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All sources NASA NTRS DOE OSTI

DOE OSTI2023

Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors

Many eukaryotic transcription factors (TF) form homodimer or heterodimer complexes to regulate gene expression. Dimerization of BASIC LEUCINE ZIPPER (bZIP) TFs are critical for their functions, but the molecular mechanism underlying the DNA binding and functional specificity of homo- versus heterodimers remains elusive. To address this gap, we present the double DNA Affinity Purification-sequencing (dDAP-seq) technique that maps heterodimer binding sites on endogenous genomic DNA. Using dDAP-seq we profile twenty pairs of C/S1 bZIP heterodimers and S1 homodimers in Arabidopsis and show that heterodimerization significantly expands the DNA binding preferences of these TFs. Analysis of dDAP-seq binding sites reveals the function of bZIP9 in abscisic acid response and the role of bZIP53 heterodimer-specific binding in seed maturation. The C/S1 heterodimers show distinct preferences for the ACGT elements recognized by plant bZIPs and motifs resembling the yeast GCN4 cis -elements. This study demonstrates the potential of dDAP-seq in deciphering the DNA binding specificities of interacting TFs that are key for combinatorial gene regulation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

A Graph Theory-Based Automated Twin Recognition Technique for Electron Backscatter Diffraction Analysis

Abstract The present article introduces a new software, Microstructure Evaluation Tool for Interface Statistics (METIS), that performs high-throughput microstructure statistical analysis from electron backscatter diffraction maps. Emphasis is placed on the detection of twin domains in hexagonal close-packed metals. The numerical framework on which METIS is built leverages graph theory, group structures, and associated numerical algorithms to automatically detect twins and unravel both their intrinsic characteristics features and those pertaining to their interactions. The proposed graphical interface allows for the detection and correction of unlikely twin/parent associations rendering the approach applicable to highly deformed microstructures. Twin statistics and microstructural data are classified and saved in a relational database that can be interrogated via either GUI or SQL requests to reveal a wide spectrum of features of the microstructure. Illustration of the approach is performed in the case of zirconium.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Automatic voltage regulation application for PV inverters in low-voltage distribution grids – A digital twin approach

This paper proposes a hierarchical coordinated control strategy for PV inverters to keep voltages in low-voltage (LV) distribution grids within specified limits. The top layer of the proposed architecture consists of the designed automatic voltage regulation (AVR) application, which has access to voltage measurements and grid parameters from the LV distribution grid, both current and historical. The AVR application solves a constrained optimization problem, which provides a set of local control set-points that bring the voltage across the grid within bounds. The middle layer consists of a local Volt/VAR controller, which is adjusted by the AVR app, while the bottom layer is the inner-loop controller of the PV inverter. The proposed method not only improves the voltage quality in the grid but also manages the reactive power outputs of PV inverters efficiently. Further, a digital twin of the cyber-physical system has also been employed that interacts with the control system to ensure its appropriate operation. The effectiveness of the proposed methodology is demonstrated on a representative low-voltage feeder located in Denmark.

24 POWER TRANSMISSION AND DISTRIBUTION↗

NASA NTRS1994

Preprocessor Program For Use With PASCO

MACPASCO is interactive, graphical preprocessor program designed to make use of Panel Analysis and Sizing Code, PASCO, (COSMIC program numbers LAR-13004, LAR-13164, and LAR-14799) faster, simpler, and less error-prone. Is Macintosh-based preprocessor program that includes graphical user interface (GUI) program to simplify specification of panel geometry, making modeling and analysis of panel designs more efficient and reducing potential for user input errors. Written in Macintosh Programmers Workbench 3.0, MPW Pascal 3.0, and MacAPP 2.0.

