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NASA NTRSDate not supplied

NASA Delay Tolerant Networks: Operational, Evolving, an Ready for Expansion

The future of humanity’s presence beyond Earth depends on the successful commercialization of space. For commercialization to succeed, companies need cost-efficient architectures to support their business models and minimize risks for human capital, design, development, and operations. An ongoing challenge to any space enterprise is the reality that terrestrial network technologies are insufficient to provide reliable communications between assets in space. Whether you need to ensure your valuable data is safely transmitted to the ground or reliably delivered between platforms in orbit, ensuring data integrity over intermittent communication links is a necessity. Current solutions to space communications rely heavily on manual recording, storing, and retrieval of data from spacecraft. The current standard in space communication protocols, Consultative Committee for Space Data Systems (CCSDS) Space Packet standard, is reliant on inflexible network architectures based around mission-critical infrastructure to ensure data delivery. However, by automating the recording, storing, retrieval, and verification of data with Delay Tolerant Networks (DTN), the operator is freed from the dependence on manual data management and expensive mission critical infrastructure. NASA has been developing delay tolerant systems since the late 1990’s. Multiple DTN implementations have been established during that time, each suited to different use cases. Most notably, the DTN deployment for the International Space Station (ISS) includes demonstration of two DTN technologies: Interplanetary Overlay Network (ION) and Delay Tolerant Network Marshall Enterprise (DTNME). Beyond ISS, there are even more NASA DTN deployments being considered. Now that DTN implementations are maturing, it is appropriate to reflect upon these decades of work, review the integration and performance of the existing ISS deployment, and explore the future possibilities for DTN deployment industry-wide. The ISS DTN deployment is a complex architecture consisting of different DTN implementations for the onboard and ground network environments. The ION DTN implementation is being used in the on-board network. The Huntsville Operations Support Center (HOSC) DTN implementation, DTNME, is used by the ground network supporting ISS and will soon be a second onboard gateway too. The two implementations work cooperatively to provide high fidelity data services to flight operations users and payload developers across the globe. Though the two implementations yield a quality service, limitations are evident. Data rate, data storage, and device management are constrained by the services themselves and the complex nature of the deployment. Evolution of operations concepts will improve system capabilities and stability, but significant improvement will require additional development to the implementations themselves and to the overall deployment architecture. Taking advantage of the ongoing development and operation of the ISS DTN service will be central to the success of the future evolutions of NASA DTN deployments while demonstrating the benefits of DTN’s low-cost reliable data communication protocols for the growing commercial space industry. A broad effort on DTN integration and support is necessary to promote expansion beyond existing applications. NASA is developing several useful DTN implementations across a number of different systems: ION, DTNME, High-Rate DTN (HDTN), Bundle Protocol Library (BPLib), and others. To prevent fragmentation, DTN implementation teams need to communicate, collaborate, and integrate with one another to build a solid operational foundation for new DTN deployments. The establishment of a group that can assist new DTN users with understanding the purpose of each DTN implementation, provide best practices, and serve as a general knowledge base is paramount. Potential use of DTN on Gateway and other future NASA missions further drives the need for streamlined communication between DTN implementation teams. A well-integrated and highly engaged NASA DTN working group should help provide system architects the best DTN solutions for future commercial space efforts. This paper will first review the history of DTN implementations, explore the shortcoming of current space networking solutions given available limits in technology, and therefore establish the need for Delay Tolerant Networking in space communications. Secondly, the authors will explore NASA’s array of DTN implementations and highlight their usefulness to space applications. Thirdly, this paper will establish general DTN implementation distinguishing factors. Fourthly, the authors will discuss attempts to create a generic DTN comparison matrix, and the authors will review potential future topics in DTN innovation and collaboration, highlighting several key future efforts. Finally, this paper will describe how the institution of a NASA DTN Working Group will benefit DTN adoption across the governmental and commercial space sector. The goal of this paper is to encourage enthusiasm for DTN, share strategies for improving DTN on both current and future applications, promote the collaboration of DTN implementation groups within the international space operations community, and open the conversations about DTN, priorities, complexities, and innovation to the wider spaceflight industry.

