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spammR: an R package designed for analysis and integration of spatial multi-omic measurements

Spatial omics is a young and evolving field and as such shows rapid development of novel technologies and analysis methods to measure transcripts, proteins, metabolites, and post-translational modifications at high spatial resolution. These advances in technology have enabled the simultaneous generation of abundance profiles for multiple different omics types and associated microscopy imaging data, as well as their analysis in a spatial context. However, most analytical tools are designed for spatial transcriptomics platforms and are challenging to use in other contexts such as mass spectrometry-based measurements or metagenomics. To this end we present spammR (spatial analysis of multi-omics measurements in R), an R package that enables end-to-end analysis with a specific focus on mass-spectrometry derived spatial omics datasets with (1) smaller sample sizes and spatial sparsity of samples, (2) considerable missingness, and (3) no a-priori knowledge about proteins or genes of interest, relying on a fully data-driven approach.

spammR↗

Fine-Tuning the Accretion Disk Clock in Hercules X-1

RXTE ASM count rates from the X-ray pulsar Her X-1 began falling consistently during the late months of 2003. The source is undergoing another state transition similar to the anomalous low state of 1999. This new event has triggered observations from both space and ground-based observatories. In order to aid data interpretation and telescope scheduling, and to facilitate the phase-connection of cycles before and after the state transition, we have re-calculated the precession ephemeris using cycles over the last 3.5 years. We report that the source has displayed a different precession period since the last anomalous event. Additional archival data from CGRO suggests that each low state is accompanied by a change in precession period and that the subsequent period is correlated with accretion flux. Consequently our analysis reveals long-term accretion disk behaviour which is predicted by theoretical models of radiation-driven warping.

Still, M.↗

Simple Pattern Traffic Generation for Automated Flight Research in Non-Towered Traffic Patterns

Research efforts into autonomous air traffic will necessitate tools for testing algorithm capabilities. Testing will require flexible methods for creating large quantities of artificial data to verify the safety of automated systems. The traffic generation method in this work was developed to test traffic prediction and replanning algorithms for an autonomous vehicle attempting to land at a non-towered airport. The traffic generation method produces airport approach trajectories supporting a wide range of pattern entry types and typical pattern modification maneuvers for multiple aircraft types with varying performance capabilities. For each aircraft there are options for choosing the approach type, modifying how the approach is flown, and imposing scenario-driven temporal constraints, such as spacing between pairs of aircraft. The tool uses simplified aircraft dynamics to produce position and velocity profiles for traffic vehicles. Additionally, the tool supports standalone simulation tests or batch/bulk testing efforts, multiple output data options, and facilitates post-processing analysis.

