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DOE OSTI2025

Structural analysis of extracellular ATP-independent chaperones of streptococcal species and protein substrate interactions

ABSTRACT During infection, bacterial pathogens rely on secreted virulence factors to manipulate the host cell. However, in gram-positive bacteria, the molecular mechanisms underlying the folding and activity of these virulence factors after membrane translocation are not clear. Here, we solved the protein structures of two secreted parvulin and two secreted cyclophilin-like peptidyl-prolyl isomerase (PPIase) ATP-independent chaperones found in gram-positive streptococcal species. The extracellular parvulin-type PPIase, PrsA inStreptococcus pneumoniaeandStreptococcus mutansmaintain dimeric crystal structures reminiscent of folding catalysts that consist of two domains, a PPIase and foldase domain. Structural comparison of the two cyclophilin-like extracellular chaperones fromS. pneumoniaeandStreptococcus pyogeneswith other cyclophilins demonstrates that this group of cyclophilin-like chaperones has novel structural appendages formed by 9- and 24-residue insertions. Furthermore, we demonstrate that deletion ofprsAandslrAgenes impairs the secretion of the cholesterol-dependent pore-forming toxin, pneumolysin inS. pneumoniae. Using protein pull-down and biophysical assays, we demonstrate a direct interaction between PrsA and SlrA with Ply. Then, we developed chaperone-assisted folding assays that show that theS. pneumoniaePrsA and SlrA extracellular chaperones accelerate pneumolysin folding. In addition, we demonstrate that SlrA and, for the first time,S. pyogenes PpiA exhibit PPIase activity and can bind the immunosuppressive drug, cyclosporine A. Altogether, these findings suggest a mechanistic role for streptococcal PPIase chaperones in the activity and folding of secreted virulence factors such as pneumolysin. IMPORTANCE Streptococcal species are a leading cause of lower respiratory infections that annually affect millions of people worldwide. During infection, streptococcal species secrete a medley of virulence factors that allow the bacteria to colonize and translocate to deeper tissues. In many gram-positive bacteria, virulence factors are secreted from the cytosol across the bacterial membrane in an unfolded state. The bacterial membrane-cell wall interface is exposed to the potentially harsh extracellular environment, making it difficult for native virulence factors to fold before being released into the host. ATP-independent PPIase-type chaperones, PrsA and SlrA, are thought to facilitate folding and stabilization of several unfolded proteins to promote the colonization and spread of streptococci. Here, we present crystal structures of the molecular chaperones of PrsA and SlrA homologs from streptococcal species. We provide evidence that theStreptococcus pyogenesSlrA homolog, PpiA, has PPIase activity and binds to cyclosporine A. In addition, we show thatStreptococcus pneumoniaePrsA and SlrA directly interact and fold the cholesterol-dependent pore-forming toxin and critical virulence determinant, pneumolysin.

Microbiology↗

DOE OSTI2025

Extending High-Level Synthesis with AI/ML Methods

Artificial Intelligence (AI) and Machine Learning (ML) methods provide significant opportunities of improving quality of results when performing high-level synthesis (HLS). For example, they can be used to model and predict metrics of the final design (e.g., area, considering aspects such as interconnect overhead for different device technologies), facilitating exploration when searching for the best design trade-offs. They can also enable identifying hidden correlations across the various phases of the synthesis and the various optimizations performed, identifying the most effective pipelines. Finally, in more general terms, bio-inspired heuristic algorithms can improve the design space exploration for the synthesis process in terms of time and quality of the result. This paper discusses opportunities and challenges to augment HLS with AI/ML using as example flow the SODA Synthesizer, an open-source hardware generation toolchain which includes SODA-OPT, a hardware/software partitioning and pre-optimization tool developed with the MLIR framework, and PandA-Bambu, a state-of-the art HLS tool. SODA interfaces with OpenROAD to provide a complete end-to-end toolchain.

artificial intelligence↗

DOE OSTI2021

Knowledge Beacons: Web services for data harvesting of distributed biomedical knowledge