DTN↗
NASA NTRSDate not supplied

NASA Delay Tolerant Networks: Operational, Evolving, an Ready for Expansion

The future of humanity’s presence beyond Earth depends on the successful commercialization of space. For commercialization to succeed, companies need cost-efficient architectures to support their business models and minimize risks for human capital, design, development, and operations. An ongoing challenge to any space enterprise is the reality that terrestrial network technologies are insufficient to provide reliable communications between assets in space. Whether you need to ensure your valuable data is safely transmitted to the ground or reliably delivered between platforms in orbit, ensuring data integrity over intermittent communication links is a necessity. Current solutions to space communications rely heavily on manual recording, storing, and retrieval of data from spacecraft. The current standard in space communication protocols, Consultative Committee for Space Data Systems (CCSDS) Space Packet standard, is reliant on inflexible network architectures based around mission-critical infrastructure to ensure data delivery. However, by automating the recording, storing, retrieval, and verification of data with Delay Tolerant Networks (DTN), the operator is freed from the dependence on manual data management and expensive mission critical infrastructure. NASA has been developing delay tolerant systems since the late 1990’s. Multiple DTN implementations have been established during that time, each suited to different use cases. Most notably, the DTN deployment for the International Space Station (ISS) includes demonstration of two DTN technologies: Interplanetary Overlay Network (ION) and Delay Tolerant Network Marshall Enterprise (DTNME). Beyond ISS, there are even more NASA DTN deployments being considered. Now that DTN implementations are maturing, it is appropriate to reflect upon these decades of work, review the integration and performance of the existing ISS deployment, and explore the future possibilities for DTN deployment industry-wide. The ISS DTN deployment is a complex architecture consisting of different DTN implementations for the onboard and ground network environments. The ION DTN implementation is being used in the on-board network. The Huntsville Operations Support Center (HOSC) DTN implementation, DTNME, is used by the ground network supporting ISS and will soon be a second onboard gateway too. The two implementations work cooperatively to provide high fidelity data services to flight operations users and payload developers across the globe. Though the two implementations yield a quality service, limitations are evident. Data rate, data storage, and device management are constrained by the services themselves and the complex nature of the deployment. Evolution of operations concepts will improve system capabilities and stability, but significant improvement will require additional development to the implementations themselves and to the overall deployment architecture. Taking advantage of the ongoing development and operation of the ISS DTN service will be central to the success of the future evolutions of NASA DTN deployments while demonstrating the benefits of DTN’s low-cost reliable data communication protocols for the growing commercial space industry. A broad effort on DTN integration and support is necessary to promote expansion beyond existing applications. NASA is developing several useful DTN implementations across a number of different systems: ION, DTNME, High-Rate DTN (HDTN), Bundle Protocol Library (BPLib), and others. To prevent fragmentation, DTN implementation teams need to communicate, collaborate, and integrate with one another to build a solid operational foundation for new DTN deployments. The establishment of a group that can assist new DTN users with understanding the purpose of each DTN implementation, provide best practices, and serve as a general knowledge base is paramount. Potential use of DTN on Gateway and other future NASA missions further drives the need for streamlined communication between DTN implementation teams. A well-integrated and highly engaged NASA DTN working group should help provide system architects the best DTN solutions for future commercial space efforts. This paper will first review the history of DTN implementations, explore the shortcoming of current space networking solutions given available limits in technology, and therefore establish the need for Delay Tolerant Networking in space communications. Secondly, the authors will explore NASA’s array of DTN implementations and highlight their usefulness to space applications. Thirdly, this paper will establish general DTN implementation distinguishing factors. Fourthly, the authors will discuss attempts to create a generic DTN comparison matrix, and the authors will review potential future topics in DTN innovation and collaboration, highlighting several key future efforts. Finally, this paper will describe how the institution of a NASA DTN Working Group will benefit DTN adoption across the governmental and commercial space sector. The goal of this paper is to encourage enthusiasm for DTN, share strategies for improving DTN on both current and future applications, promote the collaboration of DTN implementation groups within the international space operations community, and open the conversations about DTN, priorities, complexities, and innovation to the wider spaceflight industry.

