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INCREASING THE TRANSPARENCY AND REPRODUCIBILITY OF SPACE RADIATION SCIENCE: THE RADIATION BIOLOGY ONTOLOGY

Among the primary objectives of the Open/Open-Source Science paradigm are making scientific investigation data transparent and results reproducible [1], objectives shared by the FAIR principles [2]. To accomplish this, the conceptual framework that includes all the investigation objects needs to be accurately captured and communicated to all data consumers. A large part of this requires using metadata standards to annotate data collected. These standards should be readily accessible, informed by scientific community consensus and sufficiently specific to encompass all of the important aspects of the investigation. Starting in 2020 we have been co-leading an open consortium to develop a new metadata standard, the Radiation Biology Ontology (RBO), through the Open Biological and Biomedical Ontologies (OBO) Foundry [3]. We began by transforming many of the terms from the National Council on Radiation Protection and Measurement into concepts that can be formally related to existing OBO Foundry classes or attributes. We then identified and imported into the RBO existing OBO Foundry classes that have obvious relevance for radiation biomedicine (for example, concepts from the Environment Ontology that describe radiative processes, and concepts from the Gene Ontology dealing with molecular and cellular responses to radiation). Finally, we scrutinized datasets from investigations of radiation effects held in NASA GeneLab and LSDA repositories and added additional classes, instances, and attributes into the RBO that should be used to annotate these data. We developed the RBO using the open-source tools of GitHub and publish the RBO periodically through the NIH/NCBI BioPortal website, so systems worldwide can leverage the knowledge it contains [4]. This initial phase of concept modeling has yielded an RBO that at present has more than 300 declared concepts, with more than 3500 additional concepts imported from other OBO Foundry ontologies. While this first phase has focused on concepts for annotating samples, environments, exposures, and measurements, the next phase will center on supporting annotation of results and findings, such as concept models of molecular, cellular and tissue effects. The value of the RBO will be determined in part by our ability to engage the community in its development, and we have established a Radiobiology Informatics Consortium with unrestricted membership as the owner of the RBO in order to encourage investigators, system owners and other to join in this effort. Anyone can report issues or request new concept modeling or other features directly on GitHub. By using the BioPortal application programming interface, systems can pose dynamic queries to the latest version of the RBO for information on individual classes or entire hierarchies; this design eliminates the need for systems to be updated in order to use newer versions of the RBO. We hope to contribute to the advancement of open radiobiological science through the continued, open development of the RBO, that will provide more precise, machine-interpretable descriptions of investigations, as well as support data meta-analysis through machine learning or other artificial intelligence methods. REFERENCES [1] Open science in space. Nature Medicine, 2021. 27(9): p. 1485-1485. [2] Wilkinson, M.D., et al., The FAIR Guiding Principles for scientific data management and stewardship. Sci Data, 2016. 3: p. 160018. [3] Smith, B., et al., The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol, 2007. 25(11): p. 1251-5. [4] Whetzel, P.L., et al., BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res, 2011. 39(Web Server issue): p. W541-5.

informatics↗

NASA NTRS2017

Validation of a Manually Oscillating Chair for In-The-Field Assessment of Dynamic Visual Acuity on Crewmembers Within Hours of Returning From Long-Duration Spaceflight

Long-duration spaceflight results in sensorimotor adaptations, which cause functional deficits during gravitational transitions, such as landing on a planetary surface after long-duration microgravity exposure. Both the vestibular system and the central nervous system are affected by gravitational transitions. These systems are responsible for coordinating head and eye movements via the vestibulo-ocular reflex (VOR) and go through an adaptation period upon exposure to microgravity. Consequently, they must also re-adapt to Earth's gravitational environment upon landing. This re-adaptation causes decrements in gaze control and dynamic visual acuity, with crewmembers reporting oscillopsia and blurred vision caused by retinal slip, or the inability to keep an image focused on their retina. This is thought to drive motion sickness symptoms experienced by most crewmembers following landing. Retinal slip can be estimated by dynamic visual acuity (DVA); visual acuity while in motion. Previously, DVA has been assessed in the laboratory where subjects walked at 6.4 km/hr on a motorized treadmill. Using this method, Peters et al. (2011) found that DVA is worsened in astronauts by an average of 0.75 eye-chart lines one day after landing. However, it is believed that re-adaptation occurs quickly and that DVA might be worse immediately upon re-exposure to a gravitational environment. Since many crewmembers are unable to walk safely upon landing, it was necessary to develop a method for replicating the vertical head movements associated with walking. In addition, the use of a chair to imitate the head displacement caused by walking isolates eye-head interactions without allowing for trunk and lower-body compensation, as seen with treadmill walking (Mulavara & Bloomberg 2003). Therefore, a modality for assessing DVA in the field within a few hours of landing was developed. In this study, we validated the ability of a manually operated oscillating chair to reproduce the oscillatory frequency of walking on a treadmill. Healthy non-astronaut subjects (n=14) participated in one test session and completed three static (seated) and three dynamic (walking/oscillated) visual acuity tests. DVA was assessed using a motorized treadmill, an automated oscillating chair, and a manually operated chair, both developed in the Neuroscience Laboratory at JSC. The automated chair was motor-driven and set to oscillate vertically at 2 Hz with a vertical displacement of +/- 5 cm to simulate vertical translation while walking. The manually operated chair was oscillated vertically by a test operator to the beat of a metronome at 120 beats/min (2 Hz) and a vertical displacement of approximately +/- 5 cm. As the subject was oscillated, they were asked to discern the direction gap of Landolt-C optotypes of varying sizes and verbally reported the direction while an operator recorded their response using a gamepad. Subjects were outfitted with accelerometers (sampling rate = 128 Hz) on their head, trunk and lumbar spine. A fast Fourier transform was performed on the vertical trunk acceleration to compare the peak and spread of the distribution of oscillation frequencies for each oscillating condition. The spread of the frequency distribution for the manual chair was not significantly different from either the treadmill or the automated chair. However, all three conditions had similar non-zero standard error values, suggesting a variance in head movement frequency which may affect DVA. The average oscillation frequency of the manual chair (1.85 Hz) was significantly different (α=0.05) from that of treadmill walking (2.24 Hz), but not significantly different from that of the automated chair (1.85 Hz) and all three conditions had small standard errors (SEM = 0.04, 0.06, and 0.08 Hz for manual, treadmill, and automated respectively). This implies that both chairs oscillate at a frequency below that of treadmill walking, but are comparable to each other and reproducible across sessions. Additionally, DVA scores did not vary significantly across conditions. The smaller spread values of the oscillating chairs' frequencies indicated mitigation of variation induced by locomotor strategies, which enables better examination of the issue of VOR adaptation. Furthermore, due to the deconditioned state of crewmembers in the initial hours after landing, it is easier to transport a manual bouncing chair into the field and safer to perform a vision test while seated in a chair versus walking on a treadmill. Therefore, the manually oscillating chair has been deemed to meet and exceed the DVA testing capabilities previously obtained by treadmill walking.