The continually expanding distributed global compendium of biomedical knowledge is diffuse, heterogeneous and huge, posing a serious challenge for biomedical researchers in knowledge harvesting: accessing, compiling, integrating and interpreting data, information and knowledge. In order to accelerate research towards effective medical treatments and optimizing health, it is critical that efficient and automated tools for identifying key research concepts and their experimentally discovered interrelationships are developed. As an activity within the feasibility phase of a project called “Translator” (https://ncats.nih.gov/translator) funded by the National Center for Advancing Translational Sciences (NCATS) to develop a biomedical science knowledge management platform, we designed a Representational State Transfer (REST) web services Application Programming Interface (API) specification, which we call a Knowledge Beacon. Knowledge Beacons provide a standardized basic API for the discovery of concepts, their relationships and associated supporting evidence from distributed online repositories of biomedical knowledge. This specification also enforces the annotation of knowledge concepts and statements to the NCATS endorsed the Biolink Model data model and semantic encoding standards (https://biolink.github.io/biolink-model/). Implementation of this API on top of diverse knowledge sources potentially enables their uniform integration behind client software which will facilitate research access and integration of biomedical knowledge.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2025

Electron Energy-Loss Spectroscopy and Differential Phase Contrast Imaging with Active Decision in Multimodal Electron Microscopy: Isotopic detection at the atomic scale

Isotopic engineering provides a powerful route to control phonon behavior in crystalline solids, enabling fundamental studies of lattice dynamics and heat transport at the atomic scale. Here, we directly visualize isotope-dependent phonon propagation in epitaxial Cr 2 O 3 using aberration-corrected scanning transmission electron microscopy (STEM) combined with monochromated, high-energy-resolution electron energy-loss spectroscopy (EELS). Guided by ab initio phonon calculations, we demonstrate that optical phonon modes above 70 meV are predominantly oxygen-derived and exhibit measurable redshifts upon substitution of natural 16 O by enriched 18 O. Spatially resolved vibrational spectrum imaging reveals isotope-enriched tracer layers within Cr 2 O 3 thin films, correlating isotope concentration with phonon intensity variations and vibrational energy shifts. At the nanometer and atomic scales, vibrational EELS mapping uncovers coherent phonon propagation across isotopic interfaces, consistent with theoretical phonon density of states and dispersion relations. These results establish vibrational EELS as a quantitative probe for isotope-dependent phonon transport in materials, opening new possibilities for studying energy dissipation and lattice dynamics.

36 MATERIALS SCIENCE↗

DOE OSTI2024

An Advanced Synchronized Time Digital Grid Twin Testbed for Relay Misoperation Analysis of Electrical Fault Type Detection Algorithms

Distributed energy resources and the number of relays are expected to rise in modern electrical grids; consequently, relay misoperations are also expected to grow. Relays can detect electrical fault types using an internal algorithm and can display the result using light indicators on the front of the relay. However, some relays’ internal algorithms for predicting types of electrical faults could be improved. This study assesses a relay’s external and internal algorithms with an Advanced Synchronized Time Digital Grid Twin (ASTDGT) testbed with paired relays. A misoperation relay analysis focused on measuring the accuracy of using the boundary admittance (the external algorithm) versus the set-default (the internal algorithm) relay method to determine the electrical fault types was performed. In this study, the internal and external relay algorithms were assessed with a synchronized time digital grid twin testbed using a real-time simulator. This testbed evaluated two sets of logic at the same time with the digital grid twin and paired relays in the loop. Different types of electrical faults were simulated, and the relays’ recorded events and electrical fault light indicator states were collected from the human–machine interfaces. This ASTDGT testbed with paired relays successfully evaluated the relay algorithm misoperations. The boundary admittance method had an accuracy of 100% for line-to-line, line-to-ground, and line-to-line ground faults.

