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At least 1,333 records · Page 74

MolViewSpec: a Mol* extension for describing and sharing molecular visualizations

Data visualization is a pivotal component of a structural biologist’s arsenal. The Mol* Viewer makes molecular visualizations available to broader audiences via most web browsers. While Mol* provides a wide range of functionality, it has a steep learning curve and is only available via a JavaScript interface. To enhance the accessibility and usability of web-based molecular visualization, we introduce MolViewSpec (molstar.org/mol-view-spec), a standardized approach for defining molecular visualizations that decouples the definition of complex molecular scenes from their rendering. Scene definition can include references to commonly used structural, volumetric, and annotation data formats together with a description of how the data should be visualized and paired with optional annotations specifying colors, labels, measurements, and custom 3D geometries. Developed as an open standard, this solution paves the way for broader interoperability and support across different programming languages and molecular viewers, enabling more streamlined, standardized, and reproducible visual molecular analyses. MolViewSpec is freely available as a Mol* extension and a standalone Python package.

Midlik, Adam [European Bioinformatics Institute (U↗

Scalable standard optical sources in the VUV: Emissions from electron impact on metals

The use of electron impact on metals in the development of a compact optical standard lamp in the vacuum ultraviolet is described. Two different mechanisms are exploited, transition radiation and bremsstrahlung. Transition radiation will be used as a primary standard from 1200A to 3000A using 10 keV electron impact on tungsten. Bremsstrahlung will be used in the soft X-ray region below 1200A to less than 5A as an optical transfer standard from 4 keV electron impact on tantalum or tungsten.

Hughes, R.↗

A fast Monte Carlo cell-by-cell simulation for radiobiological effects in targeted radionuclide therapy using pre-calculated single-particle track standard DNA damage data

Introduction: We developed a new method that drastically speeds up radiobiological Monte Carlo radiation-track-structure (MC-RTS) calculations on a cell-by-cell basis. Methods: The technique is based on random sampling and superposition of single-particle track (SPT) standard DNA damage (SDD) files from a “pre-calculated” data library, constructed using the RTS code TOPAS-nBio, with “time stamps” manually added to incorporate dose-rate effects. This time-stamped SDD file can then be input into MEDRAS, a mechanistic kinetic model that calculates various radiation-induced biological endpoints, such as DNA double-strand breaks (DSBs), misrepairs and chromosomal aberrations, and cell death. As a benchmark validation of the approach, we calculated the predicted energy-dependent DSB yield and the ratio of direct-to-total DNA damage, both of which agreed with published in vitro experimental data. We subsequently applied the method to perform a superfast cell-by-cell simulation of an experimental in vitro system consisting of neuroendocrine tumor cells uniformly incubated with 177 Lu. Results and discussion: The results for residual DSBs, both at 24 and 48 h post-irradiation, are in line with the published literature values. Our work serves as a proof-of-concept demonstration of the feasibility of a cost-effective “in silico clonogenic cell survival assay” for the computational design and development of radiopharmaceuticals and novel radiotherapy treatments more generally.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Guide to Developing Energy Services Interfaces

This document provides guidance to develop communications interfaces that are highly interoperable and adhere to a set of energy services interface (ESI) principles. It can be applied in the context of information and communications technology interface standards and implementation profiles that enable the integration of a facility with responsive distributed energy resources (DER) into an electric power system consistent with the fundamental ESI principles. In this context, a DER facility may consist of a single DER with a communicating controller or may be as complex as a microgrid campus with several buildings and many DERs. This document is not a technical interface standard, but the requirements described can be used to check that existing, augmented, or new interface standards meet the interoperability requirements of the ESI concept. In this way, this guide for the ESI specification can support future advancements in developing interoperability standards and implementation profiles. The intended audience for this document is DER integration practitioners and ecosystem groups that are in the business of developing and implementing communications interfaces for DER integration. It is intended that these groups apply the information and processes in this document to develop communications standards and implementation profiles that are consistent with fundamental ESI principles.