DTN↗
DOE OSTI2022

BASS. XXV. DR2 Broad-line-based Black Hole Mass Estimates and Biases from Obscuration

We present measurements of broad emission lines and virial estimates of supermassive black hole masses (M BH ) for a large sample of ultrahard X-ray-selected active galactic nuclei (AGNs) as part of the second data release of the BAT AGN Spectroscopic Survey (BASS/DR2). Our catalog includes M BH estimates for a total of 689 AGNs, determined from the Hα, Hβ, Mg II λ2798, and/or C IV λ1549 broad emission lines. The core sample includes a total of 512 AGNs drawn from the 70 month Swift/BAT all-sky catalog. We also provide measurements for 177 additional AGNs that are drawn from deeper Swift/BAT survey data. We study the links between M BH estimates and line-of-sight obscuration measured from X-ray spectral analysis. We find that broad Hα emission lines in obscured AGNs ($\mathrm{log}({N}_{{\rm{H}}}/{\mathrm{cm}}^{-2})\gt 22.0$) are on average a factor of ${8.0}_{-2.4}^{+4.1}$ weaker relative to ultrahard X-ray emission and about ${35}_{-12}^{\,+7}$% narrower than those in unobscured sources (i.e., $\mathrm{log}({N}_{{\rm{H}}}/{\mathrm{cm}}^{-2})\lt 21.5$). This indicates that the innermost part of the broad-line region is preferentially absorbed. Consequently, current single-epoch M BH prescriptions result in severely underestimated (>1 dex) masses for Type 1.9 sources (AGNs with broad Hα but no broad Hβ) and/or sources with $\mathrm{log}({N}_{{\rm{H}}}/{\mathrm{cm}}^{-2})\gtrsim 22.0$. We provide simple multiplicative corrections for the observed luminosity and width of the broad Hα component (L[bHα] and FWHM[bHα]) in such sources to account for this effect and to (partially) remedy M BH estimates for Type 1.9 objects. As a key ingredient of BASS/DR2, our work provides the community with the data needed to further study powerful AGNs in the low-redshift universe.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1994

Automated protein crystal growth facility

A customer for the protein crystal growth facility fills the specially designed chamber with the correct solutions, fills the syringes with their quenching solutions, and submits the data needed for the proper growth of their crystal. To make sure that the chambers and syringes are filled correctly, a NASA representative may assist the customer. The data needed is the approximate growth time, the growth temperature, and the desired crystal size, but this data can be changed anytime from the ground, if needed. The chambers are gathered and placed into numbered slots in special drawers. Then, data is entered into a computer for each of the chambers. Technicians map out when each chamber's growth should be activated so that all of the chambers have enough time to grow. All of this data is up-linked to the space station when the previous growth session is over. Anti-vibrational containers need to be constructed for the high forces encountered during the lift off and the landing of the space shuttle, and though our team has not designed these containers, we do not feel that there is any reason why a suitable one could not be made. When the shuttle reaches the space station, an astronaut removes a drawer of quenched chambers from the growth facility and inserts a drawer of new chambers. All twelve of the drawers can be replaced in this fashion. The optical disks can also be removed this way. The old drawers are stored for the trip back to earth. Once inside the growth facility, a chamber is removed by the robot and placed in one of 144 active sites at a time previously picked by a technician. Growth begins when the chamber is inserted into an active site. Then, the sensing system starts to determine the size of the protein crystal. All during the crystal's growth, the customer can view the crystal and read all of the crystal's data, such as growth rate and crystal size. When the sensing system determines that the crystal has reached the predetermined size, the robot is told to pick up a syringe filled with the correct quenchant solution and inject it into the chamber to stop the crystal growth. The chamber is then removed from the active site and placed into its original storage slot. Another chamber is then placed into the active site and the process is repeated in all of the active sites until all of the chambers have complted their growth. After ninety days (the scheduled time between shuttle visits), the crystal growth is completed, and the old drawers are replaced with new ones. Once the customer extracts the crystals, the chambers are retrieved for future customers.

