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International Research Results and Accomplishments From the International Space Station - A New Compilation

In 2016, the International Space Station (ISS) partnership published the first-ever compilation of international ISS research publications resulting from research performed on the ISS through 2011 (Expeditions 0 through 30). International Space Station Research Accomplishments: An Analysis of Results. From 2000-2011 is a collection of over 1,200 journal publications that describe ISS research in the areas of biology and biotechnology; Earth and space science; educational activities and outreach; human research; physical sciences; technology development and demonstration; and, results from ISS operations. This paper will summarize the ISS results publications obtained through 2011 on behalf of the ISS Program Science Forum that is made up of senior science representatives across the international partnership. NASA's ISS Program Science office maintains an online experiment database (www.nasa.gov/iss- science) that tracks and communicates ISS research activities across the entire ISS partnership, and it is continuously updated by cooperation and linking with the results tracking activities of each partner. It captures ISS experiment summaries and results and includes citations to the journals, conference proceedings, and patents as they become available. This content is obtained through extensive and regular journal and patent database searches, and input provided by the ISS international partners ISS scientists themselves. The International Space Station Research Accomplishments: An Analysis of Results From 2000-2011 is a testament to the research that was underway even as the ISS laboratory was being built. It rejects the scientific knowledge gained from ISS research, and how it impact the fields of science in both space and traditional science disciplines on Earth. Now, during a time when utilization is at its busiest, and with extension of the ISS through at least 2024, the ISS partners work together to track the accomplishments and the new knowledge gained in a way that will impact humanity like no laboratory on Earth. Examples of the highest pro le publications to date from each discipline will also be presented. As ISS research activities and operations continue, scientific data derived from earlier experiments will continuously be re-examined, refined, and assembled with new data and findings, including data from other fields never considered. New results will be produced, allowing breakthroughs in new areas of research and innovative solutions to problems on Earth. The ISS Program Science Forum will continue to capture and report on these results in the form of journal publications, conference proceedings, and patents. We anticipate that successful ISS research will continue to contribute to the science literature in a way that helps to formulate new hypotheses and conclusions that will enable science advancements across a wide range of scientific disciplines both in space and on Earth.

Ruttley, Tara↗

Causal relationship between mitochondrial-associated proteins and cerebral aneurysms: a Mendelian randomization study

Background Cerebral aneurysm is a high-risk cerebrovascular disease with a poor prognosis, potentially linked to multiple factors. This study aims to explore the association between mitochondrial-associated proteins and the risk of cerebral aneurysms using Mendelian randomization (MR) methods. Methods We used GWAS summary statistics from the IEU Open GWAS project for mitochondrial-associated proteins and from the Finnish database for cerebral aneurysms (uIA, aSAH). The association between mitochondrial-associated exposures and cerebral aneurysms was evaluated using MR-Egger, weighted mode, IVW, simple mode and weighted median methods. Reverse MR assessed reverse causal relationship, while sensitivity analyses examined heterogeneity and pleiotropy in the instrumental variables. Significant causal relationship with cerebral aneurysms were confirmed using FDR correction. Results Through MR analysis, we identified six mitochondrial proteins associated with an increased risk of aSAH: AIF1 (OR: 1.394, 95% CI: 1.109–1.752, p = 0.0044), CCDC90B (OR: 1.318, 95% CI: 1.132–1.535, p = 0.0004), TIM14 (OR: 1.272, 95% CI: 1.041–1.553, p = 0.0186), NAGS (OR: 1.219, 95% CI: 1.008–1.475, p = 0.041), tRNA PusA (OR: 1.311, 95% CI: 1.096–1.569, p = 0.003), and MRM3 (OR: 1.097, 95% CI: 1.016–1.185, p = 0.0175). Among these, CCDC90B, tRNA PusA, and AIF1 demonstrated a significant causal relationship with an increased risk of aSAH (FDR q < 0.1). Three mitochondrial proteins were associated with an increased risk of uIA: CCDC90B (OR: 1.309, 95% CI: 1.05–1.632, p = 0.0165), tRNA PusA (OR: 1.306, 95% CI: 1.007–1.694, p = 0.0438), and MRM3 (OR: 1.13, 95% CI: 1.012–1.263, p = 0.0303). In the reverse MR study, only one mitochondrial protein, TIM14 (OR: 1.087, 95% CI: 1.004–1.177, p = 0.04), showed a causal relationship with aSAH. Sensitivity analysis did not reveal heterogeneity or pleiotropy. The results suggest that CCDC90B, tRNA PusA, and MRM3 may be common risk factors for cerebral aneurysms (ruptured and unruptured), while AIF1 and NAGS are specifically associated with an increased risk of aSAH, unrelated to uIA. TIM14 may interact with aSAH. Conclusion Our findings confirm a causal relationship between mitochondrial-associated proteins and cerebral aneurysms, offering new insights for future research into the pathogenesis and treatment of this condition.

