptors. Surprisingly, the effect (coefficient in the prediction model) of hypertension on telangiectasia incidence was positive in ISE and negative in MARIE. Other predictors were also not common between the 2 cohorts, illustrating that overcoming overfitting does not solve the problem of replication failure of prediction models completely. Conclusions: Overfitting and cohort heterogeneity are the 2 main causes of replication failure of prediction models across cohorts. Cross-validation and similar techniques (eg, bootstrapping) cope with overfitting, but the development of validated predictive models for radiation therapy toxicity requires strategies that deal with cohort heterogeneity.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Iron Isotope Fractionation during Fe(II) Oxidation Mediated by the Oxygen-Producing Marine Cyanobacterium Synechococcus PCC 7002

In this study, we couple iron isotope analysis to microscopic and mineralogical investigation of iron speciation during circumneutral Fe(II) oxidation and Fe(III) precipitation with photosynthetically produced oxygen. In the presence of the cyanobacterium Synechococcus PCC 7002, aqueous Fe(II) (Fe(II) aq ) is oxidized and precipitated as amorphous Fe(III) oxyhydroxide minerals (iron precipitates, Fe ppt ), with distinct isotopic fractionation (ε 56 Fe) values determined from fitting the δ 56 Fe(II) aq (1.79‰ and 2.15‰) and the δ 56 Fe ppt (2.44‰ and 2.98‰) data trends from two replicate experiments. Additional Fe(II) and Fe(III) phases were detected using microscopy and chemical extractions and likely represent Fe(II) and Fe(III) sorbed to minerals and cells. The iron desorbed with sodium acetate (FeNaAc) yielded heavier δ 56 Fe compositions than Fe(II) aq . Modeling of the fractionation during Fe(III) sorption to cells and Fe(II) sorption to Feppt, combined with equilibration of sorbed iron and with Fe(II) aq using published fractionation factors, is consistent with our resulting δ 56 FeNaAc. The δ 56 Fe ppt data trend is inconsistent with complete equilibrium exchange with Fe(II)aq. Because of this and our detection of microbially excreted organics (e.g., exopolysaccharides) coating Feppt in our microscopic analysis, we suggest that electron and atom exchange is partially suppressed in this system by biologically produced organics. These results indicate that cyanobacteria influence the fate and composition of iron in sunlit environments via their role in Fe(II) oxidation through O 2 production, the capacity of their cell surfaces to sorb iron, and the interaction of secreted organics with Fe(III) minerals.

54 ENVIRONMENTAL SCIENCES↗

A Factorial Data Rate and Dwell Time Experiment in the National Transonic Facility

This report is an introductory tutorial on the application of formal experiment design methods to wind tunnel testing, for the benefit of aeronautical engineers with little formal experiment design training. It also describes the results of a Study to determine whether increases in the sample rate and dwell time of the National Transonic Facility data system Would result in significant changes in force and moment data. Increases in sample rate from 10 samples per second to 50 samples per second were examined, as were changes in dwell time from one second per data point to two seconds. These changes were examined for a representative aircraft model in a range of tunnel operating conditions defined by angles of attack from 0 deg to 3.8 degrees, total pressure from 15.0 psi to 24.1 psi, and Mach numbers from 0.52 to 0.82. No statistically significant effect was associated with the change in sample rate. The change in dwell time from one second to two seconds affected axial force measurements, and to a lesser degree normal force measurements. This dwell effect comprises a "rectification error" caused by incomplete cancellation of the positive and negative elements of certain low frequency dynamic components that are not rejected by the one-Hz low-pass filters of the data system. These low frequency effects may be due to tunnel circuit phenomena and other sources. The magnitude of the dwell effect depends on dynamic pressure, with angle of attack and Mach number influencing the strength of this dependence. An analysis is presented which suggests that the magnitude of the rectification error depends on the ratio of measurement dwell time to the period of the low-frequency dynamics, as well as the amplitude of the dynamics The essential conclusion of this analysis is that extending the dwell time (or, equivalently, replicating short-dwell data points) reduces the rectification error.

DeLoach, R.↗

Sentinel-1 Input Data for PSInSAR Analysis

Files used to perform the Persistent Scatterer InSAR analysis with SARPROZ. The data is sourced from ESAs Sentinel-1 project and covers Brady Hot Springs and Desert Peak geothermal areas. The original titles are included for the Sentinel-1 data. The naming guide is included as a link in this submission. The data contains SAR (Radar) data from the Sentinel 1A satellite between July 2017 and December 2019. The data is necessary to replicate our results, and can be used for further PSInSAR, DInSAR and other modern interferometric analyses to determine line of sight, vertical and, possibly, East-West horizontal displacement. These displacement analysis show the soil deformation in time (including average displacement velocity), which can be used to indicate subsoil phenomena: temperature changes, subsidence, uplift, and inform other analyses like seismicity and porosity.

15 GEOTHERMAL ENERGY↗

Reynolds-number scaling of wall-pressure–velocity correlations in wall-bounded turbulence

Wall-pressure fluctuations are a practically robust input for real-time control systems aimed at modifying wall-bounded turbulence. The scaling behaviour of the wall-pressure–velocity coupling requires investigation to properly design a controller with such input data so that it can actuate upon the desired turbulent structures. A comprehensive database from direct numerical simulations (DNS) of turbulent channel flow is used for this purpose, spanning a Reynolds-number range$Re_\tau \approx 550\unicode{x2013}5200$. Spectral analysis reveals that the streamwise velocity is most strongly coupled to the linear term of the wall pressure, at a Reynolds-number invariant distance-from-the-wall scaling of$\lambda _x/y \approx 14$(and$\lambda _x/y \approx 8$for the wall-normal velocity). When extending the analysis to both homogeneous directions in$x$and$y$, the peak coherence is centred at$\lambda _x/\lambda _z \approx 2$and$\lambda _x/\lambda _z \approx 1$for$p_w$and$u$, and$p_w$and$v$, respectively. A stronger coherence is retrieved when the quadratic term of the wall pressure is concerned, but there is only little evidence for a wall-attached-eddy type of scaling. An experimental dataset comprising simultaneous measurements of wall pressure and velocity complements the DNS-based findings at one value of$Re_\tau \approx 2$k, with ample evidence that the DNS-inferred correlations can be replicated with experimental pressure data subject to significant levels of (acoustic) facility noise. It is furthermore shown that velocity-state estimations can be achieved with good accuracy by including both the linear and quadratic terms of the wall pressure. An accuracy of up to 72 % in the binary state of the streamwise velocity fluctuations in the logarithmic region is achieved; this corresponds to a correlation coefficient of$\approx$0.6. This thus demonstrates that wall-pressure sensing for velocity-state estimation – e.g. for use in real-time control of wall-bounded turbulence – has merit in terms of its realization at a range of Reynolds numbers.

Mechanics↗