Lucas, Stephen H.↗

DOE OSTI2020

Lectin Receptor-Like Kinases: The Sensor and Mediator at the Plant Cell Surface

Lectin receptor-like kinases (LecRLKs), a plant-specific receptor-like kinase (RLK) sub-family, have been recently found to play crucial roles in plant development and responses to abiotic and biotic stresses. In this review, we first describe the classification and structures of Lectin RLKs. Then we focus on the analysis of functions of LecRLKs in various biological processes and discuss the status of LecRLKs from the ligands they recognize, substrate they target, signaling pathways they are involved in, to the overall regulation of growth-defense tradeoffs. LecRLKs and the signaling components they interact with constitute recognition and protection systems at the plant cell surface contributing to the detection of environmental changes monitoring plant fitness.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Host plant genetic control of associated fungal and insect species in a Populus hybrid cross

Not Available

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2011

Telemetry and Science Data Software System

The Telemetry and Science Data Software System (TSDSS) was designed to validate the operational health of a spacecraft, ease test verification, assist in debugging system anomalies, and provide trending data and advanced science analysis. In doing so, the system parses, processes, and organizes raw data from the Aquarius instrument both on the ground and while in space. In addition, it provides a user-friendly telemetry viewer, and an instant pushbutton test report generator. Existing ground data systems can parse and provide simple data processing, but have limitations in advanced science analysis and instant report generation. The TSDSS functions as an offline data analysis system during I&T (integration and test) and mission operations phases. After raw data are downloaded from an instrument, TSDSS ingests the data files, parses, converts telemetry to engineering units, and applies advanced algorithms to produce science level 0, 1, and 2 data products. Meanwhile, it automatically schedules upload of the raw data to a remote server and archives all intermediate and final values in a MySQL database in time order. All data saved in the system can be straightforwardly retrieved, exported, and migrated. Using TSDSS s interactive data visualization tool, a user can conveniently choose any combination and mathematical computation of interesting telemetry points from a large range of time periods (life cycle of mission ground data and mission operations testing), and display a graphical and statistical view of the data. With this graphical user interface (GUI), the data queried graphs can be exported and saved in multiple formats. This GUI is especially useful in trending data analysis, debugging anomalies, and advanced data analysis. At the request of the user, mission-specific instrument performance assessment reports can be generated with a simple click of a button on the GUI. From instrument level to observatory level, the TSDSS has been operating supporting functional and performance tests and refining system calibration algorithms and coefficients, in sync with the Aquarius/SAC-D spacecraft. At the time of this reporting, it was prepared and set up to perform anomaly investigation for mission operations preceding the Aquarius/SAC-D spacecraft launch on June 10, 2011.

Bates, Lakesha↗

NASA NTRS1999

Chandra Interactive Analysis of Observations

The Chandra X-R-ay Observatory has been launched on July 23 1999. The first public release of the Chandra data analysis system, CIAO (Chandra Interactive Analysis of Observations) will be available in the near future. The XMM Science Survey Consortium is considering the possibility of using the whole or parts of CIAO to analyse observations from the XMM satellite and during the meeting we will give presentations and demonstrations of parts of CIAO, including the new GUIs developed for "FirstLook" analysis, data filtering and browsing; SHERPA, the multi-dimensional, multi-missions modelling and fitting application; CHIPS, the Chandra Imaging and Plotting System; generic data manipulation tools and other applications.

Fruscione, Antonella↗

NASA NTRS2000

Chandra Interactive Analysis of Observations (CIAO)

The Chandra X-Ray Observatory has been launched on July 23 1999. The first public release of the Chandra data analysis system, CIAO (Chandra Interactive Analysis of Observations) will be available in the near future. The XMM Science Survey Consortium is considering the possibility of using the whole or parts of CIAO to analyze observations from the XMM satellite and during the meeting we will give presentations and demonstrations of parts of CIAO, including the new GUIs developed for "First Look" analysis, data filtering and browsing; SHERPA, the multi-dimensional, multi-missions modeling and fitting application; CHIPS, the Chandra Imaging and Plotting System; generic data manipulation tools and other applications.

Fruscione, Antonella↗

NASA NTRS2009

Quantifying Therapeutic and Diagnostic Efficacy in 2D Microvascular Images

VESGEN is a newly automated, user-interactive program that maps and quantifies the effects of vascular therapeutics and regulators on microvascular form and function. VESGEN analyzes two-dimensional, black and white vascular images by measuring important vessel morphology parameters. This software guides the user through each required step of the analysis process via a concise graphical user interface (GUI). Primary applications of the VESGEN code are 2D vascular images acquired as clinical diagnostic images of the human retina and as experimental studies of the effects of vascular regulators and therapeutics on vessel remodeling.