Wang, Shuai↗

Mechanical Properties of Plasma-Sprayed ZrO2-8 wt% Y2O3 Thermal Barrier Coatings

Mechanical behavior of free standing, plasma-sprayed ZrO2-8 wt% Y2O3 thermal barrier coatings, including strength, fracture toughness, fatigue, constitutive relation, elastic modulus, and directionality, has been determined under various loading-specimen configurations. This report presents and describes a summary of mechanical properties of the plasma-sprayed coating material to provide them as a design database.

Choi, Sung R.↗

ECAR: Baseline Characterization Database Verification Report – PCEA Billet 01D3-35

The purpose of this engineering calculations and analysis report (ECAR) is to present data collected in the Baseline Graphite Characterization Program, which is directly tasked with supporting the Idaho National Laboratory’s (INL’s) research and development efforts on the Advanced Reactor Technologies (ART) Program. This program populates a comprehensive database that reflects the baseline properties of nuclear-grade graphite with regard to individual grade, billet, and position within individual billets. The physical- and mechanical-property information collected will be transferred to the Nuclear Data Management and Analysis System (NDMAS), and that database will help populate the handbook of property data available to member nations of the Generation-IV International Forum. Transfer of these data from the applicable technical lead to the dissemination databases available to other end users requires a full review of the test procedures and data-collection efforts through an analysis of the multiple summary spreadsheets and values being collected. This report represents the analysis for PCEA Billet 01D3-35 and facilitates release of associated data to the NDMAS custodians.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Evaluation of New Additions to OLI Software in Predicting Mercuric and Mercurous Species in Liquid Waste Operations

Speciation of mercury during the pretreatment steps of tank waste processing is critical to successful mercury removal prior to vitrification during Liquid Waste Operations (LWO) at SRS. OLI software has been used to predict mercury speciation and activity throughout LWO. The OLI software operates based on a thermodynamic framework called the Mixed Solvent Electrolyte (MSE) framework. The MSE framework allows prediction in theoretically infinitely dilute to concentrated mixtures (e.g., purely solute solutions). Before modification to the MSE framework databanks, certain critical mercury species were missing in the MSE databank, and some thermodynamic data needed to be updated for the OLI software to accurately predict mercury chemical species in SRS waste tanks. To better reflect streams across LWO, new mercury species were integrated into the MSE database. To evaluate the changes to the OLI MSE framework per the Technical Task Request (TTR) and the Task Technical and Quality Assurance Plan (TTQAP), waste stream compositions from Tanks 38, 43, and Tank 50 decontaminated salt solution (DSS) were used as model inputs. Models were developed and executed using both the old and new databases. Compositional analyses from caustic Tank 50 DSS and caustic Tanks 38 and 43 were used as the input streams. These streams represent the most comprehensive chemical data sets where both mercury and tank constituents were measured together. Results for Tank 50 DSS predict HgO as the predominant species in both databases. Both methyl and dimethyl Hg species are present when the new database is ‘on’ and are not predicted with the new database turned ‘off’. The new database predicts a greater amount of HgO and a greater fraction of it in the solid phase. Pourbaix diagrams (potential vs. pH) generated for each Tank 50 DSS were identical regardless of which database was used. Elemental Hg and HgO were predicted in the water stable region under basic conditions. Tanks 38 and 43 follow similar trends as the Tank 50 DSS models. Unlike Tanks 38 and 50 DSS, the Tank 43 Pourbaix plot shows a region of stability for an aqueous HgOHCO3 - species between approximately pH 7-11. In all streams, when MeHg+ is included in the inputs, the new database predicts aqueous MeHgOH as the dominant species. If elemental or dimethyl mercury is in the waste stream, the new database model predicts they are unchanged and remain in those states and quantities. Additionally, the total mercury values are reported for both the measured input data and the OLI output data for all considered tanks. The summary indicates that the percentage error between the measured and calculated values is less than 1% in all cases The reconciliations and generation of the Pourbaix diagrams for Tank 50 DSS took approximately ten times longer with the new database ‘on’. In addition, over the course of that time, models with the new database ‘on’ were more likely to crash or display an error. Some modest performance improvements were noted when modeling with an i7 processor versus an i5. An example error is found in Appendix A. Furthermore, Appendix B provides V&V for two chemical systems analyzed with the OLI software, results were satisfactory. It is recommended to utilize the new databases (i.e., HCO.ddb and SR-Hg.ddb) in future Savannah River Mission Completion applications of OLI to represent pseudo steady-state. Furthermore, the integration and utilization of the new databases (i.e., HCO.ddb and SR-Hg.ddb) in modeling applications (e.g., Aspen) is also recommended.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Enabling Efficient Sparse Computations using Linear Algebra Aware Compilers

