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At least 739 records · Page 41

Identification of a novel nematotoxic protein by challenging the model mushroom Coprinopsis cinerea with a fungivorous nematode

The dung of herbivores, the natural habitat of the model mushroom Coprinopsis cinerea, is a nutrient-rich but also very competitive environment for a saprophytic fungus. Previously we showed that C. cinerea expresses constitutive, tissue-specific armories against antagonists such as animal predators and bacterial competitors. In order to dissect the inducible armories against such antagonists, we sequenced the poly(A)-positive transcriptome of C. cinerea vegetative mycelium upon challenge with fungivorous and bacterivorous nematodes, Gram-negative and Gram-positive bacteria and mechanical damage. As a response to the fungivorous nematode Aphelenchus avenae, C. cinerea was found to specifically induce the transcription of several genes encoding previously characterized nematotoxic lectins. In addition, a previously not characterized gene encoding a cytoplasmic protein with several predicted Ricin B-fold domains, was found to be strongly up-regulated under this condition. Functional analysis of the recombinant protein revealed a high toxicity towards the bacterivorous nematode Caenorhabditis elegans. Challenge of the mycelium with A. avenae also lead to the induction of several genes encoding putative antibacterial proteins. Some of these genes were also induced upon challenge of the mycelium with the bacteria Escherichia coli and Bacillus subtilis. Lastly, these results suggest that fungi have the ability to induce specific innate defense responses similar to plants and animals.

59 BASIC BIOLOGICAL SCIENCES↗

Progress Report on Identification and Resolution of Gaps in Mechanistic Source Term Modeling for Molten Salt Reactors

This report summarizes FY23 activities to improve mechanistic source term modeling for MSR concepts. Relevant MELCOR capability enhancements made during FY23 are summarized including development of a flexible python-based EOS generator (MELEOS), porous domain modeling capabilities for validation applications, and development of a MELCOR model for the LSTL facility in anticipation of upcoming molten salt experiments.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3

In oligotrophic ocean waters where bacteria are often subjected to chronic nutrient limitation, community transcriptome sequencing has pointed to the presence of highly abundant small RNAs (sRNAs). The role of sRNAs in regulating response to nutrient stress was investigated in a model heterotrophic marine bacterium Ruegeria pomeroyi grown in continuous culture under carbon (C) and nitrogen (N) limitation. RNAseq analysis identified 99 putative sRNAs. Sixty-nine were cis-encoded and located antisense to a presumed target gene. Thirty were trans-encoded and initial target prediction was performed computationally. The most prevalent functional roles of genes anti-sense to the cis-sRNAs were transport, cell-cell interactions, signal transduction, and transcriptional regulation. Most sRNAs were transcribed equally under both C and N limitation, and may be involved in a general stress response. However, 14 were regulated differentially between the C and N treatments and may respond to specific nutrient limitations. A network analysis of the predicted target genes of the R. pomeroyi cis-sRNAs indicated that they average fewer connections than typical protein-encoding genes, and appear to be more important in peripheral or niche-defining functions encoded in the pan genome.

59 BASIC BIOLOGICAL SCIENCES↗

Identification of state variables and dynamic inflow from rotor model dynamic tests

The paper describes methods for extracting unknown state variables and parameters from dynamic rotor model tests given transient cyclic pitch stirring inputs, blade root flap-bending measurements, and the form of the dynamic rotor equations, including a rotor dynamic inflow description, when none of the physical parameters are known. A simplified version of the maximum likelihood method seems best suited for this purpose. The measurement equation error covariance matrix is assumed constant during each iteration, but updated for the subsequent iteration. A detailed analysis of the suitability of the derived techniques for studying various rotor dynamic inflow effects is provided.

Banerjee, D.↗

Report of the Subpanel on Error Characterization and Error Budgets

The state of knowledge of both user positioning requirements and error models of current and proposed satellite systems is reviewed. In particular the error analysis models for LANDSAT D are described. Recommendations are given concerning the geometric error model for the thematic mapper; interactive user involvement in system error budgeting and modeling and verification on real data sets; and the identification of a strawman mission for modeling key error sources.