2030.5↗

Comparison of ISO and ANSI/ANS Nuclear Criticality Safety Standards [Slides]

This paper provides a high-level comparison between the international and domestic nuclear criticality safety (NCS) standards, as requested by members of the Nuclear Criticality Safety Division. Currently, there are 18 enacted American National Standards Institute (ANSI)/American National Standards (ANS) standards, and 1 ANSI/ANS standard, in progress. There are 11 NCS standards from the International Organization for Standardization (ISO), Technical Committee 85 (TC85) on Nuclear Energy, Subcommittee 5 (SC5) on Nuclear Fuel Cycle, Working Group 8 (WG8). NCS standard revisions are in progress for both standards organizations. The key differences between the ISO TC85/SC5/WG8 and ANSI/ANS-8 consensus NCS standards are summarized. The hard work done by the ANS-8 and WG8 volunteers allows for applicable, high-quality consensus standards for use by the NCS community. This paper defines the current status of each ANSI/ANS and ISO standard, the work in in progress, the revisions/amendments in progress, and WG8/ANS-8 non-standard business in progress. A forthcoming paper will compare the development process for ISO and ANSI/ANS standards.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Modular space station, phase B extension. Information management advanced development. Volume 5: Software assembly

The development of uniform computer program standards and conventions for the modular space station is discussed. The accomplishments analyzed are: (1) development of computer program specification hierarchy, (2) definition of computer program development plan, and (3) recommendations for utilization of all operating on-board space station related data processing facilities.

Gerber, C. R.↗

Semicustom integrated circuits and the standard transistor array radix (STAR)

The development, application, pros and cons of the semicustom and custom approach to the integration of circuits are described. Improvements in terms of cost, reliability, secrecy, power, and size reduction are examined. Also presented is the standard transistor array radix, a semicustom approach to digital integrated circuits that offers the advantages of both custom and semicustom approaches to integration.

Edge, T. M.↗

Standards in the architectural effort

The NASA Scientific and Technical Information (STI) Project Architecture Group was established to build a framework for modernization, provide guidance and direction for standardization and integration efforts, and to develop a set of concepts, interfaces, and entities to specifiy standards. The STI data processing architecture is a set of diagrams and descriptions that characterize the principal functions and services as well as hardware and software components. The use of standards promotes scalability and interchangeability.

Markham, Howard↗

Human Exploration of Phobos

This study developed, analyzed, and compared mission architectures for human exploration of Mars' Moons within the context of an Evolvable Mars Campaign. METHODS: All trades assumed conjunction class missions to Phobos (approximately 500 days in Mars system) as it was considered the driving case for the transportation architecture. All architectures assumed that the Mars Transit Habitat would remain in a High Mars Orbit with crewmembers transferring between HMO and Phobos in a small crew taxi vehicle. A reference science / exploration program was developed including performance of a standard set of tasks at 55 locations on the Phobos surface. Detailed EVA timelines were developed using realistic flight rules to accomplish the reference science tasks using exploration systems ranging from jetpacks to multi-person pressurized excursion vehicles combined with Phobos surface and orbital (L1, L4/L5, 20km Distant Retrograde Orbit) habitat options. Detailed models of propellant mass, crew time, science productivity, radiation exposure, systems and consumables masses, and other figures of merit were integrated to enable quantitative comparison of different architectural options. Options for pre-staging assets using solar electric propulsion (SEP) vs. delivering all systems with the crew were also evaluated. Seven discrete mission architectures were evaluated. RESULTS: The driving consideration for habitat location (Phobos surface vs. orbital) was radiation exposure, with an estimated reduction in cumulative mission radiation exposure of up to 34% (vs. Mars orbital mission) when the habitat is located on the Phobos surface, compared with only 3-6% reduction for a habitat in a 20km DRO. The exploration utility of lightweight unpressurized excursion vehicles was limited by the need to remain within 20 minutes of Solar Particle Event radiation protection combined with complex GN&C systems required by the non-intuitive and highly-variable gravitational environment. Two-person pressurized excursion vehicles as well as mobile surface habitats offer significant exploration capability and operational benefits compared with unpressurized EVA mobility systems at the cost of increased system and propellant mass. Mechanical surface translation modes (i.e. hopping) were modeled and offer potentially significant propellant savings and the possibility of extended exploration operations between crewed missions. Options for extending the utilization of the crew taxi vehicle were examined, including use as an exploration asset for Phobos surface exploration (when combined with an alternate mobility system) and as an EVA platform, both on Phobos and for contingency EVA on the Mars Transit Habitat. CONCLUSIONS: Human exploration of Phobos offers a scientifically meaningful first step towards human Mars surface missions that develops and validates transportation, habitation, and exploration systems and operations in advance of the Mars landing systems.