This project developed the LAPIS compiler framework, built on the Multilevel Intermediate Representation (MLIR), to optimize sparse linear algebra operations and support performance portability across diverse architectures. The main innovation of LAPIS is the Kokkos dialect, which allows for lowering codes from a high productivity language to different architectures in an elegant way. The dialect also allows the conversion of lower-level MLIR code to C++ Kokkos code, facilitating the integration of scientific machine learning (SciML) models into applications. To extend LAPIS for distributed memory architectures, a new partition dialect was created to manage the distribution of sparse tensors and express communication patterns for sparse linear algebra operations. This dialect also supports the distributed execution of operators and includes algorithmic optimizations to minimize communication to improve performance. The project also demonstrates that MLIR can enable effective linear algebra-level optimizations, improving performance on different GPUs for both sparse and dense linear algebra kernels. Key applications of LAPIS include sparse linear algebra and graph kernels, TenSQL, a relational database management solution built on GraphBLAS, and the development of subgraph isomorphism and monomorphism kernels, showcasing performance portability. In summary, the LAPIS framework supports productivity, performance, portability, and distributed memory execution, while also enabling linear algebra-level optimizations that are challenging in traditional programming languages, with successful applications ranging from simple sparse linear algebra to complex graph kernels.

97 MATHEMATICS AND COMPUTING↗

International Research Results and Accomplishments From the International Space Station

In 2016, the International Space Station (ISS) partnership published the first-ever compilation of international ISS research publications resulting from research performed on the ISS through 2011. The International Space Station Research Accomplishments: An Analysis of Results From 2000-2011 is a collection of summaries of over 1,200 journal publications that describe ISS research in the areas of biology and biotechnology; Earth and space science; educational activities and outreach; human research; physical sciences; technology development and demonstration; and, results from ISS operations. This paper will summarize the ISS results publications obtained through 2011 on behalf of the ISS Program Science Forum that is made up of senior science representatives across the international partnership. NASA's ISS Program Science office maintains an online experiment database (www.nasa.gov/issscience) that tracks and communicates ISS research activities across the entire ISS partnership, and it is continuously updated. It captures ISS experiment summaries and results and includes citations to the journals, conference proceedings, and patents as they become available. The International Space Station Research Accomplishments: An Analysis of Results From 2000-2011 is a testament to the research that was underway even as the ISS laboratory was being built. It reflects the scientific knowledge gained from ISS research, and how it impact the fields of science in both space and traditional science disciplines on Earth. Now, during a time when utilization is at its busiest, and with extension of the ISS through at least 2024, the ISS partners work together to track the accomplishments and the new knowledge gained in a way that will impact humanity like no laboratory on Earth. The ISS Program Science Forum will continue to capture and report on these results in the form of journal publications, conference proceedings, and patents. We anticipate that successful ISS research will continue to contribute to the science literature in a way that helps to formulate new hypotheses and conclusions that will enable science advancements across a wide range of scientific disciplines both in space and on Earth.