Parsons-Wingerter, Patricia↗

NASA NTRS1992

AXAF user interfaces for heterogeneous analysis environments

The AXAF Science Center (ASC) will develop software to support all facets of data center activities and user research for the AXAF X-ray Observatory, scheduled for launch in 1999. The goal is to provide astronomers with the ability to utilize heterogeneous data analysis packages, that is, to allow astronomers to pick the best packages for doing their scientific analysis. For example, ASC software will be based on IRAF, but non-IRAF programs will be incorporated into the data system where appropriate. Additionally, it is desired to allow AXAF users to mix ASC software with their own local software. The need to support heterogeneous analysis environments is not special to the AXAF project, and therefore finding mechanisms for coordinating heterogeneous programs is an important problem for astronomical software today. The approach to solving this problem has been to develop two interfaces that allow the scientific user to run heterogeneous programs together. The first is an IRAF-compatible parameter interface that provides non-IRAF programs with IRAF's parameter handling capabilities. Included in the interface is an application programming interface to manipulate parameters from within programs, and also a set of host programs to manipulate parameters at the command line or from within scripts. The parameter interface has been implemented to support parameter storage formats other than IRAF parameter files, allowing one, for example, to access parameters that are stored in data bases. An X Windows graphical user interface called 'agcl' has been developed, layered on top of the IRAF-compatible parameter interface, that provides a standard graphical mechanism for interacting with IRAF and non-IRAF programs. Users can edit parameters and run programs for both non-IRAF programs and IRAF tasks. The agcl interface allows one to communicate with any command line environment in a transparent manner and without any changes to the original environment. For example, the authors routinely layer the GUI on top of IRAF, ksh, SMongo, and IDL. The agcl, based on the facilities of a system called Answer Garden, also has sophisticated support for examining documentation and help files, asking questions of experts, and developing a knowledge base of frequently required information. Thus, the GUI becomes a total environment for running programs, accessing information, examining documents, and finding human assistance. Because the agcl can communicate with any command-line environment, most projects can make use of it easily. New applications are continually being found for these interfaces. It is the authors' intention to evolve the GUI and its underlying parameter interface in response to these needs - from users as well as developers - throughout the astronomy community. This presentation describes the capabilities and technology of the above user interface mechanisms and tools. It also discusses the design philosophies guiding the work, as well as hopes for the future.

Mandel, Eric↗

NASA NTRS2007

State-Chart Autocoder

A computer program translates Unified Modeling Language (UML) representations of state charts into source code in the C, C++, and Python computing languages. ( State charts signifies graphical descriptions of states and state transitions of a spacecraft or other complex system.) The UML representations constituting the input to this program are generated by using a UML-compliant graphical design program to draw the state charts. The generated source code is consistent with the "quantum programming" approach, which is so named because it involves discrete states and state transitions that have features in common with states and state transitions in quantum mechanics. Quantum programming enables efficient implementation of state charts, suitable for real-time embedded flight software. In addition to source code, the autocoder program generates a graphical-user-interface (GUI) program that, in turn, generates a display of state transitions in response to events triggered by the user. The GUI program is wrapped around, and can be used to exercise the state-chart behavior of, the generated source code. Once the expected state-chart behavior is confirmed, the generated source code can be augmented with a software interface to the rest of the software with which the source code is required to interact.

Clark, Kenneth↗

NASA NTRS2006

Update On the Status of the FLUKA Monte Carlo Transport Code*

The FLUKA Monte Carlo transport code is a well-known simulation tool in High Energy Physics. FLUKA is a dynamic tool in the sense that it is being continually updated and improved by the authors. We review the progress achieved since the last CHEP Conference on the physics models, some technical improvements to the code and some recent applications. From the point of view of the physics, improvements have been made with the extension of PEANUT to higher energies for p, n, pi, pbar/nbar and for nbars down to the lowest energies, the addition of the online capability to evolve radioactive products and get subsequent dose rates, upgrading of the treatment of EM interactions with the elimination of the need to separately prepare preprocessed files. A new coherent photon scattering model, an updated treatment of the photo-electric effect, an improved pair production model, new photon cross sections from the LLNL Cullen database have been implemented. In the field of nucleus-- nucleus interactions the electromagnetic dissociation of heavy ions has been added along with the extension of the interaction models for some nuclide pairs to energies below 100 MeV/A using the BME approach, as well as the development of an improved QMD model for intermediate energies. Both DPMJET 2.53 and 3 remain available along with rQMD 2.4 for heavy ion interactions above 100 MeV/A. Technical improvements include the ability to use parentheses in setting up the combinatorial geometry, the introduction of pre-processor directives in the input stream. a new random number generator with full 64 bit randomness, new routines for mathematical special functions (adapted from SLATEC). Finally, work is progressing on the deployment of a user-friendly GUI input interface as well as a CAD-like geometry creation and visualization tool. On the application front, FLUKA has been used to extensively evaluate the potential space radiation effects on astronauts for future deep space missions, the activation dose for beam target areas, dose calculations for radiation therapy as well as being adapted for use in the simulation of events in the ALICE detector at the LHC.