Donald, Stacey↗
DOE OSTI2024

HERO WEC - Bills of Materials: WEC, RO System, and Submersible Pump

This submission includes detailed Bills of Materials for the NREL-designed and -built Hydraulic and Electric Reverse Osmosis Wave Energy Converter (HERO WEC), as well as the reverse osmosis assembly and submersible pump that are used in the HERO WEC. The WEC file is specific to the components and sub-components that are included on the in-water buoy portion of the WEC. The RO file is specific to the components and sub-components that are included on the reverse osmosis module that is used for both the hydraulic and electric configuration. The submersible pumps file is specific to the components and sub-components that are included on the submersible pump module that is used feed the reverse osmosis module when the HERO WEC is in the electric configuration. In addition to this submission, an additional submission available for the WEC model itself, including the power electronics enclosure, and reverse osmosis assembly that is needed to supply water in the electric submission. A link is provided below. More details on this project including data, CAD drawings, etc. can be found in the HERO-WEC main page link below. This data set has been developed by the National Renewable Energy Laboratory, operated by Alliance for Sustainable Energy, LLC, for the U.S. Department of Energy (DOE) under Contract No. DE-AC36-08GO28308. Funding provided U.S. Department of Energy Office of Energy Efficiency and Renewable Energy Water Power Technologies Office.

16 TIDAL AND WAVE POWER↗
NASA NTRS2003

Small Particle Response to Fluid Motion Using Tethered Particles to Simulate Microgravity

This paper reports on ground based work conducted to support the Spaceflight Definition project SHIVA (Spaceflight Holography Investigation in a Virtual Apparatus). SHIVA will advance our understanding of the movement of a particle in a fluid. Gravity usually dominates the equations of motion, but in microgravity as well as on earth other terms can become important. Through an innovative application of fractional differential equations, two members of our team produced the first analytical solution of a fundamental equation of motion, which had only been solved numerically or by approximation before. The general solution predicts that the usually neglected history term becomes important in particle response to a sinusoidal fluid movement when the characteristic viscous time is in the same order as the fluid oscillation period and peaks when the two times are equal. In this case three force terms, the Stokes drag, the added mass, and the history drag must all be included in predicting particle movement. We have developed diagnostic recording methods using holography to save all of the particle field data, allowing the experiment to essentially be transferred from space back to earth in what we call the virtual apparatus for on-earth microgravity experimentation. We can quantify precisely the three-dimensional motion of sets of particles, allowing us to test and apply the new analytical solutions. We are examining the response of particles up to 2 mm radius to fluid oscillation at frequencies up to 80 Hz with amplitudes up to 200 microns. Ground studies to support the flight development program have employed various schemes to simulate microgravity. One of the most reliable and meaningful methods uses spheres tethered to a fine hair suspended in the fluid. We have also investigated particles with nearly neutral buoyancy. Recordings are made at the peak amplitudes of vibration of the cell providing a measure of the ratio of fluid to particle amplitude. The experiment requires precise location of the particle to within microns during recording, and techniques for achieving this are one of the project challenges. Focused microscopic images and diffraction patterns are used. To make the experiment more versatile, the spaceflight system will record holograms both on film and electronically. A cross correlation procedure enables sub pixel accuracies for electronic recordings, partially accommodating the lower spatial resolution of CCDs. The electronic holograms can be down linked providing real time data. Results of the ground experiments, the flight experiment design, and data analysis procedures are reported.