Source record↗

Identification of the prooxidant site of human ceruloplasmin: a model for oxidative damage by copper bound to protein surfaces

Free transition metal ions oxidize lipids and lipoproteins in vitro; however, recent evidence suggests that free metal ion-independent mechanisms are more likely in vivo. We have shown previously that human ceruloplasmin (Cp), a serum protein containing seven Cu atoms, induces low density lipoprotein oxidation in vitro and that the activity depends on the presence of a single, chelatable Cu atom. We here use biochemical and molecular approaches to determine the site responsible for Cp prooxidant activity. Experiments with the His-specific reagent diethylpyrocarbonate (DEPC) showed that one or more His residues was specifically required. Quantitative [14C]DEPC binding studies indicated the importance of a single His residue because only one was exposed upon removal of the prooxidant Cu. Plasmin digestion of [14C]DEPC-treated Cp (and N-terminal sequence analysis of the fragments) showed that the critical His was in a 17-kDa region containing four His residues in the second major sequence homology domain of Cp. A full length human Cp cDNA was modified by site-directed mutagenesis to give His-to-Ala substitutions at each of the four positions and was transfected into COS-7 cells, and low density lipoprotein oxidation was measured. The prooxidant site was localized to a region containing His426 because CpH426A almost completely lacked prooxidant activity whereas the other mutants expressed normal activity. These observations support the hypothesis that Cu bound at specific sites on protein surfaces can cause oxidative damage to macromolecules in their environment. Cp may serve as a model protein for understanding mechanisms of oxidant damage by copper-containing (or -binding) proteins such as Cu, Zn superoxide dismutase, and amyloid precursor protein.

NASA Discipline Regulatory Physiology↗

Advanced WEC Dynamics and Controls, Test 1

Numerous studies have shown that advanced control of a wave energy converter's (WEC's) power take off (PTO) can provide significant increases (on the order of 200-300%) in WEC energy absorption. Transitioning these control approaches from simplified paper studies to application in full-scale devices remains an open and extremely challenging problem will be central to creating economically competitive WECs and delivering clean renewable energy to the US electrical grid. The Advanced WEC Dynamics and Controls project is targeted on assisting WEC developers to apply novel control systems for their devices and thus achieving major increases in performance and economic viability. The success of any control strategy is based directly upon the availability of a reduced-order model with the ability to accurately capture the dynamics of the system with sufficient accuracy. A model-scale WEC was designed and fabricated for use in studies to advance the state-of-the-art in WEC controls. This test, which is the first in a series of planned tests, focused on system identification (system ID) and model validation.

16 TIDAL AND WAVE POWER↗

ClimateNet: an expert-labeled open dataset and deep learning architecture for enabling high-precision analyses of extreme weather

Abstract. Identifying, detecting, and localizing extreme weather events is a crucial first step in understanding how they may vary under different climate change scenarios. Pattern recognition tasks such as classification, object detection, and segmentation (i.e., pixel-level classification) have remained challenging problems in the weather and climate sciences. While there exist many empirical heuristics for detecting extreme events, the disparities between the output of these different methods even for a single event are large and often difficult to reconcile. Given the success of deep learning (DL) in tackling similar problems in computer vision, we advocate a DL-based approach. DL, however, works best in the context of supervised learning – when labeled datasets are readily available. Reliable labeled training data for extreme weather and climate events is scarce. We create “ClimateNet” – an open, community-sourced human-expert-labeled curated dataset that captures tropical cyclones (TCs) and atmospheric rivers (ARs) in high-resolution climate model output from a simulation of a recent historical period. We use the curated ClimateNet dataset to train a state-of-the-art DL model for pixel-level identification – i.e., segmentation – of TCs and ARs. We then apply the trained DL model to historical and climate change scenarios simulated by the Community Atmospheric Model (CAM5.1) and show that the DL model accurately segments the data into TCs, ARs, or “the background” at a pixel level. Further, we show how the segmentation results can be used to conduct spatially and temporally precise analytics by quantifying distributions of extreme precipitation conditioned on event types (TC or AR) at regional scales. The key contribution of this work is that it paves the way for DL-based automated, high-fidelity, and highly precise analytics of climate data using a curated expert-labeled dataset – ClimateNet. ClimateNet and the DL-based segmentation method provide several unique capabilities: (i) they can be used to calculate a variety of TC and AR statistics at a fine-grained level; (ii) they can be applied to different climate scenarios and different datasets without tuning as they do not rely on threshold conditions; and (iii) the proposed DL method is suitable for rapidly analyzing large amounts of climate model output. While our study has been conducted for two important extreme weather patterns (TCs and ARs) in simulation datasets, we believe that this methodology can be applied to a much broader class of patterns and applied to observational and reanalysis data products via transfer learning.