Ruttley, Tara M.↗

NASA GRC ICME Schema for Materials Data Management: An Executive Summary

Integrated Computational Materials Engineering (ICME) has received a growing emphasis in attention due its potential impact on rapid material design, reduction in cost and time to market for new applications, and the promise of ‘fit-for-purpose’ materials coupled with recent advances in high performance computing and material characterization tools. However, for an organization to implement ICME practices for material discovery and design, a series of both technical and cultural challenges must be overcome to foster an environment that enables efficient, traceable, and predictive multiscale simulations of material behavior to enable virtual design of materials. In 2016, NASA sponsored a 2040 Vision study to define the potential 25-year future state required for integrated multiscale modeling of materials and systems to improve both the associated time and cost for aerospace and aeronautical innovation. The study envisions a cyber-physical-social ecosystem of experimentally validated computational models, tools, and techniques, along with the associated digital tapestry, that can enable rapid, optimized, ‘fit-for-purpose’ design of materials, components, and systems. A key requirement for such an ecosystem is the development of a robust information management system for materials across their full lifecycle, including material pedigree, experimental (real) and virtual (simulation) data, developed material models, and the implementation of models in engineering applications, such that process-structure-property-performance relationships can be established, thereby enabling the virtual design and optimization of materials. Such an information management system must be able to effectively capture: i) material information at each length scale; ii) test data and analysis; iii) associated material models; and iv) material and model deployment in engineering applications. These systems must also provide traceability between experimental and virtual representations of the material to ensure, when appropriate, the material digital twin is maintained. Additionally, this robust material information management system must be able to seamlessly connect with both commercial and an organization’s in-house software tools, be they analysis tools, other material databases, product lifecycle management (PLM) or simulation data management (SDM) tools, etc., such that automation of the design and analysis of a material across multiple length scales is possible. In this paper, an executive summary of the NASA GRC ICME Schema for materials information management is presented. The database best practices and schema design philosophy specifically for ICME materials data management and an overview description of each element in the schema is given, along with its associated role in an ICME workflow. Additionally, auxiliary tools that interact with the database and provide judicious automation with regards to importing, exporting, and analyzing materials data are presented. Such tools are critical to an ICME ecosystem, not only for their role in enabling optimization, but also in relieving users of tedious manual tasks, thus helping to promote adoption and combat the cultural challenges organizations face in enabling ICME.

Materials↗

BIO-Plex Information System Concept

This paper describes a suggested design for an integrated information system for the proposed BIO-Plex (Bioregenerative Planetary Life Support Systems Test Complex) at Johnson Space Center (JSC), including distributed control systems, central control, networks, database servers, personal computers and workstations, applications software, and external communications. The system will have an open commercial computing and networking, architecture. The network will provide automatic real-time transfer of information to database server computers which perform data collection and validation. This information system will support integrated, data sharing applications for everything, from system alarms to management summaries. Most existing complex process control systems have information gaps between the different real time subsystems, between these subsystems and central controller, between the central controller and system level planning and analysis application software, and between the system level applications and management overview reporting. An integrated information system is vitally necessary as the basis for the integration of planning, scheduling, modeling, monitoring, and control, which will allow improved monitoring and control based on timely, accurate and complete data. Data describing the system configuration and the real time processes can be collected, checked and reconciled, analyzed and stored in database servers that can be accessed by all applications. The required technology is available. The only opportunity to design a distributed, nonredundant, integrated system is before it is built. Retrofit is extremely difficult and costly.

Jones, Harry↗

Travel Patterns and Characteristics of Elderly Population in New York State: 2017 Update

According to US Census Bureau, the elderly population (individuals 65 years and older) has grown by over a third during the past decade (2010 to 2019), and by 3.2% from 2018 to 2019. It is essential for policymakers and planners to understand transportation issues associated with the elderly to meet their increasing travel demands. These issues include transportation and mobility of the elderly population, factors impacting their travel behavior, and transportation safety. In this study, Oak Ridge National Laboratory was tasked by the New York State Department of Transportation (NYSDOT) to conduct a detailed examination of travel behaviors and identify patterns and trends of its elderly residents. The National Household Travel Survey (NHTS) was used as the primary data source to analyze subjects and address questions such as: Are there differences in traveler demographics between the elderly population and those of younger age groups who live in various New York State (NYS) regions, e.g., New York City (NYC), other urban areas of NYS, or other parts of the country? How do they compare with the population at large? Are there any regional differences (e.g., urban versus rural)? Do any unique travel characteristics or patterns exist within the elderly group? How did these patterns change over time? In addition to the analysis of NHTS data, roadway travel safety concerns associated with elderly travelers were also investigated. Specifically, data on crashes involving the elderly (including drivers, passengers, and pedestrians) as captured in the Fatal Analysis Reporting System database was analyzed to examine elderly drivers and elderly pedestrian travel safety issues in NYS. This study report provides a summary of travel behavior and social-demographic characteristics of NYS elderly residents. These statistics could be used to examine equity issue concerning elderly New Yorkers, as well as to evaluate how well their mobility needs are being met. With a deeper understanding of issues and needs that this special population group is facing, policymakers and transportation planners would be able to make informed decisions on transportation investments and design services that could better address them.