Ferrari, A.↗

NASA NTRSDate not supplied

Enabling a Voice Management System for Space Applications

The sustainable missions beyond Low Earth Orbit (LEO) envisioned for NASA’s Artemis program will require autonomous capabilities. Moreover, Artemis mission crews will need a means to efficiently interact with a spacecraft’s autonomous systems. This interaction can be facilitated by voice and speech communications because voice-based controls enable users to interact hands- and eyes-free, allowing the user to better focus on critical tasks. The goal of our project was to explore the knowledge and technology needed to successfully design effective Voice User Interfaces (VUIs) for autonomous systems utilizing Human Centered Design (HCD) principles. The focus of the human factors’ aspect of engineering, pays close attention to psychological and physiological principles in the development of autonomous crew operation systems. A main objective was to understand how a crew member, through voice interaction, could efficiently and intuitively communicate with a notional autonomous vehicle system manager. This project was a part of the NASA Moon to Mars eXploration Systems and Habitation (M2M X-Hab) 2020 Academic Innovation Challenge. The work from the BLiSS Team, at the University of Michigan, resulted in the design of a system persona, Diego, to which an astronaut may quickly build trust with autonomous systems, to alleviate known stressors on mental health expected during long duration space missions. Optimal software to facilitate integration of the system persona into a reference Lunar orbiting Gateway station was defined. Additionally, a Speech to Text (STT) system and a Graphical User Interface (GUI) that could be implemented in future missions was developed on an Internet of Things (IOT) platform. The Voice User Interface (VUI) design for the M2M X-Hab 2020 project leveraged previous technology developed by the BLiSS team to incorporate a voice-based interface into NASA’s Platform for Autonomous Systems (NPAS) software. This required technologies to convert voice to text, conduct semantic interpretations, and convert responses from the autonomous system to text and to speech; additionally, the spacecraft background noise environment was assessed, a noise mitigation technique was developed, and a relatable personality for the autonomous system was developed in order to facilitate human-like conversations. The success of our effort was largely due to the diversity of the team that included expertise in Space Systems Engineering, Human Computer Interaction, Aerospace Engineering, Computer Science, Biomedical Engineering, and Applied Physics. The diverse perspectives fostered elaborate discussions, resulting in the conception of three main subsystems: (1) User-System, (2) NPAS-System, and (3) Environment-System. The VUI was unique and had to be efficient and intuitive. For this project, 5 subteams were formed, each with a separate objective, Voice Design team, Background Noise Mitigation team, Software Integration team and Graphical User Interface team. The BLiSS team crafted a personality for the VUI to enable human-like conversation and drive user adoption and trust. User surveys were completed and used to help determine the required VUI system personality traits by capturing perspectives and expectations of prospective “Artemis Generation Astronauts”. To further simulate human-like conversations, the system had to be able to quickly interpret user speech and be able to integrate with NASA’s NPAS platform for quick and reliable information transfer. The outcomes of our research were: (1) a working prototype user interface, that is compatible with NASA’s NPAS platform; (2) software that demonstrates the ability of the VUI system to interpret user requests and respond appropriately; (3) the capability to implement fully expanded conversations between user and system using intuitive communication in four request categories; and (4) software and hardware recommendations that optimize the system’s ability to operate in a noisy environment. Our research has laid the foundation for the development of VUI’s for autonomy, and provides a baseline for future VUI developments.

