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At least 199 records · Page 11

Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting

Single-cell multiomics provides comprehensive insights into gene regulatory networks, cellular diversity, and temporal dynamics. While tools for co-profiling single-cell genomes, transcriptomes, and epigenomes are available, accessing proteomes in parallel is more challenging. We developed nanoSPLITS (nanodroplet SPlitting for Linked-multimodal Investigations of Trace Samples), an integrated platform that enables global profiling of the transcriptome and proteome from same single cells using RNA sequencing and mass spectrometry-based proteomics, respectively. nanoSPLITS can precisely quantify over 5000 genes, 2000 proteins, and 140 phosphopeptides per single cell and identify candidate cell markers from these modalities. By exploring Cdk1-mediated cell cycle arrest, we demonstrate how nanoSPLITS single-cell multiomics can provide comprehensive cellular characterization with insights into covarying protein/gene clusters, unique phosphorylation events, and mitotic pathways.

59 BASIC BIOLOGICAL SCIENCES↗

High level cognitive information processing in neural networks

Two related research efforts were addressed: (1) high-level connectionist cognitive modeling; and (2) local neural circuit modeling. The goals of the first effort were to develop connectionist models of high-level cognitive processes such as problem solving or natural language understanding, and to understand the computational requirements of such models. The goals of the second effort were to develop biologically-realistic model of local neural circuits, and to understand the computational behavior of such models. In keeping with the nature of NASA's Innovative Research Program, all the work conducted under the grant was highly innovative. For instance, the following ideas, all summarized, are contributions to the study of connectionist/neural networks: (1) the temporal-winner-take-all, relative-position encoding, and pattern-similarity association techniques; (2) the importation of logical combinators into connection; (3) the use of analogy-based reasoning as a bridge across the gap between the traditional symbolic paradigm and the connectionist paradigm; and (4) the application of connectionism to the domain of belief representation/reasoning. The work on local neural circuit modeling also departs significantly from the work of related researchers. In particular, its concentration on low-level neural phenomena that could support high-level cognitive processing is unusual within the area of biological local circuit modeling, and also serves to expand the horizons of the artificial neural net field.

Barnden, John A.↗

The Conference Proceedings of the 2003 Air Transport Research Society (ATRS) World Conference, Volume 5

The UNO Aviation Institute Monograph Series began in 1994 as a key component of the education outreach and information transfer missions of the Aviation Institute and the NASA Nebraska Space Grant & EPSCoR Programs. The series is an outlet for aviation materials to be indexed and disseminated through an efficient medium. Publications are welcome in all aspects of aviation. Publication formats may include, but are not limited to, conference proceedings, bibliographies, research reports, manuals, technical reports, and other documents that should be archived and indexed for future reference by the aviation and world wide communities. The Conference proceedings of the 2003 Air Transport Research Society (ATRS) world conference, volume 5 is presented. The topics include: 1) The Temporal Configuration of Airline Networks in Europe; 2) Determination and Applications of Environmental Costs at Different Sized Airports-Aircraft Noise and Engine Emissions; 3) Cost Effective Measures to Reduce CO2 Emissions in the Air Freight Sector; 4) An Assessment of the Sustainability of Air Transport System: Quantification of Indicators; 5) Regulation, Competition and Network Evolution in Aviation; 6) Regulation in the Air: Price and Frequency Cap; 7) Industry Consolidation and Future Airline Network Structures in Europe; 8) Application of Core Theory to the U.S. Airline Industry; 9) Air Freight Transshipment Route Choice Analysis; 10) A Fuzzy Approach of the Competition on Air Transport Market; and 11) Developing Passenger Demand Models for International Aviation from/to Egypt: A Case Study of Cairo Airport and Egyptair.