Trolinger, James↗
NASA NTRS2003

Cost and Performance Comparison of an Earth-Orbiting Optical Communication Relay Transceiver and a Ground-Based Optical Receiver Subnet

Optical communications can provide high-data-rate telemetry from deep-space probes with subsystems that have lower mass, consume less power, and are smaller than their radio frequency (RF) counterparts. However, because optical communication is more a.ected by weather than is RF communication, it requires groundstation site diversity to mitigate the adverse e.ects of inclement weather on the link. An optical relay satellite is not a.ected by weather and can provide 24-hour coverage of deep-space probes. Using such a relay satellite for the deep-space link and an 8.4-GHz (X-band) link to a ground station would support high-data-rate links from small deep-space probes with very little link loss due to inclement weather. We have reviewed past JPL-funded work on RF and optical relay satellites, and on proposed clustered and linearly dispersed optical subnets. Cost comparisons show that the life cycle costs of a 7-m optical relay station based on the heritage of the Next Generation Space Telescope is comparable to that of an 8-station subnet of 10- m optical ground stations. This makes the relay link an attractive option vis- a-vis a ground-station network.

Wilson, K. E.↗
DOE OSTI2016

T.Rex

T.Rex is used to explore tabular data sets containing up to ten million records to help rapidly understand a previously unknown data set. Analysis can quickly identify patterns of interest and the records and fields that capture those patterns. T.Rex contains a growing set of deep analytical tools and supports robust export capabilities that selected data can be incorporated into to other specialized tools for further analysis. T.Rex is flexible in ingesting different types and formats of data, allowing the user to interactively experiment and perform trial and error guesses on the structure of the data; and also has a variety of linked visual analytic tools that enable exploration of the data to find relevant content, relationships among content, trends within the content, and capture knowledge about the content. Finally, T.Rex has a rich export capability, to extract relevant subsets of a larger data source, to further analyze their data in other analytic tools.

Source record↗
NASA NTRS2004

Integrated Antenna/Solar Array Cell (IA/SAC) System for Flexible Access Communications

Present satellite communications systems normally use separate solar cells and antennas. Since solar cells generally account for the largest surface area of the spacecraft, co-locating the antenna and solar cells on the same substrate opens the possibility for a number of data-rate-enhancing communications link architecture that would have minimal impact on spacecraft weight and size. The idea of integrating printed planar antenna and solar array cells on the same surface has been reported in the literature. The early work merely attempted to demonstrate the feasibility by placing commercial solar cells besides a patch antenna. Recently, Integrating multiple antenna elements and solar cell arrays on the same surface was reported for both space and terrestrial applications. The application of photovoltaic solar cell in a planar antenna structure where the radiating patch antenna is replaced by a Si solar cell has been demonstrated in wireless communication systems (C. Bendel, J. Kirchhof and N. Henze, 3rd Would Photovotaic Congress, Osaka, Japan, May 2003). Based on a hybrid approach, a 6x1 slot array with circularly polarized crossdipole elements co-located on the same surface of the solar cells array has been demonstrated (S. Vaccaro, J. R. Mosig and P. de Maagt, IEEE Trans. Ant. and Propag., Vol. 5 1, No. 8, Aug. 2003). Amorphous silicon solar cells with about 5-10% efficiency were used in these demonstrations. This paper describes recent effort to integrate advanced solar cells with printed planar antennas. Compared to prior art, the proposed WSAC concept is unique in the following ways: 1) Active antenna element will be used to achieve dynamic beam steering; 2) High efficiency (30%) GaAs multi-junction solar cells will be used instead of Si, which has an efficiency of about 15%; 3) Antenna and solar cells are integrated on a common GaAs substrate; and 4) Higher data rate capability. The IA/SAC is designed to operate at X-band (8-12 GH) and higher frequencies Higher operating frequencies enable greater bandwidth and thus higher data transfer rates. The first phase of the effort involves the development of GaAs solar cell MIMs (Monolithically Integrated Module) with a single patch antenna on the opposite side of the substrate. Subsequent work will involve the integration of MIMs and antennas on the same side of the substrate. Results from the phase one efforts will be presented.