Abercromby, Andrew F. J.↗

Data & Reasoning Fabric Minimum Viable Product

A Data & Reasoning Fabric (DRF) is envisioned to enable the full potential of air mobility by providing all data and reasoning where they are needed. The DRF provides a marketplace based on an open foundational ecosystem of data and reasoning exchange between the many systems that must seamlessly interplay to manage the complex and dense airspace operations required to achieve advanced air mobility goals. The DRF marketplace is decentralized and will not be owned by any single party. To deliver reference designs and development environments that catalyze broad private and public sector buy-in and self-sustaining development of DRF and associated standards, DRF activities will collaboratively test these technologies, open standards and architectures, and an integrated framework with end-users. The DRF activity is developing a Minimum Viable Product (MVP) called the DRF Accelerator which will enable the rapid deployment of candidate data and reasoning services to test and evaluate the DRF core system functionality. The DRF Project is engaging with government and industry end-users and stakeholders, to: (1) assess the technical feasibility of the DRF Accelerator; (2) assess the likelihood of adoption, through shared test and evaluation; and (3) identify what data and services can be shared across DRF.

DRF↗

Editorial: Towards the rapid and systematic assessment of vaccine technologies

The COVID-19 pandemic highlighted both the extraordinary potential of modern vaccinology and persistent challenges in how vaccine technologies are assessed. While vaccines can be developed and deployed at unprecedented speed, our ability to predict efficacy in a population is constrained by methodological difficulties, underreporting of negative results, and limited comparability across studies. This editorial introduces a Research Topic that brings together an interdisciplinary collection of experimental, computational, and theoretical contributions spanning multiple pathogens and vaccine platforms. Across these contributions, emerging themes emphasize the need for standardized immunogenicity metrics, transparent reporting including negative findings, and harmonized experimental protocols to support meaningful comparisons. This editorial highlights community practices and shared commitments – supported by researchers, funders, and journals – that could strengthen reproducibility, transparency, and cumulative learning in vaccine research.

59 BASIC BIOLOGICAL SCIENCES↗

Simulation and Flight Test Data Collection Review for Supporting Phase 1 Detect and Avoid MOPS

RTCA Special Committee 228 is a consortium of government, industry, and academic organizations tasked to develop minimum operational performance standards for UAS detect and avoid systems. The UAS in the NAS (National Airspace System) project is studying the minimum operational performance standards for unmanned aerial systems (UAS's) detect-and-avoid (DAA) system in order to operate in the National Airspace System. Over the past 3 years, the project has executed a series of fast-time simulation, human-in-the-loop experiments, and flight tests in support of this effort. The purpose of this briefing is to summarize the models developed and data collected to overcome UAS integration barriers, so UAS can remain well clear of all traffic.

Santiago, Confesor↗

The Value of Data and Metadata Standardization for Interoperability in Giovanni Or: Why Your Product's Metadata Causes Us Headaches!

Giovanni is a data exploration and visualization tool at the NASA Goddard Earth Sciences Data Information Services Center (GES DISC). It has been around in one form or another for more than 15 years. Giovanni calculates simple statistics and produces 22 different visualizations for more than 1600 geophysical parameters from more than 90 satellite and model products. Giovanni relies on external data format standards to ensure interoperability, including the NetCDF CF Metadata Conventions. Unfortunately, these standards were insufficient to make Giovanni's internal data representation truly simple to use. Finding and working with dimensions can be convoluted with the CF Conventions. Furthermore, the CF Conventions are silent on machine-friendly descriptive metadata such as the parameter's source product and product version. In order to simplify analyzing disparate earth science data parameters in a unified way, we developed Giovanni's internal standard. First, the format standardizes parameter dimensions and variables so they can be easily found. Second, the format adds all the machine-friendly metadata Giovanni needs to present our parameters to users in a consistent and clear manner. At a glance, users can grasp all the pertinent information about parameters both during parameter selection and after visualization.