Bowen, Brent↗

NASA Tech Briefs, November 2012

The topics include: Visual System for Browsing, Analysis, and Retrieval of Data (ViSBARD); Time-Domain Terahertz Computed Axial Tomography NDE System; Adaptive Sampling of Time Series During Remote Exploration; A Tracking Sun Photometer Without Moving Parts; Surface Temperature Data Analysis; Modular, Autonomous Command and Data Handling Software with Built-In Simulation and Test; In-Situ Wire Damage Detection System; Amplifier Module for 260-GHz Band Using Quartz Waveguide Transitions; Wideband Agile Digital Microwave Radiometer; Buckyball Nucleation of HiPco Tubes; FACT, Mega-ROSA, SOLAROSA; An Integrated, Layered-Spinel Composite Cathode for Energy Storage Applications; Engineered Multifunctional Surfaces for Fluid Handling; Polyolefin-Based Aerogels; Adjusting Permittivity by Blending Varying Ratios of SWNTs; Gravity-Assist Mechanical Simulator for Outreach; Concept for Hydrogen-Impregnated Nanofiber/Photovoltaic Cargo Stowage System; DROP: Durable Reconnaissance and Observation Platform; Developing Physiologic Models for Emergency Medical Procedures Under Microgravity; Spectroscopic Chemical Analysis Methods and Apparatus; Low Average Sidelobe Slot Array Antennas for Radiometer Applications; Motion-Corrected 3D Sonic Anemometer for Tethersondes and Other Moving Platforms; Water Treatment Systems for Long Spaceflights; Microchip Non-Aqueous Capillary Electrophoresis (MicronNACE) Method to Analyze Long-Chain Primary Amines; Low-Cost Phased Array Antenna for Sounding Rockets, Missiles, and Expendable Launch Vehicles; Mars Science Laboratory Engineering Cameras; Seismic Imager Space Telescope; Estimating Sea Surface Salinity and Wind Using Combined Passive and Active L-Band Microwave Observations; A Posteriori Study of a DNS Database Describing Super critical Binary-Species Mixing; Scalable SCPPM Decoder; QuakeSim 2.0; HURON (HUman and Robotic Optimization Network) Multi-Agent Temporal Activity Planner/Scheduler; MPST Software: MoonKommand

Source record↗

Using Machine Learning to Predict Future Temperature Outputs in Geothermal Systems

Optimizing the power output, and economic value, of geothermal power plants over decades of operation is a major challenge in renewable energy. Optimizing the output requires the ability to predict the mass flow rates and the output temperatures of production wells based on the inputs of injection wells, as well as the time history of the system. Machine Learning (ML) that incorporates the known physics of geothermal systems is one possible solution to this challenge. In this work, we explore the ability of ML algorithms to predict future temperature outputs based on historical data. Considering the challenges with obtaining an empirical dataset from field data that is large enough to enable reliable ML, we propose an alternate approach: developing a high-fidelity reservoir model and using computational resources to build a dataset that enables ML. As a first step towards achieving this goal, we present preliminary results from applying ML to predict the temperature timeseries of simple modeled geothermal systems. We describe the application of relevant state-of-the-art ML approaches, such as the Long Short-Term Memory (LSTM) networks and Convolutional Neural Networks (CNN), to extract temporal structures in the model data. We assess the accuracy of the forecasts we obtain, compare the selected approaches, and share the lessons learned that would inform the process of training and utilizing ML algorithms for larger and more complex geothermal systems.

GEOTHERMAL ENERGY↗

Gaining the most utility from our geospace observational system: Network analysis of total electron content as a means to understand space weather to the point of prediction

We present the first network analysis of interplanetary magnetic field (IMF) clock angle dependent, high-latitude, hemispheric-specific total electron content (TEC) data. We examine network parameters to describe spatio-temporal correlations in the TEC data for January 2016. We find that significant network structure exists distinguishing the dayside and nightside ionosphere, and specific features in the high-latitudes (cusp/ionospheric footpoints of magnetospheric boundary layers, polar cap, and auroral zone), and that these features vary with IMF clock angle. In this brief summary paper, we provide proof of concept results and identify important areas of future research, providing a basis for the discussion of network analysis and machine learning approaches for space weather applications.

Malik, Nishant↗

Data-driven modeling of coarse mesh turbulence for reactor transient analysis using convolutional recurrent neural networks

Advanced nuclear reactors often exhibit complex thermal-fluid phenomena during transients. To accurately capture such phenomena, a coarse-mesh three-dimensional (3-D) modeling capability is desired for modern nuclear-system code. In the coarse-mesh 3-D modeling of advanced-reactor transients that involve flow and heat transfer, accurately predicting the turbulent viscosity is a challenging task that requires an accurate and computationally efficient model to capture the unresolved fine-scale turbulence. In this work, we propose a data-driven coarse-mesh turbulence model based on local flow features for the transient analysis of thermal mixing and stratification in a sodium-cooled fast reactor. The model has a coarse mesh setup to ensure computational efficiency, while it is trained by fine-mesh computational fluid dynamics (CFD) data to ensure accuracy. A novel neural network architecture, combining a densely connected convolutional network and a long-short-term-memory network, is developed that can efficiently learn from the spatial temporal CFD transient simulation results. The neural network model was trained and optimized on a loss-of flow transient and demonstrated high accuracy in predicting the turbulent viscosity field during the whole transient. The trained model's generalization capability was also investigated on two other transients with different inlet conditions. The study demonstrates the potential of applying the proposed data-driven approach to support the coarse-mesh multi-dimensional modeling of advanced reactors.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Predicting material microstructure evolution via data-driven machine learning