Autonomous Vehicle↗

NASA Tech Briefs, January 2013

Topics include: Single-Photon-Sensitive HgCdTe Avalanche Photodiode Detector; Surface-Enhanced Raman Scattering Using Silica Whispering-Gallery Mode Resonators; 3D Hail Size Distribution Interpolation/Extrapolation Algorithm; Color-Changing Sensors for Detecting the Presence of Hypergolic Fuels; Artificial Intelligence Software for Assessing Postural Stability; Transformers: Shape-Changing Space Systems Built with Robotic Textiles; Fibrillar Adhesive for Climbing Robots; Using Pre-Melted Phase Change Material to Keep Payloads in Space Warm for Hours without Power; Development of a Centrifugal Technique for the Microbial Bioburden Analysis of Freon (CFC-11); Microwave Sinterator Freeform Additive Construction System (MS-FACS); DSP/FPGA Design for a High-Speed Programmable S-Band Space Transceiver; On-Chip Power-Combining for High-Power Schottky Diode-Based Frequency Multipliers; FPGA Vision Data Architecture; Memory Circuit Fault Simulator; Ultra-Compact Transputer-Based Controller for High-Level, Multi-Axis Coordination; Regolith Advanced Surface Systems Operations Robot Excavator; Magnetically Actuated Seal; Hybrid Electrostatic/Flextensional Mirror for Lightweight, Large-Aperture, and Cryogenic Space Telescopes; System for Contributing and Discovering Derived Mission and Science Data; Remote Viewer for Maritime Robotics Software; Stackfile Database; Reachability Maps for In Situ Operations; JPL Space Telecommunications Radio System Operating Environment; RFI-SIM: RFI Simulation Package; ION Configuration Editor; Dtest Testing Software; IMPaCT - Integration of Missions, Programs, and Core Technologies; Integrated Systems Health Management (ISHM) Toolkit; Wind-Driven Wireless Networked System of Mobile Sensors for Mars Exploration; In Situ Solid Particle Generator; Analysis of the Effects of Streamwise Lift Distribution on Sonic Boom Signature; Rad-Tolerant, Thermally Stable, High-Speed Fiber-Optic Network for Harsh Environments; Towed Subsurface Optical Communications Buoy; High-Collection-Efficiency Fluorescence Detection Cell; Ultra-Compact, Superconducting Spectrometer-on-a-Chip at Submillimeter Wavelengths; UV Resonant Raman Spectrometer with Multi-Line Laser Excitation; Medicine Delivery Device with Integrated Sterilization and Detection; Ionospheric Simulation System for Satellite Observations and Global Assimilative Model Experiments - ISOGAME; Airborne Tomographic Swath Ice Sounding Processing System; flexplan: Mission Planning System for the Lunar Reconnaissance Orbiter; Estimating Torque Imparted on Spacecraft Using Telemetry; PowderSim: Lagrangian Discrete and Mesh-Free Continuum Simulation Code for Cohesive Soils; Multiple-Frame Detection of Subpixel Targets in Thermal Image Sequences; Metric Learning to Enhance Hyperspectral Image Segmentation; Basic Operational Robotics Instructional System; Sheet Membrane Spacesuit Water Membrane Evaporator; Advanced Materials and Manufacturing for Low-Cost, High-Performance Liquid Rocket Combustion Chambers; Motor Qualification for Long-Duration Mars Missions.

Source record↗

Conditional diffusion machine-learning framework for mapping valence electron distribution from convergent beam electron diffraction

Quantitative convergent beam electron diffraction (CBED) enables determination of aspherical valence electron distributions through refinement of low-order structure factors, which are highly sensitive to chemical bonding and charge density variations. However, conventional quantitative CBED (QCBED) requires solving a highly nonlinear inverse problem with many coupled parameters, and computationally intensive dynamical diffraction calculations, making it time-consuming and difficult to apply to complex systems. More broadly, reconstructing charge density and orbital electron distribution from diffraction data has long been a central challenge in both x-ray and electron crystallography. Here, in this study, we introduce an artificial-intelligence (AI)-based framework that replaces traditional refinement with a data-driven inverse solver. Using a large synthetic CBED dataset generated by Bloch-wave simulations, we train a conditional diffusion model to directly infer crystal structural parameters and multipole density formalism parameters, and hence valence electron distributions, from CBED patterns alone. By learning from forward simulations across realistic parameter space, the model effectively solves the inverse problem. Compared with direct regression approaches, the diffusion-based framework provides posterior parameter distributions for rigorous uncertainty quantification while preserving quantitative fidelity and reducing analysis time by orders of magnitude. By eliminating the need for external single-crystal x-ray diffraction data and complex nonlinear refinement, this approach enables practical, high-throughput, and in situ quantitative CBED, enabling real-time mapping of valence electron distributions and their correlation with functional responses in quantum and energy materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Energy Storage Grand Challenge: Energy Storage Market Report