24 POWER TRANSMISSION AND DISTRIBUTION↗

NASA NTRS1973

Information Management System for the California State Water Resources Control Board (SWRCB)

A study was made to establish the requirements for an integrated state-wide information management system for water quality control and water quality rights for the State of California. The data sources and end requirements were analyzed for the data collected and used by the numerous agencies, both State and Federal, as well as the nine Regional Boards under the jurisdiction of the State Board. The report details the data interfaces and outlines the system design. A program plan and statement of work for implementation of the project is included.

Heald, T. C.↗

NASA NTRS1986

Physics through the 1990s: Condensed-matter physics

The volume presents the current status of condensed-matter physics from developments since the 1970s to opportunities in the 1990s. Topics include electronic structure, vibrational properties, critical phenomena and phase transitions, magnetism, semiconductors, defects and diffusion, surfaces and interfaces, low-temperature physics, liquid-state physics, polymers, nonlinear dynamics, instabilities, and chaos. Appendices cover the connections between condensed-matter physics and applications of national interest, new experimental techniques and materials, laser spectroscopy, and national facilities for condensed-matter physics research. The needs of the research community regarding support for individual researchers and for national facilities are presented, as are recommendations for improved government-academic-industrial relations.

Source record↗

NASA NTRS1989

Design of a final approach spacing tool for TRACON air traffic control

This paper describes an automation tool that assists air traffic controllers in the Terminal Radar Approach Control (TRACON) Facilities in providing safe and efficient sequencing and spacing of arrival traffic. The automation tool, referred to as the Final Approach Spacing Tool (FAST), allows the controller to interactively choose various levels of automation and advisory information ranging from predicted time errors to speed and heading advisories for controlling time error. FAST also uses a timeline to display current scheduling and sequencing information for all aircraft in the TRACON airspace. FAST combines accurate predictive algorithms and state-of-the-art mouse and graphical interface technology to present advisory information to the controller. Furthermore, FAST exchanges various types of traffic information and communicates with automation tools being developed for the Air Route Traffic Control Center. Thus it is part of an integrated traffic management system for arrival traffic at major terminal areas.

Davis, Thomas J.↗

NASA NTRS1989

A system architecture for a planetary rover

Each planetary mission requires a complex space vehicle which integrates several functions to accomplish the mission and science objectives. A Mars Rover is one of these vehicles, and extends the normal spacecraft functionality with two additional functions: surface mobility and sample acquisition. All functions are assembled into a hierarchical and structured format to understand the complexities of interactions between functions during different mission times. It can graphically show data flow between functions, and most importantly, the necessary control flow to avoid unambiguous results. Diagrams are presented organizing the functions into a structured, block format where each block represents a major function at the system level. As such, there are six blocks representing telecomm, power, thermal, science, mobility and sampling under a supervisory block called Data Management/Executive. Each block is a simple collection of state machines arranged into a hierarchical order very close to the NASREM model for Telerobotics. Each layer within a block represents a level of control for a set of state machines that do the three primary interface functions: command, telemetry, and fault protection. This latter function is expanded to include automatic reactions to the environment as well as internal faults. Lastly, diagrams are presented that trace the system operations involved in moving from site to site after site selection. The diagrams clearly illustrate both the data and control flows. They also illustrate inter-block data transfers and a hierarchical approach to fault protection. This systems architecture can be used to determine functional requirements, interface specifications and be used as a mechanism for grouping subsystems (i.e., collecting groups of machines, or blocks consistent with good and testable implementations).

Smith, D. B.↗

NASA NTRS1989

Transportable telemetry workstation

The goal was to complete the design of a prototype for a Transportable Telemetry Workstation (TTW). The Macintosh 2 is used to provide a low-cost system which can house real-time cards mounted on the NuBus inside the Macintosh 2 plus provide a standardized user interface on the Macintosh 2 console. Prior to a telemetry run, the user will be able to configure his real-time telemetry processing functions from the Macintosh 2 console. During a telemetry run, the real-time cards will store the telemetry data directly on a hard disk while permitting viewing of the data cards on the Macintosh 2 console on various selectable formats. The user will view the cards in terms of the functions they perform and the selectable paths through the cards, it is not required to become involved directly in hardware issue except in terms of the functional configuration of the system components. The TTW will accept telemetry data from an RS422 serial input data bus, pass it through a frame synchronizer card and on to a real time controller card via a telemetry backplane bus. The controller card will then route the data to a hard disk through a SCSI interface, and/or to a user interface on the Macintosh 2 console by way of the Macintosh 2 NuBus. The three major components to be designed, therefore, are the TTW Controller Card, the TTW Synchronizer Card, and the NuBus/Macintosh 2 User Interface. Design and prototyping of this state-of-the-art, transportable, low-cost, easy-to-use multiprocessor telemetry system is continuing. Other functions are planned for the future.