The recent rapid rise in data-driven practices in the materials science domain has led to the development of efficient, generalizable, and accurate approaches for several applications, including: material property prediction, mining (micro)structure- property and (micro)structure-processing relationships, and characterization of material microstructures. Central to the materials science domain is linking microstructure to properties and performance, and critical to building such linkages is understanding how microstructures evolve as a function of environmental exposure or processing conditions (e.g., time, temperature, applied stress or strain, irradiation). This preview article summarizes recent work on the development of recurrent neural networks for predicting spatio-temporal microstructure evolution detailed by Yang et al in their manuscript entitled 'Self-supervised Learning and Prediction of Microstructure Evolution with Recurrent Neural Networks'.

machine learning (ML), materials characterization↗

Volterra network modeling of the nonlinear finite-impulse reponse of the radiation belt flux

We show how a general class of spatio-temporal nonlinear impulse-response forecast networks (Volterra networks) can be constructed from a taxonomy of nonlinear autoregressive integrated moving average with exogenous inputs (NAR-MAX) input-output equations, and used to model the evolution of energetic particle f uxes in the Van Allen radiation belts. We present initial results for the nonlinear response of the radiation belts to conditions a month earlier. The essential features of spatio-temporal observations are recovered with the model echoing the results of state space models and linear f nite impulse-response models whereby the strongest coupling peak occurs in the preceding 1-2 days. It appears that such networks hold promise for the development of accurate and fully data-driven space weather modelling, monitoring and forecast tools.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Multi-Domain Routing in Delay Tolerant Networks

The goal of Delay Tolerant Networking (DTN) is to provide the missing ingredient for the ever-growing collection of communicating nodes in our solar system to become a Solar System Internet (SSI). Great strides have been made in modeling particular types of DTNs, such as schedule- or discovery-based. Now, analogously to the Internet, these smaller DTNs can be considered routing domains which must be stitched together to form the overall SSI. In this paper, we propose a framework for cross-domain routing in DTNs as well as methodologies for detecting these sub-domains. Example time-varying networks are given to demonstrate the techniques proposed. A basic component is the mathematical theory of sheaves, which unifies the underlying model of DTN routing algorithms, by giving rise to routing sheaves – these can be defined for the dynamic and scheduled networks as noted above, and can also be used to define the interfaces between these domains in order to route across them. An immediate application would be routing across discovery-based networks connected by scheduled networks. These DTN subdomains remain elusive, however, and need to become well-defined and properly sized for tractable computability. In particular, a balance must be determined between areas that are too large (i.e. large matrix computations) versus areas that are too small (i.e. “many” single-noded domains). Moreover, the connections between the domains should, at least locally, be chosen to optimize data flow and connectivity: we address this in three ways. First, tools from persistent homology are given to understand underlying structures, reminiscent of hierarchies in the Internet Protocol (IP) addressing. Second, we construct a notion of temporal graph curvature based on network geometry to analyze flows induced by dynamical processes on these networks. Finally, Schrodinger Bridges, a tool arising from statistical physics, are proposed as a method of constructing flows on time-evolving networks with desirable properties such as speed, robustness, and load sensitivity. We construct an approach to temporal hypergraphs to simultaneously model unicast, multicast, and broadcast, using the language of scheme theory, and then consider DTN network coding as a way to achieve network-level computation and organization. The paper concludes with a discussion and ideas for future work.