Lee, Ricard Q.↗
DOE OSTI2024

Carbon Transport and Storage Planning and Viability Support Tools

The EDX disCO2ver Carbon Transport and Storage Planning and Viability Support Tools are made up of the Carbon Storage Planning Inquiry Tool (CS PlanIT, Justman et al. 2024) and the Carbon Storage Technical Viability Approach Support Tool (CS TVA). Together, these tools support data access to support understanding data availability to support planning efforts for carbon transport and storage. The Carbon Storage Planning Inquiry Tool (CS PlanIT) is an online web mapping application designed to help users explore, query, and evaluate multiple data layers to support and accelerate carbon storage resource and feasibility assessments and planning efforts. CS PlanIT currently contains a range of datasets associated with geologic, technical, and infrastructure factors. The data sets can be filtered geographically for an area of interest to update statistics and charts within the dashboard. The dashboard is divided into different sections called widgets, relating to different steps in the carbon storage planning process. The resources in this submission include a link to PlanIT, as well as a data catalog and link to user documentation. The original citation for the CS PlanIT tool, which has now been integrated into the toolset here, was: - Devin Justman, Scott Pantaleone, Maneesh Sharma, Lucy Romeo, Paige Morkner, CS PlanIT (Carbon Storage Planning Inquiry Tool) , 6/28/2024, https://edx.netl.doe.gov/dataset/cs-planit-carbon-storage-planning-inquiry-tool, DOI: 10.18141/2377953 The Carbon Storage Technical Viability Approach Support (CS TVA) Tool displays spatial data availability for the many components of Geologic Carbon Storage (GCS) technical viability assessment (Creason al 2025). Identifying sites suitable for GCS requires evaluating the intersection of myriad factors, including reservoir conditions, subsurface and surface hazards, infrastructure requirements, and energy community metrics. The technical viability of a site can only be confirmed for instances where all these factors have data available, and where those data support viability. Additional Resources related to the Technical Viability Assessment Tool: - Julia Mulhern, Casey White, Araceli Lara, Neyda Cordero Rodriguez, Zachary Jackson, Jacob Shay, Gabriel Creason, MacKenzie Mark-Moser, Paige Morkner, Kelly Rose, Carbon Storage Technical Viability Approach (CS TVA) Database, 3/26/2025, https://edx.netl.doe.gov/dataset/edx4ccs-carbon-storage-technical-viability-approach-database , DOI:10.18141/1984655 - Julia Mulhern, MacKenzie Mark-Moser, Gabriel Creason, Casey White, Araceli Lara, Neyda Cordero Rodriguez, Zach Jackson, Paige Morkner, Kelly Rose, Carbon Storage Technical Viability Approach (CS TVA) Matrix, 3/27/2025, https://edx.netl.doe.gov/dataset/carbon-storage-technical-viability-approach-cs-tva-matrix , DOI: 10.18141/2539979 - Gabriel Creason, Zach Jackson, Neyda Cordero Rodriguez, Julia Mulhern, Casey White, Araceli Lara, MacKenzie Mark-Moser, Paige Morkner, Kelly Rose, Carbon Storage Technical Viability Approach (CS TVA) Data Availability Results Database, 3/27/2025, https://edx.netl.doe.gov/dataset/carbon-storage-technical-viability-approach-cs-tva-data-availability-results-database, DOI:10.18141/2538557

Carbon storage↗
DOE OSTI2017

Observational Signatures of Cloud–Cloud Collision in the Extended Star-forming Region S235