99 GENERAL AND MISCELLANEOUS↗

A Complete Public Archive for the Einstein Imaging Proportional Counter

Consistent with our proposal to the Astrophysics Data Program in 1992, we have completed the design, construction, documentation, and distribution of a flexible and complete archive of the data collected by the Einstein Imaging Proportional Counter. Along with software and data delivered to the High Energy Astrophysics Science Archive Research Center at Goddard Space Flight Center, we have compiled and, where appropriate, published catalogs of point sources, soft sources, hard sources, extended sources, and transient flares detected in the database along with extensive analyses of the instrument's backgrounds and other anomalies. We include in this document a brief summary of the archive's functionality, a description of the scientific catalogs and other results, a bibliography of publications supported in whole or in part under this contract, and a list of personnel whose pre- and post-doctoral education consisted in part in participation in this project.

Helfand, David J.↗

Second Generation RLV Program

During the time period covered by this report, SAIC: 1) Continued to develop and assess processes and approaches that can be applied to Second Generation Reuseable Launch Vehicles (RLV) technologies prioritization. An approach based on the use of analytic Saaty scale functions has been defined and is being investigated. 2) Planned and facilitated technologies prioritization workshops, supported development of systems program algorithms based on the concept of influence diagramming, and assessment of analogies between aircraft and space systems developments. 3) Video interviews held with X-37 personnel at Dryden. The CD-ROM is being concluded and a near-final review disc is expected soon. 4) CD-ROMS were produced by Engineered Multimedia, Inc. (EMI) under subcontract to SAIC. These two CD-ROM products, "Microgravity" and "New Horizons", were delivered to MSFS technical representatives at a briefing at SAID on January 18, 2001. 5) Presentation brochure, "Aviation/Space Analog Team Interim Report" was provided to Space Propulsion Synergy Team (SPST) members and to NASA personnel. Wrap-up of effort will be a mid-April briefing to both MSFC and the full SPST membership. Support to Phase 2 of CCPD ends 3/31/01. Phase 3 continuation effort planned with emphasis on technical info content. 6) Recommended that eliminating the B-52 flights of the X-37 in favor of alternate approached be evaluated. Discovered that a required change to the thruster valves of the X-37 had not been made. Repair work continues on the lower fuselage section of the X-37, in the areas that experienced core collapse. The currently catalogued potential weight increases and decreases are about equal, but this does not include the impact of the cable weight underestimate reported earlier. The CFD for RCS testing correlates well with the wind tunnel data. 7) The Level IV CCB approved SCN-4 to the MC-1 Engine SPecification. Approved changes have been incorporated into the specification, and Revision D has been released to the Repository. Billy Gonterman, SAIC, traveled to SSC to perform a five-day readiness assessment on the progress of facilities activation. Implemented modifications to the MC-1 Engine TPA Component Database. 8) Replaced 25 Combined-Cycle Propulsion Database (CCPD) documents; modified the low-on screen to include a direct email link for user contact; prepared a summary presentation of current and proposed tasks.

Laue, Jay↗

Theoretical Studies of Molecular Spectra

This summary describes the research activities of the principal investigator during the reporting period. The research includes spectroscopy, management of molecular databases, and generation of spectral line profiles and opacity data. The spectroscopy research includes oxygen broadening of nitric oxide (NO), analysis of CO2 spectra, analysis of HNO3 spectra, and analysis of CO spectra.

McKay, Christopher↗

Numerical Predictions of Wind Turbine Power and Aerodynamic Loads for the NREL Phase II and IV Combined Experiment Rotor

Accurate, reliable and robust numerical predictions of wind turbine rotor power remain a challenge to the wind energy industry. The literature reports various methods that compare predictions to experiments. The methods vary from Blade Element Momentum Theory (BEM), Vortex Lattice (VL), to variants of Reynolds-averaged Navier-Stokes (RaNS). The BEM and VL methods consistently show discrepancies in predicting rotor power at higher wind speeds mainly due to inadequacies with inboard stall and stall delay models. The RaNS methodologies show promise in predicting blade stall. However, inaccurate rotor vortex wake convection, boundary layer turbulence modeling and grid resolution has limited their accuracy. In addition, the inherently unsteady stalled flow conditions become computationally expensive for even the best endowed research labs. Although numerical power predictions have been compared to experiment. The availability of good wind turbine data sufficient for code validation experimental data that has been extracted from the IEA Annex XIV download site for the NREL Combined Experiment phase II and phase IV rotor. In addition, the comparisons will show data that has been further reduced into steady wind and zero yaw conditions suitable for comparisons to "steady wind" rotor power predictions. In summary, the paper will present and discuss the capabilities and limitations of the three numerical methods and make available a database of experimental data suitable to help other numerical methods practitioners validate their own work.