54 ENVIRONMENTAL SCIENCES↗

Model correlation and damage location for large space truss structures: Secant method development and evaluation

On-orbit testing of a large space structure will be required to complete the certification of any mathematical model for the structure dynamic response. The process of establishing a mathematical model that matches measured structure response is referred to as model correlation. Most model correlation approaches have an identification technique to determine structural characteristics from the measurements of the structure response. This problem is approached with one particular class of identification techniques - matrix adjustment methods - which use measured data to produce an optimal update of the structure property matrix, often the stiffness matrix. New methods were developed for identification to handle problems of the size and complexity expected for large space structures. Further development and refinement of these secant-method identification algorithms were undertaken. Also, evaluation of these techniques is an approach for model correlation and damage location was initiated.

Smith, Suzanne Weaver↗

Discovering State-Parameter Mappings in Subsurface Models Using Generative Adversarial Networks

A fundamental problem in geophysical modeling is related to the identification and approximation of causal structures among physical processes. However, resolving the bidirectional mappings between physical parameters and model state variables (i.e., solving the forward and inverse problems) is challenging, especially when parameter dimensionality is high. Deep learning has opened a new door toward knowledge representation and complex pattern identification. In particular, the recently introduced generative adversarial networks (GANs) hold strong promises in learning cross-domain mappings for image translation. This study presents a state-parameter identification GAN (SPID-GAN) for simultaneously learning bidirectional mappings between a high-dimensional parameter space and the corresponding model state space. SPID-GAN is demonstrated using a series of representative problems from subsurface flow modeling. Results show that SPID-GAN achieves satisfactory performance in identifying the bidirectional state-parameter mappings, providing a new deep-learning-based, knowledge representation paradigm for a wide array of complex geophysical problems.

58 GEOSCIENCES↗

Advanced WEC Dynamics & Controls FY16 Testing Report

A model-scale wave tank test was conducted in the interest of improving control systems design of wave energy converters (WECs). The success of most control strategies is based directly upon the availability of a reduced-order model with the ability to capture the dynamics of the system with sufficient accuracy. For this reason, the test described in this report, which is the first in a series of planned tests on WEC controls, focused on system identification (system ID) and model validation.

42 ENGINEERING↗

Affinity propagation clustering of full-field, high-spatial-dimensional measurements for robust output-only modal identification: A proof-of-concept study

Determination of the model order is a challenging problem in system identification, especially in output-only or operational modal identification where some modes are weakly excited. While existing methods such as the stabilization diagram method (spectral information) are effective, they do not scale to high-dimensional data, which is usually needed for high-fidelity characterization of structural dynamics and has been made available in the emerging full-field measurement techniques using optical methods such as photogrammetry and laser vibrometers. In this proof-of-concept study we present a new non-parametric, data-driven approach for robust output-only identification of high-spatial-dimensional modal parameters of basic structures by efficiently processing and interactively exploiting the full-field measurement (i.e., very dense spatial measurement points). Specifically, we first over-estimate the system model once, producing a pool of candidate modes associated with their modal frequencies and full-field, high-spatial-dimensional mode shapes. This is accomplished by a data-driven method termed affinity propagation clustering (APC), where the active clusters, which are the active modes in our formulations, emerge from the "message-passing" procedure and does not require a pre-determination of the cluster number (mode or model order). Next, rather than using the spectral information to distinguish the physical and spurious modes in the stabilization diagram method, we exploit and visualize the spatial, full-field mode shape associated with each candidate mode to do so. We conduct extensive experiments on basic structural models with comparisons to a few existing methods. The results indicate that the new method is computationally efficient for identifying high-spatial-dimensional modal parameters, and robust to identify weak modes by exploiting the full-field measurement. We also discuss its applicability and limitations for structures with complex geometry (shapes).

42 ENGINEERING↗

Online Static Load Model Estimation in Distribution Systems: Preprint

The paper focuses on parameter identification for time varying voltage dependent polynomial load models, namely the constant impedance (Z), constant current (I), and constant power (P), in the distribution systems. Typically, parameter identification has been done for aggregated loads at substations for the transmission planning studies. Given the higher voltage volatility faced by active distribution systems, this paper takes the load model estimation to the distribution networks. The paper assumes the presence of measurements at the distribution nodes from various sources, each at varying temporal resolutions. Least squares estimation (LSE) method with bounded variables is used to convert the measurements into ZIP parameter estimations for loads at various locations of the feeder. The results and discussions focus on some of the estimation issues faced in a distribution system due to varying voltage sensitivities of loads along a feeder, measurement resolution, impact of window size and sampling rate of measurement data, and the use of dynamic simulations to create synthetic measurement data in the absence of real ones.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Non-disruptive error field identification based on magnetic island healing