Alan Hylton↗

Identifying emerging phenomenon in long temporal phenotyping experiments

Abstract Motivation The rapid improvement of phenotyping capability, accuracy and throughput have greatly increased the volume and diversity of phenomics data. A remaining challenge is an efficient way to identify phenotypic patterns to improve our understanding of the quantitative variation of complex phenotypes, and to attribute gene functions. To address this challenge, we developed a new algorithm to identify emerging phenomena from large-scale temporal plant phenotyping experiments. An emerging phenomenon is defined as a group of genotypes who exhibit a coherent phenotype pattern during a relatively short time. Emerging phenomena are highly transient and diverse, and are dependent in complex ways on both environmental conditions and development. Identifying emerging phenomena may help biologists to examine potential relationships among phenotypes and genotypes in a genetically diverse population and to associate such relationships with the change of environments or development. Results We present an emerging phenomenon identification tool called Temporal Emerging Phenomenon Finder (TEP-Finder). Using large-scale longitudinal phenomics data as input, TEP-Finder first encodes the complicated phenotypic patterns into a dynamic phenotype network. Then, emerging phenomena in different temporal scales are identified from dynamic phenotype network using a maximal clique based approach. Meanwhile, a directed acyclic network of emerging phenomena is composed to model the relationships among the emerging phenomena. The experiment that compares TEP-Finder with two state-of-art algorithms shows that the emerging phenomena identified by TEP-Finder are more functionally specific, robust and biologically significant. Availability and implementation The source code, manual and sample data of TEP-Finder are all available at: http://phenomics.uky.edu/TEP-Finder/. Supplementary information Supplementary data are available at Bioinformatics online.

Biochemistry & Molecular Biology↗

Assessment of long-term spatio-temporal radiofrequency electromagnetic field exposure

Highlights: • A year's worth of RF-EMF data is collected in an urban sensor network is analysed. • A full spatio-temporal model of the RF-EMF exposure in the study area is built. • Short-term variations of the RF-EMF exposure are collected in temporal profiles. • Models using data collected at different instants are improved by adjusting for time. As both the environment and telecommunications networks are inherently dynamic, our exposure to environmental radiofrequency (RF) electromagnetic fields (EMF) at an arbitrary location is not at all constant in time. In this study, more than a year's worth of measurement data collected in a fixed low-cost exposimeter network distributed over an urban environment was analysed and used to build, for the first time, a full spatio-temporal surrogate model of outdoor exposure to downlink Global System for Mobile Communications (GSM) and Universal Mobile Telecommunications System (UMTS) signals. Though no global trend was discovered over the measuring period, the difference in measured exposure between two instances could reach up to 42 dB (a factor 12,000 in power density). Furthermore, it was found that, taking into account the hour and day of the measurement, the accuracy of the surrogate model in the area under study was improved by up to 50% compared to models that neglect the daily temporal variability of the RF signals. However, further study is required to assess the extent to which the results obtained in the considered environment can be extrapolated to other geographic locations.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Deep convolutional neural networks for multi-scale time-series classification and application to tokamak disruption prediction using raw, high temporal resolution diagnostic data

In this paper we discuss recent advances in deep convolutional neural networks (CNN) for sequence learning, which allow identifying long-range, multi-scale phenomena in long sequences, such as those found in fusion plasmas. We point out several benefits of these deep CNN architectures, such as not requiring experts such as physicists to hand-craft input data features, the ability to capture longer range dependencies compared to the more common sequence neural networks (recurrent neural networks like long short-term memory (LSTM) networks), and the comparative computational efficiency. We apply this neural network architecture to the popular problem of disruption prediction in fusion energy tokamaks, utilizing raw data from a single diagnostic, the Electron Cyclotron Emission imaging (ECEi) diagnostic from the DIII-D tokamak. Initial results trained on a large ECEi dataset show promise, achieving an F 1 -score of ~91% on individual time-slices using only the ECEi data. This indicates the ECEi diagnostic by itself can be sensitive to a number of pre-disruption markers useful for predicting disruptions on timescales not only for mitigation but also avoidance. Future opportunities for utilizing these deep CNN architectures with fusion data are outlined, including impact of recent upgrades to the ECEi diagnostic.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

GLM Proxy Data Generation: Methods for Stroke/Pulse Level Inter-Comparison of Ground-Based Lightning Reference Networks

In order to produce useful proxy data for the GOES-R Geostationary Lightning Mapper (GLM) in regions not covered by VLF lightning mapping systems, we intend to employ data produced by ground-based (regional or global) VLF/LF lightning detection networks. Before using these data in GLM Risk Reduction tasks, it is necessary to have a quantitative understanding of the performance of these networks, in terms of CG flash/stroke DE, cloud flash/pulse DE, location accuracy, and CLD/CG classification error. This information is being obtained through inter-comparison with LMAs and well-quantified VLF/LF lightning networks. One of our approaches is to compare "bulk" counting statistics on the spatial scale of convective cells, in order to both quantify relative performance and observe variations in cell-based temporal trends provided by each network. In addition, we are using microsecond-level stroke/pulse time correlation to facilitate detailed inter-comparisons at a more-fundamental level. The current development status of our ground-based inter-comparison and evaluation tools will be presented, and performance metrics will be discussed through a comparison of Vaisala s Global Lightning Dataset (GLD360) with the NLDN at locations within and outside the U.S.