Voice user interface↗

NASA NTRS2013

A System for Fault Management for NASA's Deep Space Habitat

NASA's exploration program envisions the utilization of a Deep Space Habitat (DSH) for human exploration of the space environment in the vicinity of Mars and/or asteroids. Communication latencies with ground control of as long as 20+ minutes make it imperative that DSH operations be highly autonomous, as any telemetry-based detection of a systems problem on Earth could well occur too late to assist the crew with the problem. A DSH-based development program has been initiated to develop and test the automation technologies necessary to support highly autonomous DSH operations. One such technology is a fault management tool to support performance monitoring of vehicle systems operations and to assist with real-time decision making in connection with operational anomalies and failures. Toward that end, we are developing Advanced Caution and Warning System (ACAWS), a tool that combines dynamic and interactive graphical representations of spacecraft systems, systems modeling, automated diagnostic analysis and root cause identification, system and mission impact assessment, and mitigation procedure identification to help spacecraft operators (both flight controllers and crew) understand and respond to anomalies more effectively. In this paper, we describe four major architecture elements of ACAWS: Anomaly Detection, Fault Isolation, System Effects Analysis, and Graphic User Interface (GUI), and how these elements work in concert with each other and with other tools to provide fault management support to both the controllers and crew. We then describe recent evaluations and tests of ACAWS on the DSH testbed. The results of these tests support the feasibility and strength of our approach to failure management automation and enhanced operational autonomy.

Fault management↗

NASA NTRS2013

A System for Fault Management and Fault Consequences Analysis for NASA's Deep Space Habitat

System Effects Analysis↗

DOE OSTI2016

Knockdown of a laccase in Populus deltoides confers altered cell wall chemistry and increased sugar release

Summary Plant laccases are thought to function in the oxidation of monolignols which leads to higher order lignin formation. Only a hand‐full of laccases in plants have been functionally evaluated, and as such little is known about the breadth of their impact on cell wall chemistry or structure. Here, we describe a previously uncharacterized laccase from Populus , encoded by locus Potri.008G064000, whose reduced expression resulted in transgenic Populus trees with changes in syringyl/guaiacyl ratios as well as altered sugar release phenotypes. These phenotypes are consistent with plant biomass exhibiting reduced recalcitrance. Interestingly, the transgene effect on recalcitrance is dependent on a mild pretreatment prior to chemical extraction of sugars. Metabolite profiling suggests the transgene modulates phenolics that are associated with the cell wall structure. We propose that this particular laccase has a range of functions related to oxidation of phenolics and conjugation of flavonoids that interact with lignin in the cell wall.

09 BIOMASS FUELS↗

DOE OSTI2023

Virtual Engineering Software Framework for Integrated Biomass Conversion Modeling

This presentation covers the design and implementation of a software tool to systematically connect computational models of unit operations to simulate an integrated process of low-temperature conversion of biomass to fuel. This virtual engineering (VE) software was designed with the overarching goal of connecting unit models written in various programming languages and requiring different computational resources within a single, flexible framework. The models and features currently considered for the VE library include mechanistic models for pretreatment, enzymatic hydrolysis, and aerobic bioreaction; high-fidelity computational fluid dynamics (CFD) simulations for enzymatic hydrolysis and aerobic bioreaction; and the capability to perform techno-economic analyses (TEA) using Aspen Plus, a commercial software package. The CFD models require access to high-performance computing (HPC) resources, so in addition to handling multiple programming languages and interfaces, the VE software must also be capable of interacting with an HPC scheduler to submit, run, and post-process jobs. Using the Python programming language, a new VE software package has been developed that contains functionality to manage the input-output communication between various unit models, schedule simulations to run on NREL's HPC and analyze those results, and interface with existing TEA software workflows. A Jupyter-notebook GUI was also created to solicit user input and provide documentation. In cases where multiple models for a particular unit-operation exist, selection between models is accomplished through a simple checkbox, with the appropriate inputs and outputs being parsed and converted seamlessly in the background. Each operation makes use of a different programming language, but the flow of information from pretreatment to enzymatic hydrolysis to bioreaction is managed with an intuitive, centralized file-communication strategy. In this talk, the programming approach and implementation details of the notebook are presented for multiple possibilities of the conversion process, including a demonstration of the ability to manage HPC resources. Additionally, an example of a sensitivity study of treatment parameters governing the overall conversion outcome is shown which highlights the ease of defining new problems using the VE Notebook workflow and leads into a discussion of ongoing work to enable outer-loop optimization studies.

biofuel↗