As part of the Department of Energy's (DOE) Energy Storage Grand Challenge (ESGC), DOE intends to synthesize and disseminate best available energy storage data, information, and analysis to inform decision-making and accelerate technology adoption. The ESGC Roadmap provides options for addressing technology development, commercialization, manufacturing, valuation, and workforce challenges to position the United States for global leadership in the energy storage technologies of the future. This report provides a baseline understanding of the numerous, dynamic energy storage markets that fall within the scope of the ESGC via an integrated presentation of deployment, investment, and manufacturing data from the best, publicly-available sources. This report covers the following energy storage technologies: lithium ion batteries, lead acid batteries, pumped storage hydropower, comrpessed air energy storage, redox flow batteries, hydrogen, building thermal energy storage, and select long duration energy storage technologies. Not all energy storage technologies and markets could be addressed in this report. Due to the wide array of energy technologies, market niches, and data availability issues, this market report only included a select group of technologies. For example, thermal energy storage technologies are very broadly defined and cover a wide range of potential markets, technology readiness levels, and primary energy sources. In other areas, data scarcity necessitates a greater understanding of future applications and emerging science. Future efforts will update data presented in this report and be expanded to include other energy storage technologies. This data-driven assessment of the current status of energy storage markets is essential to track progress toward the goals described in the Energy Storage Grand Challenge and inform the decision-making of a broad range of stakeholders. At the same time, gaps identified through the development of this report can point to areas where further data collection and analysis could provide an even greater level of understanding of the full range of markets and technologies. Finally, numerous complementary analyses are planned, underway, or completed that will provide a deeper understanding of the specific technologies and markets covered at a high-level in this report.

25 ENERGY STORAGE↗

The Diverse Data, User Driven Services and the Power of Giovanni at NASA GES DISC

This presentation provides an overview of remote sensing and model data at GES (Goddard Earth Sciences) DISC (Data and Information Services Center); Overview of data services at GES DISC (Registration with NASA data system; Searching and downloading data); Giovanni (Geospatial Interactive Online VisualizationANd aNalysis Infrastructure): online data exploration tool; and NASA Earth Data and Information System.

model↗

An automatically curated first-principles database of ferroelectrics

Ferroelectric materials have technological applications in information storage and electronic devices. The ferroelectric polar phase can be controlled with external fields, chemical substitution and size-effects in bulk and ultrathin film form, providing a platform for future technologies and for exploratory research. In this work, we integrate spin-polarized density functional theory (DFT) calculations, crystal structure databases, symmetry tools, workflow software, and a custom analysis toolkit to build a library of known, previously-proposed, and newly-proposed ferroelectric materials. With our automated workflow, we screen over 67,000 candidate materials from the Materials Project database to generate a dataset of 255 ferroelectric candidates, and propose 126 new ferroelectric materials. We benchmark our results against experimental data and previous first-principles results. The data provided includes atomic structures, output files, and DFT values of band gaps, energies, and the spontaneous polarization for each ferroelectric candidate. Finally, we contribute our workflow and analysis code to the open-source python packages atomate and pymatgen so others can conduct analogous symmetry driven searches for ferroelectrics and related phenomena.

36 MATERIALS SCIENCE↗

Enhanced Preparation for Intelligent Cybermanufacturing Systems (EPICS)

Opportunities exist for realizing transformative advances in productivity and reductions in energy footprint through ubiquitous sensing in manufacturing environments. Enhanced Preparation for Intelligent Cybermanufacturing Systems (EPICS) is a 21-month (4 academic semesters, plus one summer) experience for graduate students that focuses on scaling the knowledge, understanding and leadership skills in the cyber manufacturing area. Masters students (8/year, 32 total) complete 2-year projects on industrially-driven project topics, rotating to internships in summer semester to work on scoping and implementation at project partners. Students complete academic training in embedded systems, process modeling, data science, and cloud-based systems design. Their projects are targeted toward sensor retrofit, process monitoring, root cause analysis, and sensor fusion.

Advanced Manufacturing↗

An efficient microcomputer system for the analysis of particle image velocimetry specklegrams

An efficient image processing system is described for the automatic analysis of particle image velocimetry (PIV) fringe patterns. Each interrogation point takes 1 second to analyze; a complete specklegram can be interrogated at 1000 points in approximately 15 minutes. Incorporated in the analysis is a means for automatic replacement of spurious velocity vectors without either re-interrogation of the specklegram or interpolation between neighboring data points. The sucess of the above system is demonstrated by application of the PIV technique to the study of the sink-driven cavity flow. This flow is studied as part of a larger program to investigate trapped vortex flows as a means of lift enhancement on swept wings.