Collins, Aaron S.↗

NASA NTRS1993

DESSY: Making a real-time expert system robust and useful

As the complexity and expected life-span of modern space systems continue to increase, the need for real-time data monitoring and failure analysis becomes more critical to their successful operation. The DEcision Support SYstem (DESSY) is a joint effort by the Intelligent Systems Branch/ER2 and the Remote Manipulator System (RMS) Section/DF44 to develop an expert system for the monitoring of the Payload Deployment and Retrieval System (PDRS). DESSY users, the RMS flight controllers, are provided with user interface enhancements and automated monitoring of system state (physical orientation) and status (operational health). Currently, a DESSY prototype for the Manipulator Positioning Mechanism (MPM) and Manipulator Retention Latches (MRL) of the PDRS has been developed and successfully demonstrated during the STS-49 and STS-46 missions. Expert systems for monitoring real-time operations must not only accurately represent domain knowledge, but also address the challenges of using unfiltered real-time data as input. This paper describes the methods and design strategies developed to overcome problems with real-time data in the NASA Mission Control Center. Types of data problems addressed are as follows: (1) loss of data; (2) erratic data; and (3) data lags and irregularities during state transition. Methods used to handle data problems include rule disabling for ignoring data when data quality is uncertain, context-sensitive bounded pattern recognition for minimizing incorrect conclusions based on bad data, and graceful recovery through system correction when reliable data returns. This combination of methods with an object-based modular DESSY design assures a robust program capable of lengthy periods of uninterrupted use in operations.

Land, Sherry A.↗

NASA NTRS1993

Cost effective data system design approach for EOS AM-1

The question of how to design a cost-effective data system for a space-based application with a high aggregate data rate is addressed. The steps used by the EOS AM-1 design team are defined. A summary of the design as of January 1993 is outlined. The AM-1 Science Data system is comprised of one subsystem that ingests, formats, and routes data - the Science Formatting Equipment (SFE), and another that records the data. Key interfaces are the interfaces to the high rate science instruments, the real-time transmitters, and the internal interface between the SFR and the Solid State Recorder. A cost-effective design approach for the AM-1 data system must take into account impacts on ground systems, data processing facilities, availability of data for real-time users, and future spacecraft designs.

Westmeyer, Paul A.↗

NASA NTRS1993

Biogeochemical cycles of carbon, sulfur, and free oxygen in a microbial mat

Complete budgets for carbon and oxygen have been constructed for cyanobacterial mats dominated by Microcoleus chthonoplastes from the evaporating ponds of a salt works. We infer from the data the various sinks for O2 as well as the sources of carbon for primary production. Although seasonal variability exists, a major percentage of the O2 produced during the day did not diffuse out of the mat but was used within the mat to oxidize both organic carbon and the sulfide produced by sulfate reduction. At night, most of the O2 that diffused into the mat was used to oxidize sulfide, with O2 respiration of minor importance. During the day, the internal mat processes of sulfate reduction and O2 respiration generated as much or more inorganic carbon (DIC) for primary production as diffusion into the mat. Oxygenic photosynthesis was the most important process of carbon fixation. At night, the DIC lost from the mat was mostly from sulfate reduction. Elemental fluxes across the mat/brine interface indicated that carbon with an oxidation state of greater than zero was taken up by the mat during the day and liberated from the mat at night. Overall, carbon with an average oxidation state of near zero accumulated in the mat. Both carbon fixation and carbon oxidation rates varied with temperature by a similar amount.