interoperability↗

The Generality of the GUGA MRCI Approach in COLUMBUS for Treating Complex Quantum Chemistry

The core part of the program system COLUMBUS allows highly efficient calculations using variational multireference (MR) methods in the framework of configuration interaction with single and double excitations (MR-CISD) and averaged quadratic coupled-cluster calculations (MR-AQCC), based on uncontracted sets of configurations and the graphical unitary group approach (GUGA). The availability of analytic MR-CISD and MR-AQCC energy gradients and analytic nonadiabatic couplings for MR-CISD enables exciting applications including, e.g., investigations of π-conjugated biradicaloid compounds, calculations of multitudes of excited states, development of diabatization procedures, and furnishing the electronic structure information for on-the-fly surface nonadiabatic dynamics. With fully variational uncontracted spin-orbit MRCI, COLUMBUS provides a unique possibility of performing high-level calculations on compounds containing heavy atoms up to lanthanides and actinides. Crucial for carrying out all of these calculations effectively is the availability of an efficient parallel code for the CI step. Configuration spaces of several billion in size now can be treated quite routinely on standard parallel computer clusters. Emerging developments in COLUMBUS, including the all configuration mean energy multiconfiguration self-consistent field method and the graphically contracted function method, promise to allow practically unlimited configuration space dimensions. Spin density based on the GUGA approach, analytic spin-orbit energy gradients, possibilities for local electron correlation MR calculations, development of general interfaces for nonadiabatic dynamics, and MRCI linear vibronic coupling models conclude this overview.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Assessment of Immune Status, Latent Viral Reactivation and Stress during Long Duration Bed Rest as an Analog for Spaceflight

As logistical access for in-flight space research becomes more limited, the use of ground based spaceflight analogs for life science studies will increase. These studies are particularly important as NASA progresses towards the Lunar and eventually Mars missions outlined in the 2005 Vision for Space Exploration. Countermeasures must be developed to mitigate the clinical risks associated with exploration class space missions. In an effort to coordinate studies across multiple disciplines, NASA has selected 90-day bed rest as the analog of choice, and initiated the Flight Analogs Project to implement research studies with or without the evaluation of countermeasures. Although bed rest is not the analog of choice to evaluate spaceflight-associated immune dysfunction, a standard Immune Assessment was developed for subjects participating in the 90-day bed best studies. The Immune Assessment consists of: leukocyte subset distribution, T cell functional responses, intracellular cytokine production profiles, latent viral reactivation, virus specific T cell levels, virus specific T cell function, stress hormone levels and a behavioral assessment using stress questionnaires. The purpose of the assessment during the initial studies (without countermeasure) is to establish control data against which future studies (with countermeasure) will be evaluated. It is believed that some of the countermeasures planned to be evaluated in future studies, such as exercise, pharmacologic intervention or nutritional supplementation, have the ability to impact immune function. Therefore immunity will likely be monitored during those studies. The data generated during the first three control studies showed that the subjects in general did not display altered peripheral leukocyte subsets, constitutive immune activation, significant latent viral reactivation (EBV, VZV) or altered T cell function. Interestingly, for some subjects the level of constitutively activated T cells (CD8+/CD69+) and virus-specific T cells (CMV and EBV) both decreased during the studies. This likely reflects the isolation of the subjects (from an immunological perspective) and absence of everyday subclinical challenges to the immune system. Cortisol levels (plasma and saliva) did not vary significantly during the studies. This probably reflects a lack of physiological stress during the study and the stress of readaptation to the 1xG environment at R+1. These data demonstrate the absence of significant immune alteration during 90-day bed rest, and establish control data against which future studies (including countermeasures) may be compared.