Duque, Earl P. N.↗

Observations on the Application of Machine Learning Techniques to Aviation Operations

There is an increasing interest in applying methods based on Machine Learning Techniques (MLT) to problems in aviation operations. The current interest is based on developments in Cloud Computing, the availability of open software and the success of MLT in automation, consumer behavior and finance involving large database. Historically aviation operations have been analyzed using physics-based models and provide information for making operational decisions. This talk describes issues to be addressed in applying either model-driven or data-driven methods. Aviation operations involving many decision makers, multiple objectives, poor or unavailable physics-based models and a rich historical database are prime candidates for analysis using data-driven methods. The issues are illustrated by a detailed example and summary of current research in the area. The application of MLT to aviation operations falls into two categories: (a) based on the lack of a physics-based model, MLT is the favored approach and (b) marginal difference between regression methods using physics-based models and MLT. Further research is needed in the selection of MLT to critical aviation operations. As always, the best approach depends on the task, the physical understanding of the problem and the quality and quantity of the available data.

Sridhar, Banavar↗

Application of Machine Learning Techniques to Aviation Operations: A Case Study

There is an increasing interest in applying methods based on Machine Learning Techniques (MLT) to problems in aviation operations. The current interest is based on developments in Cloud Computing, the availability of open software and the success of MLT in automation, consumer behavior and finance involving large database. Historically aviation operations have been analyzed using physics-based models and provide information for making operational decisions. This talk describes issues to be addressed in applying either model-driven or data-driven methods. Aviation operations involving many decision makers, multiple objectives, poor or unavailable physics-based models and a rich historical database are prime candidates for analysis using data-driven methods. The issues are illustrated by a detailed example and summary of current research in the area. The application of MLT to aviation operations falls into two categories 58; (a) based on the lack of a physics-based model, MLT is the favored approach and (b) marginal difference between regression methods using physics-based models and MLT. Further research is needed in the selection of MLT to critical aviation operations. As always, the best approach depends on the task, the physical understanding of the problem and the quality and quantity of the available data.

Sridhar, Banavar↗

Jet-Surface Interaction - High Aspect Ratio Nozzle Test: Test Summary

The Jet-Surface Interaction High Aspect Ratio Nozzle Test was conducted in the Aero-Acoustic Propulsion Laboratory at the NASA Glenn Research Center in the fall of 2015. There were four primary goals specified for this test: (1) extend the current noise database for rectangular nozzles to higher aspect ratios, (2) verify data previously acquired at small-scale with data from a larger model, (3) acquired jet-surface interaction noise data suitable for creating verifying empirical noise models and (4) investigate the effect of nozzle septa on the jet-mixing and jet-surface interaction noise. These slides give a summary of the test with representative results for each goal.

aircraft↗

Genomic Language model for Annotation of Repetitive Elements (GLARE) v1.0

GLARE (Genomic Language model for Annotation of Repetitive Elements) is a tool that classifies transposable elements (TEs)—the mobile, repetitive DNA sequences that make up large fractions of eukaryotic genomes. GLARE fine-tunes the NTv3-650M genomic language model on a harmonized collection of curated TE sequences from the PanTEon and Repbase reference databases, assigning each input sequence to one of 11 orders and 32 superfamilies in a Wicker-compatible taxonomy. Features. From nucleotide FASTA input, GLARE outputs per-sequence predictions, class summaries, composition figures, and an annotated FASTA. It provides calibrated confidence scores with optional abstention and runs on CPU or GPU. Uses. GLARE serves as a classification component in genome-annotation pipelines, downstream of TE discovery, supporting genome annotation and comparative and evolutionary genomics. Advantages. GLARE is the first repeat-element classifier to leverage a pretrained genomic language model. Combined with multi-database training, this approach outperformed all nine classifiers in the PanTEon benchmark, generalized better to unseen taxonomic clades, and remained robust to sequence orientation—a common failure mode of existing tools.

Bruna, Tomas [Lawrence Berkeley National Laborator↗