Here a technique to identify intrinsic error fields (EFs) in tokamaks with minimized risk of disruption is demonstrated on the DIII-D tokamak. The method extends the conventional driven magnetic island ‘compass scan’ approach by modifying asynchronous control waveforms to enable prompt healing of the island instability. Healing of the island is achieved by reducing the imposed non-axisymmetric coil current and raising the density (here via gas fueling). The method is also shown to support multiple island threshold measurements per pulse, thus reducing the number of dedicated pulses necessary to conduct an EF identification. Non-linear modeling with the TM1 code reproduces the experimental results and approximately recovers the critical density required for island healing. Island healing is explained in the non-linear modeling by an increase in the viscous coupling between the static island and the nearby flowing plasma, thus healing the island as it accelerates into the plasma frame. Due to both simplicity and risk minimization, this technique is suitable for plasma-based EF identification in the early commissioning stages of future disruption-averse tokamaks such as ITER and SPARC.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Reduced-Order Aerodynamic Modeling Based on CFD Frequency Responses from Multisine Inputs

A system identification analysis was performed to determine reduced-order models of a computational fluid dynamics (CFD) solver for linear aeroelastic analysis and control design. The application was to the FUN3D code and the flexible half-span wind tunnel test article, in transonic flow conditions, used in the NASA-Boeing collaboration called the Integrated Adaptive Wing Technology Maturation (IAWTM) project. Multiple inputs (structural mode displacements and control surface deflections) were simultaneously excited with orthogonal phase-optimized multisines and multiple outputs (generalized aerodynamic forces) were recorded, from which the matrix of frequency responses were computed using a single CFD run. A state-space model was then fit to the frequency response data using a maximum-likelihood estimator.

System identification↗

Simulation of the Impact of Point Defects and Edge Dislocations on X-Ray Diffraction in Hexagonal (Ni,Co) 1+2 x Ti 1– x O 3 Thin Films

In this work, a computer code for simulating high-resolution X-ray diffraction (XRD) data from disordered crystals with arbitrary spatial composition and local lattice parameters is developed. Simulated patterns are compared with the experimental data collected on a single phase, highly crystalline (Ni 0.42 Co 0.58 ) 2.22 Ti 0.39 O 3 solid-solution thin film exhibiting a large number of subsidiary minima. As a case study, the edge dislocations in hexagonal (Ni,Co) 3 O 3 thin films with Burgers vector parallel and perpendicular to the a-axis and c-axis, respectively, are modeled. No peak profiles are assumed and thus issues related to profile fitting are avoided. Both macroscopic features, such as film thickness, and atomic-scale structure, such as dislocations, are simultaneously modeled. Simulations are run on a desktop machine. Commonly applied database-based phase identification routines can result in wrong phase identification, unless intensities are properly modeled. Modeling tools of diffractometer manufacturers are compared with the present approach. An example of how simulated reciprocal lattice patterns can be used to choose relevant measurement geometries in defected thin films is given.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Development and Validation of Home Comfort System for Total Performance Deficiency/Fault Detection and Optimal Comfort Control

In this project, we developed and tested a learning-based home thermal model that facilitates the operation of a model predictive control (MPC)-based optimization agent and an automated fault detection and diagnosis (AFDD) agent. The home thermal model was constructed using a two-node resistor-capacitor model. Moreover, two accompanying parameter identification methods were introduced, least-squares and optimization. Based on the home thermal model, the MPC-based optimization agent was developed to optimize residential HVAC operation. Using two FDD methods, the AFDD agent was constructed to detect and diagnose two prevalent residential AC faults, airflow reduction and refrigerant undercharge. The home thermal model, along with the MPC-based optimization agent and AFDD agent, were tested at the Norman Test House, Miami Test House, Pacific Northwest National Laboratory (PNNL) Test House A, and PNNL Test House B. Finally, they were also field tested in nine demonstration homes with real occupants.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Using support vector machines to improve elemental ion identification in macromolecular crystal structures

A method to automatically identify possible elemental ions in X-ray crystal structures has been extended to use support vector machine (SVM) classifiers trained on selected structures in the PDB, with significantly improved sensitivity over manually encoded heuristics. In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