Cummins, Kenneth L.↗

Hydrologic connectivity and dynamics of solute transport in a mountain stream: Insights from a long-term tracer test and multiscale transport modeling informed by machine learning

The movement of solutes in a watershed is a complex process with multiple interactions and feedbacks across spatial and temporal scales. Modeling the dynamics of solute transport along diverse hydrologic pathways within watersheds – from hillslopes to stream channels and in and out of the hyporheic zones – is challenging but critically important, as these processes integrate and contribute to the biogeochemical functioning of the river corridor up to the river network scale. Here we use results from a long-term network-scale tracer test at the H.J. Andrews experimental forest in western Cascade Mountains, Oregon, USA to inform a multiscale framework for transport in stream corridors. The framework uses a Lagrangian-based subgrid model to represent the effects of hyporheic exchange flow and advective transport at stream network scales. The spatially and temporally resolved stream discharge needed for the transport model is imputed across the river system by an entity-aware long short-term memory network. Modeled concentrations show good agreements with the observations and exhibit power scaling laws indicative of a very wide range of timescales over which hyporheic exchange flow occurs. Our results demonstrate a data-informed modeling framework that links dynamical processes occurring at small scales to a network context to help understand how changes at reach scale cascade into network-scale effects, providing a useful tool for sustainable river basin management.

54 ENVIRONMENTAL SCIENCES↗

Forecasting high-dimensional spatio-temporal systems from sparse measurements

This paper introduces a new neural network architecture designed to forecast high-dimensional spatio-temporal data using only sparse measurements. The architecture uses a two-stage end-to-end framework that combines neural ordinary differential equations (NODEs) with vision transformers. Initially, our approach models the underlying dynamics of complex systems within a low-dimensional space; and then it reconstructs the corresponding high-dimensional spatial fields. Many traditional methods involve decoding high-dimensional spatial fields before modeling the dynamics, while some other methods use an encoder to transition from high-dimensional observations to a latent space for dynamic modeling. In contrast, our approach directly uses sparse measurements to model the dynamics, bypassing the need for an encoder. This direct approach simplifies the modeling process, reduces computational complexity, and enhances the efficiency and scalability of the method for large datasets. We demonstrate the effectiveness of our framework through applications to various spatio-temporal systems, including fluid flows and global weather patterns. Although sparse measurements have limitations, our experiments reveal that they are sufficient to forecast system dynamics accurately over long time horizons. Our results also indicate that the performance of our proposed method remains robust across different sensor placement strategies, with further improvements as the number of sensors increases. This robustness underscores the flexibility of our architecture, particularly in real-world scenarios where sensor data is often sparse and unevenly distributed.

97 MATHEMATICS AND COMPUTING↗

Statistical Evaluation of Combined Daily Gauge Observations and Rainfall Satellite Estimations over Continental South America

This paper describes a comprehensive assessment of a new high-resolution, high-quality gauge-satellite based analysis of daily precipitation over continental South America during 2004. This methodology is based on a combination of additive and multiplicative bias correction schemes in order to get the lowest bias when compared with the observed values. Inter-comparisons and cross-validations tests have been carried out for the control algorithm (TMPA real-time algorithm) and different merging schemes: additive bias correction (ADD), ratio bias correction (RAT) and TMPA research version, for different months belonging to different seasons and for different network densities. All compared merging schemes produce better results than the control algorithm, but when finer temporal (daily) and spatial scale (regional networks) gauge datasets is included in the analysis, the improvement is remarkable. The Combined Scheme (CoSch) presents consistently the best performance among the five techniques. This is also true when a degraded daily gauge network is used instead of full dataset. This technique appears a suitable tool to produce real-time, high-resolution, high-quality gauge-satellite based analyses of daily precipitation over land in regional domains.

Vila, Daniel↗

Software Development Technologies for Reactive, Real-Time, and Hybrid Systems: Summary of Research

This research is directed towards the implementation of a comprehensive deductive-algorithmic environment (toolkit) for the development and verification of high assurance reactive systems, especially concurrent, real-time, and hybrid systems. For this, we have designed and implemented the STCP (Stanford Temporal Prover) verification system. Reactive systems have an ongoing interaction with their environment, and their computations are infinite sequences of states. A large number of systems can be seen as reactive systems, including hardware, concurrent programs, network protocols, and embedded systems. Temporal logic provides a convenient language for expressing properties of reactive systems. A temporal verification methodology provides procedures for proving that a given system satisfies a given temporal property. The research covered necessary theoretical foundations as well as implementation and application issues.

Manna, Zohar↗