Wadcock, Alan J.↗

An Overview of the Runtime Verification Tool Java PathExplorer

We present an overview of the Java PathExplorer runtime verification tool, in short referred to as JPAX. JPAX can monitor the execution of a Java program and check that it conforms with a set of user provided properties formulated in temporal logic. JPAX can in addition analyze the program for concurrency errors such as deadlocks and data races. The concurrency analysis requires no user provided specification. The tool facilitates automated instrumentation of a program's bytecode, which when executed will emit an event stream, the execution trace, to an observer. The observer dispatches the incoming event stream to a set of observer processes, each performing a specialized analysis, such as the temporal logic verification, the deadlock analysis and the data race analysis. Temporal logic specifications can be formulated by the user in the Maude rewriting logic, where Maude is a high-speed rewriting system for equational logic, but here extended with executable temporal logic. The Maude rewriting engine is then activated as an event driven monitoring process. Alternatively, temporal specifications can be translated into efficient automata, which check the event stream. JPAX can be used during program testing to gain increased information about program executions, and can potentially furthermore be applied during operation to survey safety critical systems.

Havelund, Klaus↗

Advancing Open Science through Public-Private Partnerships

Rapid technology developments are changing the way data-driven research is performed within the science community. With the emergence of cloud computing, this has quickly become a viable approach for enabling “science at scale”. Researchers are no longer hindered by obstacles of data management and data wrangling, allowing them to quickly discover, access and perform analysis on extremely large datasets. Infrastructures that move data out of institutional silos and into a computational platform, will ensure that data and tools are accessible to all users. NASA’s Interagency Implementation and Advanced Concepts Team (IMPACT) seeks to address these rapid technology developments by establishing Space Act Agreements with selected partners from the public-private sector working in the area of cloud computing. These agreements aim to explore new opportunities with commercial cloud providers to accelerate open science and enable discovery, access and use of data sets on the cloud. In addition, they will also help establish training workshops for the science community to help researchers utilize the cloud for science. In this talk, we will present an overview of current and new partnerships we are developing to support open science and open data initiatives.

Elizabeth Fancher↗

Satellite-Based Spatiotemporal Trends in PM2.5 Concentrations: China 2004-2013

Three decades of rapid economic development is causing severe and widespread PM2.5(particulate matter (is) less than 2.5 ) pollution in China. However, research on the health impacts of PM2.5 exposure has been hindered by limited historical PM2.5 concentration data. We estimated ambient PM2.5 concentrations from 2004 to 2013 in China at 0.1 deg resolution using the most recent satellite data and evaluated model performance with available ground observations. We developed a two-stage spatial statistical model using the Moderate Resolution Imaging Spectroradiometer (MODIS) Collection 6 aerosol optical depth (AOD) and assimilated meteorology, land use data, and PM2.5 concentrations from China's recently established ground monitoring network. An inverse variance weighting (IVW) approach was developed to combine MODIS Dark Target and Deep Blue AOD to optimize data coverage. We evaluated model predicted PM2.5 concentrations from 2004 to early 2014 using ground observations. The overall model cross-validation R(sup 2) and relative prediction error were 0.79 and 35.6%, respectively. Validation beyond the model year (2013) indicated that it accurately predicted PM(sub 2.5) concentrations with little bias at the monthly (R(sup 2) = 0.73), regression slope = 0.91) and seasonal (R(sup 2) = 0.79), regression slope = 0.92) levels. Seasonal variations revealed that winter was the most polluted season and that summer was the cleanest season. Analysis of predicted PM2.5 levels showed a mean annual increase of 1.97 micro-g/cu cm between 2004 and 2007 and a decrease of 0.46 micro-g/cu cm between 2008 and 2013. Our satellite-driven model can provide reliable historical PM2.5 estimates in China at a resolution comparable to those used in epidemiologic studies on the health effects of long-term PM2.5 exposure in North America. This data source can potentially advance research on PM2.5 health effects in China.