Kreutzberg, G. A.↗

NASA NTRS2014

The CCSDS Next Generation Space Data Link Protocol (NGSLP)

The CCSDS space link protocols i.e., Telemetry (TM), Telecommand (TC), Advanced Orbiting Systems (AOS) were developed in the early growth period of the space program. They were designed to meet the needs of the early missions, be compatible with the available technology and focused on the specific link environments. Digital technology was in its infancy and spacecraft power and mass issues enforced severe constraints on flight implementations. Therefore the Telecommand protocol was designed around a simple Bose, Hocquenghem, Chaudhuri (BCH) code that provided little coding gain and limited error detection but was relatively simple to decode on board. The infusion of the concatenated Convolutional and Reed-Solomon codes5 for telemetry was a major milestone and transformed telemetry applications by providing them the ability to more efficiently utilize the telemetry link and its ability to deliver user data. The ability to significantly lower the error rates on the telemetry links enabled the use of packet telemetry and data compression. The infusion of the high performance codes for telemetry was enabled by the advent of digital processing, but it was limited to earth based systems supporting telemetry. The latest CCSDS space link protocol, Proximity-1 was developed in early 2000 to meet the needs of short-range, bi-directional, fixed or mobile radio links characterized by short time delays, moderate but not weak signals, and short independent sessions. Proximity-1 has been successfully deployed on both NASA and ESA missions at Mars and is planned to be utilized by all Mars missions in development. A new age has arisen, one that now provides the means to perform advanced digital processing in spacecraft systems enabling the use of improved transponders, digital correlators, and high performance forward error correcting codes for all communications links. Flight transponders utilizing digital technology have emerged and can efficiently provide the means to make the next leap in performance for space link communications. Field Programmable Gate Arrays (FPGAs) provide the capability to incorporate high performance forward error correcting codes implemented within software transponders providing improved performance in data transfer, ranging, link security, and time correlation. Given these synergistic technological breakthroughs, the time has come to take advantage of them in applying them to both on going (e.g., command, telemetry) and emerging (e.g., space link security, optical communication) space link applications. However one of the constraining factors within the Data Link Layer in realizing these performance gains is the lack of a generic transfer frame format and common supporting services amongst the existing CCSDS link layer protocols. Currently each of the four CCSDS link layer protocols (TM, TC, AOS, and Proximity-1) have unique formats and services which prohibits their reuse across the totality of all space link applications of CCSDS member space agencies. For example, Mars missions. These missions implement their proximity data link layer using the Proximity-1 frame format and the services it supports but is still required to support the direct from Earth (TC) protocols and the Direct To Earth (AOS/TM) protocols. The prime purpose of this paper, is to describe a new general purpose CCSDS Data Link layer protocol, the NGSLP that will provide the required services along with a common transfer frame format for all the CCSDS space links (ground to/from space and space to space links) targeted for emerging missions after a CCSDS agency-wide coordinated date. This paper will also describe related options that can be included for the Coding and Synchronization sub-layer of the Data Link layer to extend the capacities of the link and additionally provide an independence of the transfer frame sub-layer from the coding sublayer. This feature will provide missions the option of running either the currently performed synchronous coding and transfer frame data link or an asynchronous coding/frame data link, in which the transfer frame length is independent of the block size of the code. The benefits from the elimination of this constraint (frame synchronized to the code block) will simplify the interface between the transponder and the data handling equipment and reduce implementation costs and complexities. The benefits include: inclusion of encoders/decoders into transmitters and receivers without regard to data link protocols, providing the ability to insert latency sensitive messages into the link to support launch, landing/docking, telerobotics. and Variable Coded Modulation (VCM). In addition the ability to transfer different sized frames can provide a backup for delivering stored anomaly engineering data simultaneously with real time data, or relaying of frames from various sources onto a trunk line for delivery to Earth.

Kazz, Greg J.↗