Crucian, Brian E.↗

The Evolution of Payload Data Capabilities on the Commercial Visiting Vehicles that Service the International Space Station

For over 10 years, NASA has been working with U.S.-based commercial companies to support the design, development, and operations of new commercial space vehicles. The purpose of these vehicles is to provide cargo and crew transportation services to the International Space Station (ISS) and to stimulate the commercial space transportation industry to Low-Earth Orbit (LEO). Along with the ability to provide a couple tons of cargo to the ISS each mission, the commercial visiting vehicles also provide the ability to transfer NASA payloads to and from the ISS in an active, powered state. To take advantage of this capability, NASA requirements for the data services that payloads need while they are integrated into the visiting vehicles have grown with each set of commercial contracts. Today, NASA desires for payload data services encompass a variety of capabilities including payload health and status (H&S) telemetry monitoring, visiting vehicle environment data monitoring, and payload commanding. The intent of these capabilities is to provide payload developers with situational awareness and the ability to quickly diagnose any problems with payload operations prior to vehicle docking or post-landing to support immediate troubleshooting response. As new requirements for payload data services have emerged over the years, the ISS Payload Operations Integration Center (POIC) at the NASA Marshall Space Flight Center (MSFC) has established ground segment interfaces to the visiting vehicle control centers to enable payload developers to use these services. Many technical and programmatic challenges have been faced while establishing these interfaces. The most significant challenge faced has been in finding the right balance amongst providing interfaces to payloads that are compatible with the ISS so that payload hardware or software changes are not necessary to ensure compatibility with the visiting vehicles; keeping POIC ground system development costs low by standardizing implementation approaches across commercial vehicle partners; and fostering commercialization through supporting vendor-unique implementations that are commercially economical. This paper will first detail the data services that will be available to payload users under each commercial visiting vehicle contract. Secondly, this paper will offer discussion of the most significant technical and programmatic challenges faced to-date in offering these new data services to payload developers.

Wiggins, Lindsay M.↗

Mercury Atomic Frequency Standards for Space Based Navigation and Timekeeping

A low power Mercury Atomic Frequency Standard (MAFS) has been developed and demonstrated on the path towards future space clock applications. A self contained mercury ion breadboard clock: emulating flight clock interfaces, steering a USO local oscillator, and consuming approx 40 Watts has been operating at JPL for more than a year. This complete, modular ion clock instrument demonstrates that key GNSS size, weight, and power (SWaP) requirements can be achieved while still maintaining short and long term performance demonstrated in previous ground ion clocks. The MAFS breadboard serves as a flexible platform for optimizing further space clock development and guides engineering model design trades towards fabrication of an ion clock for space flight.

Global Positioning Systems (GPS)↗

The Artificial Intelligence Ontology: LLM-Assisted Construction of AI Concept Hierarchies

The Artificial Intelligence Ontology (AIO) is a systematization of artificial intelligence (AI) concepts, methodologies, and their interrelations. Developed via manual curation, with the additional assistance of large language models (LLMs), AIO aims to address the rapidly evolving landscape of AI by providing a comprehensive framework that encompasses both technical and ethical aspects of AI technologies. The primary audience for AIO includes AI researchers, developers, and educators seeking standardized terminology and concepts within the AI domain. We use the term “branches” for classes, and their subclasses, in our ontology that are subclasses of owl:Thing. AIO contains eight branches: Bias, Layer, Machine Learning Task, Mathematical Function, Model, Network, Preprocessing, and Training Strategy, each designed to support the modular composition of AI methods and facilitate a deeper understanding of deep learning architectures and ethical considerations in AI. AIO uses the Ontology Development Kit (ODK) for its creation and maintenance, with its content being more easily updated through AI-driven curation support. This approach not only ensures the ontology's relevance amidst the fast-paced advancements in AI but also significantly enhances its utility for researchers, developers, and educators by simplifying the integration of new AI concepts and methodologies. The ontology's utility is demonstrated through the annotation of AI methods data in a catalog of AI research publications and the integration into the BioPortal ontology resource, highlighting its potential for cross-disciplinary research. The AIO ontology is open source and is available on GitHub ( https://w3id.org/aio/ ) and BioPortal ( https://bioportal.bioontology.org/ontologies/AIO ).

Joachimiak, Marcin P. [Biosystems Data Science Dep↗