We present a multi-wavelength data analysis of the extended star-forming region S235 (hereafter E-S235), where two molecular clouds are present. In E-S235, using the {sup 12}CO (1–0) and {sup 13}CO (1–0) line data, a molecular cloud linked with the site “S235main” is traced in a velocity range [−24, −18] km s{sup −1}, while the other one containing the sites S235A, S235B, and S235C (hereafter “S235ABC”) is depicted in a velocity range [−18, −13] km s{sup −1}. In the velocity space, these two clouds are separated by ∼4 km s{sup −1}, and are interconnected by a lower-intensity intermediate velocity emission, tracing a broad bridge feature. In the velocity channel maps, a possible complementary molecular pair at [−21, −20] km s{sup −1} and [−16, −15] km s{sup −1} is also evident. The sites, “S235ABC,” east 1, and south–west, are spatially seen in the interface of two clouds. Together, these observed features are consistent with the predictions of numerical models of the cloud–cloud collision (CCC) process, favoring the onset of the CCC in E-S235 about 0.5 Myr ago. Deep UKIDSS near-infrared photometric analysis of point-like sources reveals significant clustering of young stellar populations toward the sites located at the junction, and the “S235main.” The sites “S235ABC” harbor young compact H ii regions with dynamical ages of ∼0.06–0.22 Myr, and these sites (including south–west and east 1) also contain dust clumps (having M {sub clump} ∼ 40 to 635 M{sub ⊙}). Our observational findings suggest that the star formation activities (including massive stars) appear to be influenced by the CCC mechanism at the junction.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1974

Integrated source and channel encoded digital communications system design study

Studies on the digital communication system for the direct communication links from ground to space shuttle and the links involving the Tracking and Data Relay Satellite (TDRS). Three main tasks were performed:(1) Channel encoding/decoding parameter optimization for forward and reverse TDRS links,(2)integration of command encoding/decoding and channel encoding/decoding; and (3) modulation coding interface study. The general communication environment is presented to provide the necessary background for the tasks and to provide an understanding of the implications of the results of the studies.

Huth, G. K.↗
DOE OSTI2020

BioHackathon 2015: Semantics of data for life sciences and reproducible research

We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Development and data path integration test of the global Feature EXtractor for the ATLAS Level-1 calorimeter trigger system Phase-I upgrade

The global Feature Extractor (gFEX) is a component of the Phase-I upgrade of the Level-1 Calorimeter (L1Calo) trigger system for the ATLAS experiment at the Large Hadron Collider (LHC) at CERN. The gFEX is used to identify patterns of energy associated with the hadronic decays of high momentum Higgs, W and Z bosons, top quarks, and exotic particles in real time at the 40 MHz LHC bunch crossing rate. Three prototypes were implemented and tested from 2014 to 2017. With the lessons learned from the prototypes, the final gFEX production board has been implemented at the end of 2017. The gFEX receives up to 300 fiber optical links from the calorimeter and transmits trigger data on 96 links to the ATLAS Level-1 Topological [1] (L1Topo) trigger at a rate of up to 12.8 Gb/s. There are also 24 electrical links on board for communication between two FPGAs running at speeds of up to 25.6 Gb/s. Here, the hardware functionality and performance of the production board have been evaluated. A data path integration test between the Liquid Argon Digital Processing Blade (LDPB) [2] and the Front End LInk eXchange (FELIX) [3] was performed successfully at CERN in 2018.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2011

Oxidized low-density lipoprotein-induced periodontal inflammation is associated with the up-regulation of cyclooxygenase-2 and microsomal prostaglandin synthase 1 in human gingival epithelial cells

Highlights: {yields} OxLDL-induced responses in human gingival epithelial cells were studied. {yields} OxLDL enhanced the production of IL-8, IL-1{beta} and PGE{sub 2} in Ca9-22 cells. {yields} An NF-{kappa}B inhibitor suppressed the expression of COX-2 and mPGES1 induced by oxLDL. {yields} Unlike the case in macrophages, oxLDL did not increase the CD36 level. -- Abstract: Periodontitis is characterized by chronic gingival tissue inflammation, and inflammatory mediators such as IL-8 and prostaglandin E{sub 2} (PGE{sub 2}) are associated with disease progression. Previously we showed that oxidatively modified low-density lipoprotein (oxLDL) was present in gingival crevicular fluid. In this study, the role of oxLDL in the gingival epithelial cell inflammatory response was further investigated using Ca9-22 cells and primary human oral keratinocytes (HOK). Treatment of Ca9-22 cells and HOK with oxLDL induced an up-regulation of IL-8 and the PGE{sub 2}-producing enzymes, cyclooxygenase-2 and microsomal PGE{sub 2} synthase-1. These responses induced by oxLDL were significantly suppressed by a nuclear factor-kappa B (NF-{kappa}B) inhibitor. However, unlike the result in macrophages, oxLDL did not lead to an increase in CD36 expression in these two cells. These results suggest that oxLDL elicits gingival epithelial cell inflammatory responses through an activation of the NF-{kappa}B pathway. These data suggest a mechanistic link between periodontal disease and lipid metabolism-related disorders, including atherosclerosis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