satellite remote sensing↗

Characterizing skyrmion flow phases with principal component analysis

Principal component analysis (PCA) is a powerful method that can identify patterns in large, complex data sets by constructing low-dimensional order parameters from higher-dimensional feature vectors. There are increasing efforts to use space-and-time-dependent PCA to detect transitions in nonequilibrium systems that are difficult to characterize with equilibrium methods. Here, we demonstrate that feature vectors incorporating the position and velocity information of driven skyrmions moving through random disorder permit PCA to resolve different types of disordered skyrmion motion as a function of driving force and the ratio of the Magnus force to the dissipation. Since the Magnus force creates gyroscopic motion and a finite Hall angle, skyrmions can exhibit a greater range of flow phases than what is observed in overdamped driven systems with quenched disorder. We show that in addition to identifying previously known skyrmion flow phases, PCA detects several additional phases, including different types of channel flow, moving fluids, and partially ordered states. Guided by the PCA analysis, we further characterize the disordered flow phases to elucidate the different microscopic dynamics and show that the changes in the PCA-derived order parameters can be connected to features in bulk transport measures, including the transverse and longitudinal velocity-force curves, differential conductivity, topological defect density, and changes in the skyrmion Hall angle as a function of drive. We discuss how asymmetric feature vectors can be used to improve the resolution of the PCA analysis, and how this technique can be extended to find disordered phases in other nonequilibrium systems with time-dependent dynamics.

36 MATERIALS SCIENCE↗

RADAMS: Resilient and adaptive alert and attention management strategy against Informational Denial-of-Service (IDoS) attacks

Attacks exploiting human attentional vulnerability have posed severe threats to cybersecurity. In this work, we identify and formally define a new type of proactive attentional attacks called Informational Denial-of-Service (IDoS) attacks that generate a large volume of feint attacks to overload human operators and hide real attacks among feints. Here, we incorporate human factors (e.g., levels of expertise, stress, and efficiency) and empirical psychological results (e.g., the Yerkes-Dodson law and the sunk cost fallacy) to model the operators’ attention dynamics and their decision-making processes along with the real-time alert monitoring and inspection. To assist human operators in dismissing the feints and escalating the real attacks timely and accurately, we develop a Resilient and Adaptive Data-driven alert and Attention Management Strategy (RADAMS) that de-emphasizes alerts selectively based on the abstracted category labels of the alerts. RADAMS uses reinforcement learning to achieve a customized and transferable design for various human operators and evolving IDoS attacks. The integrated modeling and theoretical analysis lead to the Product Principle of Attention (PPoA), fundamental limits, and the tradeoff among crucial human and economic factors. Experimental results corroborate that the proposed strategy outperforms the default strategy and can reduce the IDoS risk by as much as 20%. Besides, the strategy is resilient to large variations of costs, attack frequencies, and human attention capacities. We have recognized interesting phenomena such as attentional risk equivalency, attacker’s dilemma, and the half-truth optimal attack strategy.

97 MATHEMATICS AND COMPUTING↗

Soil Moisture Buffers the Impact of Precipitation Variability on Ecosystem Productivity

Water availability governs ecosystem productivity, yet estimates of vegetation sensitivity to water can differ greatly depending on whether the sensitivity is examined spatially or temporally. In particular, the spatial sensitivity is often reported to be much stronger than temporal sensitivities, leading to highly uncertain projections of ecosystem responses to future climate change when using space-for-time substitution. The large difference between spatial and temporal sensitivities remains unexplained. Prior research, however, primarily relied on precipitation as the water availability proxy, whereas vegetation responds to soil moisture. Here, we combined satellite estimates of vegetation productivity with soil moisture data across water-limited ecosystems of the continental United States (CONUS) to identify a convergent sensitivity of productivity to water availability. Using precipitation, we show that temporal sensitivity is 66% lower than spatial sensitivity overall. Our analysis identified the cause of the difference to be primarily driven by the seasonal variability of water availability, rooting depth, and soil properties. When using soil moisture instead of precipitation, we observed widespread convergence in the spatial and temporal sensitivities—that is, the two sensitivities became much more similar in magnitude across all water-limited ecosystems within CONUS. These results show that overlooking soil hydrology can inflate perceived discrepancies between spatial and temporal vegetation sensitivities, leading to biased projections of ecosystem dynamics under future hydro-climatic change.