Canfield, Donald E.↗

NASA NTRS1998

Antiterrorist Software

In light of the escalation of terrorism, the Department of Defense spearheaded the development of new antiterrorist software for all Government agencies by issuing a Broad Agency Announcement to solicit proposals. This Government-wide competition resulted in a team that includes NASA Lewis Research Center's Computer Services Division, who will develop the graphical user interface (GUI) and test it in their usability lab. The team launched a program entitled Joint Sphere of Security (JSOS), crafted a design architecture (see the following figure), and is testing the interface. This software system has a state-ofthe- art, object-oriented architecture, with a main kernel composed of the Dynamic Information Architecture System (DIAS) developed by Argonne National Laboratory. DIAS will be used as the software "breadboard" for assembling the components of explosions, such as blast and collapse simulations.

Clark, David A.↗

NASA NTRS2006

Numerical Methodology for Coupled Time-Accurate Simulations of Primary and Secondary Flowpaths in Gas Turbines

Detailed information of the flow-fields in the secondary flowpaths and their interaction with the primary flows in gas turbine engines is necessary for successful designs with optimized secondary flow streams. Present work is focused on the development of a simulation methodology for coupled time-accurate solutions of the two flowpaths. The secondary flowstream is treated using SCISEAL, an unstructured adaptive Cartesian grid code developed for secondary flows and seals, while the mainpath flow is solved using TURBO, a density based code with capability of resolving rotor-stator interaction in multi-stage machines. An interface is being tested that links the two codes at the rim seal to allow data exchange between the two codes for parallel, coupled execution. A description of the coupling methodology and the current status of the interface development is presented. Representative steady-state solutions of the secondary flow in the UTRC HP Rig disc cavity are also presented.

Przekwas, A. J.↗

NASA NTRS2008

Design of Test Articles and Monitoring System for the Characterization of HIRF Effects on a Fault-Tolerant Computer Communication System

This report describes the design of the test articles and monitoring systems developed to characterize the response of a fault-tolerant computer communication system when stressed beyond the theoretical limits for guaranteed correct performance. A high-intensity radiated electromagnetic field (HIRF) environment was selected as the means of injecting faults, as such environments are known to have the potential to cause arbitrary and coincident common-mode fault manifestations that can overwhelm redundancy management mechanisms. The monitors generate stimuli for the systems-under-test (SUTs) and collect data in real-time on the internal state and the response at the external interfaces. A real-time health assessment capability was developed to support the automation of the test. A detailed description of the nature and structure of the collected data is included. The goal of the report is to provide insight into the design and operation of these systems, and to serve as a reference document for use in post-test analyses.

Torres-Pomales, Wilfredo↗

NASA NTRS2010

Overview and Software Architecture of the Copernicus Trajectory Design and Optimization System

The Copernicus Trajectory Design and Optimization System represents an innovative and comprehensive approach to on-orbit mission design, trajectory analysis and optimization. Copernicus integrates state of the art algorithms in optimization, interactive visualization, spacecraft state propagation, and data input-output interfaces, allowing the analyst to design spacecraft missions to all possible Solar System destinations. All of these features are incorporated within a single architecture that can be used interactively via a comprehensive GUI interface, or passively via external interfaces that execute batch processes. This paper describes the Copernicus software architecture together with the challenges associated with its implementation. Additionally, future development and planned new capabilities are discussed. Key words: Copernicus, Spacecraft Trajectory Optimization Software.

Williams, Jacob↗

DOE OSTI2019

Optical quantification of interfacial charge states

Methods of generating second harmonic generation (SHG) signals from interfaces formed with, or formed over, a noncentrosymmetric material, e.g., α-quartz, are provided. The methods make use of the noncentrosymmetric material as an internal phase reference for the determination of a variety of interfacial electrostatic parameters, including interfacial potential, interfacial charge density, and the sign of the interfacial charge (i.e., net positive or net negative).

Geiger, Franz M.↗