A secretome analysis reveals that PPARα is upregulated by fractionated-dose γ-irradiation in three-dimensional keratinocyte cultures

Studies have shown that γ-irradiation induces various biological responses, including oxidative stress and apoptosis, as well as cellular repair and immune system responses. However, most such studies have been performed using traditional two-dimensional cell culture systems, which are limited in their ability to faithfully represent in vivo conditions. A three-dimensional (3D) environment composed of properly interconnected and differentiated cells that allow communication and cooperation among cells via secreted molecules would be expected to more accurately reflect cellular responses. Here, we investigated γ-irradiation–induced changes in the secretome of 3D-cultured keratinocytes. An analysis of keratinocyte secretome profiles following fractionated-dose γ-irradiation revealed changes in genes involved in cell adhesion, angiogenesis, and the immune system. Notably, peroxisome proliferator-activated receptor-α (PPARα) was upregulated in response to fractionated-dose γ-irradiation. This upregulation was associated with an increase in the transcription of known PPARα target genes in secretome, including angiopoietin-like protein 4, dermokine and kallikrein-related peptide 12, which were differentially regulated by fractionated-dose γ-irradiation. Collectively, our data imply a mechanism linking γ-irradiation and secretome changes, and suggest that these changes could play a significant role in the coordinated cellular responses to harmful ionizing radiation, such as those associated with radiation therapy. This extension of our understanding of γ-irradiation-induced secretome changes has the potential to improve radiation therapy strategies. - Highlights: • γ-irradiation induced changes of cell adhesion, angiogenesis, and immune system in secretome of 3D-cultured keratinocytes. • Peroxisome proliferator-activated receptor-α (PPARα) was upregulated in response to fractionated-dose γ-irradiation. • The known PPARα target genes were differentially regulated by fractionated-dose γ-irradiation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

The SCF ubiquitin ligase Slimb controls Nerfin-1 turnover in Drosophila

Highlights: • Slimb associates with Nerfin-1 and promotes Nerfin-1 turnover. • The C-terminal half of Nerfin-1 is required for Slimb-binding and Slimb-mediated degradation by UPS. • Slimb regulates Nerfin-1 activity in vivo. The C2H2 type zinc-finger transcription factor Nerfin-1 expresses dominantly in Drosophila nervous system and plays an important role in early axon guidance decisions and preventing neurons dedifferentiation. Recently, increasing reports indicated that INSM1 (homologue to nerfin-1 in mammals) is a useful marker for prognosis of neuroendocrine tumors. The dynamic expression of Nerfin-1 is regulated post-transcriptionally by multiple microRNAs; however, its post-translational regulation is still unclear. Here we showed that the protein turnover of Nerfin-1 is regulated by Slimb, the substrate adaptor of SCF{sup Slimb} ubiquitin ligase complex. Mechanistically, Slimb associates with Nerfin-1 and promotes it ubiquitination and degradation in Drosophila S2R{sup +} cells. Furthermore, we determined that the C-terminal half of Nerfin-1 (Nerfin-1{sup CT}) is required for its binding to Slimb. Genetic epistasis assays showed that Slimb misexpression antagonizes, while knock-down enhances the activity of Nerfin-1{sup CT} in Drosophila eyes. Our data revealed a new link to understand the underlying mechanism for Nerfin-1 turnover in post-translational level, and provided useful insights in animal development and disease treatment by manipulating the activity of Slimb and Nerfin-1.

60 APPLIED LIFE SCIENCES↗