Wang, Huiqi [University of California, Berkeley, C↗

Tracking structural solvent reorganization and recombination dynamics following e – photoabstraction from aqueous I – with femtosecond x-ray spectroscopy and scattering

Here we present a sub-picosecond resolved investigation of the structural solvent reorganization and geminate recombination dynamics following 400 nm two-photon excitation and photodetachment of a valence p electron from the aqueous atomic solute, I–(aq). The measurements utilized time-resolved X-ray Absorption Near Edge Structure (TR-XANES) spectroscopy and X-ray Solution Scattering (TR-XSS) at the Linac Coherent Light Source x-ray free electron laser in a laser pump/x-ray probe experiment. The XANES measurements around the L 1 -edge of the generated nascent iodine atoms (I 0 ) yield an average electron ejection distance from the iodine parent of 7.4 ± 1.5 Å with an excitation yield of about 1/3 of the 0.1M NaI aqueous solution. The kinetic traces of the XANES measurement are in agreement with a purely diffusion-driven geminate iodine–electron recombination model without the need for a long-lived (I 0 :e–) contact pair. Nonequilibrium classical molecular dynamics simulations indicate a delayed response of the caging H 2 O solvent shell and this is supported by the structural analysis of the XSS data: We identify a two-step process exhibiting a 0.1 ps delayed solvent shell reorganization time within the tight H-bond network and a 0.3 ps time constant for the mean iodine–oxygen distance changes. The results indicate that most of the reorganization can be explained classically by a transition from a hydrophilic cavity with a well-ordered first solvation shell (hydrogens pointing toward I–) to an expanded cavity around I 0 with a more random orientation of the H 2 O molecules in a broadened first solvation shell.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An Applied Strategy for Using Empirical and Hybrid Models in Online Monitoring

The monitoring of plant equipment for failure prediction is one of the key contributors to operation and maintenance (O&M) costs for a nuclear power plant (NPP) because O&M monitoring depends on labor-intensive activities that are required to meet high equipment reliability standards. These activities rely primarily on humans for information gathering, condition diagnosis, and predictive analysis. Online monitoring aims to automate these activities by relying on sensors to replace human information gathering and machine learning to replace human analysis and decision making. To facilitate automated monitoring, a systematic strategy for anomaly detection is needed to optimally use the available sensor data, empirical models, and physics-supported models. This strategy is essential to provide credible reasoning on why and when an empirical (i.e., purely data-driven) versus hybrid (i.e., physics-supported) approach should be used and to determine the ideal mix of these two approaches for a defined anomaly detection scope. The extant methods usually adopt an ad hoc trial-and-error approach that, in addition to being time-consuming and costly, is also highly subjective; it is impacted by the background and the skill set of the personnel making the decisions. Thus, such an approach cannot guarantee an optimum outcome. This represents the motivation of the current research effort, which is focused on devising a scientifically supported strategy for the optimum selection of anomaly detection methods. This report presents a detailed assessment of the main anomaly detection techniques within the empirical or hybrid method streams. Empirical methods include pattern, statistical, and causal inference. Hybrid methods include the use of physics models to train and test data methods, reduce data dimensionality, reduce data-model complexity, augment data, and reduce empirical uncertainty; hybrid methods also include the use of data to tune physics models. The listed techniques within these two streams represent the vast majority of techniques performed for anomaly detection. Using the techniques as outcomes, a strategy was developed to enable a systematic decision-making process to lead to one of these techniques. The strategy is driven by key decision points related to data relevance, simple modeling feasibility, data inference, physics-modeling value, data dimensionality, physics knowledge, method of validation, performance, data availability and suitability for training and testing, cause-effect, entropy inference, and model fitting. Each of these decision points in the strategy is explained in detail in this report with examples, along with the scientific basis behind the decisions and outcomes in common and simplified terminology. The strategy is developed for use by any NPP staff with basic engineering or science knowledge. A user-friendly graphical state flow diagram was also developed as a visual presentation of the strategy. The strategy was tested and demonstrated through two pilot projects for the application of anomaly detection at an NPP. Each pilot had two use cases: an initial case in which certain decisions were made that resulted in one or more empirical techniques and a revised use case where one or more key decisions were modified resulting in using a set of hybrid methods.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