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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

An archaeal genetic code with all TAG codons as pyrrolysine

Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archaea consistently incorporate pyrrolysine (Pyl) at TAG codons, supporting an alternative archaeal genetic code that we designate the Pyl code. This genetic code has 62 sense codons encoding 21 amino acids. In contrast to monophyletic genetic code distributions in bacteria, the archaeal Pyl code occurs sporadically, indicating that it arose independently in multiple lineages. We discovered that more than 1800 archaeal proteins contain Pyl, increasing the number of such proteins by two orders of magnitude. Additionally, five Pyl transfer RNA (tRNA) pyrrolysyl–tRNA synthetase pairs from Pyl-code archaea were used to introduce Pyl analogs into proteins in Escherichia coli.

Kivenson, Veronika [University of California, Berk↗
DOE OSTI2022

Complete Genome Sequences of the Soil Oxalotrophic Bacterium Cupriavidus oxalaticus Strain Ox1 and Its Derived mCherry-Tagged Strain

Here, we report the complete genome sequences of the soil oxalotrophic bacterium Cupriavidus oxalaticus Ox1 and a derived mCherry-tagged strain. The genome size is approximately 6.69 Mb, with a GC content of 66.9%. The genome sequence of C. oxalaticus Ox1 contains a complete operon for the degradation and assimilation of oxalate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Tagged deep inelastic scattering measurement on deuterium with the LAD experiment

Here, the origin of the modification of the quark structure of nucleons in the nuclear medium can be tested with tagged recoil nucleon measurements from deep inelastic scattering off electrons on deuterium. The LAD experiment at the Thomas Jefferson National Laboratory (JLab) will measure the modification of the neutron structure function for high-momentum, highly-virtual neutrons by measuring the spectator recoil protons in coincidence with the scattered electron. An update on the experimental setup and projected results is presented. The experiment will collect data in Fall 2024.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Tracking moisture sources of precipitation over Central Asia: A study based on the water-source-tagging method

Central Asia is a semi-arid to arid region that is sensitive to hydrological changes. We use the Community Atmosphere Model version 5 (CAM5), equipped with a water tagging capability, to investigate the major moisture sources for climatological precipitation and its long-term trends over Central Asia. Europe, the north Atlantic and local evaporation, which explain 33.2±1.5%, 23.0±2.5% and 19.4±2.2% of the precipitation, respectively, are identified as the most dominant moisture sources for northern Central Asia (NCA). For precipitation over southern Central Asia (SCA), Europe, the north Atlantic and local evaporation contributes 25.4±2.7%, 18.0±1.7% and 14.7±1.9%, respectively. In addition, the contributions of South Asia (8.6±1.7%) and Indian Ocean (9.5±2.0%) are also substantial for SCA. Modulated by the seasonal meridional shift of subtropical westerly jet, moisture originating from low- and mid-latitude is important in winter, spring and autumn, while northern Europe contributes more in summer. We also explain the observed drying trends over southeastern Central Asia in spring and over NCA in summer during 1956-2005. The drying trend over the southeastern Central Asia in spring is mainly due to the decrease of local evaporation and weakened moisture fluxes from the Arabian Peninsula and Arabian Sea associated with the warming Western Pacific. The drying trend over NCA in summer can be attributed to the decrease of local evaporation and reduced moisture from northern Europe due to the southward shift of the subtropical westerly jet.

Jiang, Jie↗
DOE OSTI2021

OWD.2 TAG Expression

During the transformation of wild-type (WT) Arabidopsis thaliana, a T-DNA containing OLEOSIN-GFP (OLE1-GFP) was inserted by happenstance within the GBSS1 gene, resulting in significant reduction in amylose and increase in leaf oil content in the transgenic line (OG). The synergistic effect on oil accumulation of combining gbss1 with the expression of OLE1-GFP was confirmed by transforming an independent gbss1 mutant (GABI_914G01) with OLE1-GFP. The resulting OLE1-GFP/gbss1 transgenic lines showed higher leaf oil content than the individual OLE1-GFP/WT or single gbss1 mutant lines. Further stacking of the lipogenic factors WRINKLED1, Diacylglycerol O-Acyltransferase (DGAT1), and Cys-OLEOSIN1 (an engineered sesame OLEOSIN1) in OG significantly elevated its oil content in mature leaves to 2.3% of dry weight, which is 15 times higher than that in WT Arabidopsis. Inducible expression of the same lipogenic factors was shown to be an effective strategy for triacylglycerol (TAG) accumulation without incurring growth, development, and yield penalties.

Biomass Analytics↗
DOE OSTI2025

Hypersonic wake velocity measurements using acetone molecular tagging velocimetry

Molecular tagging velocimetry, a minimally intrusive laser diagnostic, was used to find quantitative off-body velocity measurements in the wake of both strut-mounted and free-flight spheres in hypersonic flow. Acetone gas seeded in the flow was excited using the fourth harmonic of a pulse-burst Nd:YAG laser. The experimental tests were validated and compared to simulations using a continuous Galerkin flow solver and an adaptive mesh refinement process. Near the centerline in the wake of the sphere, velocities between −105 and 65 m/s were observed due to reverse flow in the viscous shear layer. Similarly, the simulated data showed negative velocity values in the shear layer region. Outside of the shear layer, average velocities of 730 m/s were observed in both the experimental and simulated results. The overall average uncertainty for the strut-mounted and free-flight cases was estimated to have an accuracy of ±4% (±35.5m/s or 4.9%). In conclusion, this non-intrusive technique provides a velocity map of the wake behind a sphere under hypersonic conditions.

42 ENGINEERING↗
DOE OSTI2025

Nitric oxide molecular tagging velocimetry of a free-flight model in a reflected shock tunnel

Nitric oxide molecular tagging velocimetry (NO MTV) is used to characterize the wake behind a free-flight spherical model in the test section of a free-piston reflected shock tunnel using a burst-mode laser operated at 100 kHz. A novel (to our knowledge) multi-delay timing scheme was implemented to measure velocity in a varying collisional environment in the wake of the free-flight model. Four simultaneous velocity profiles were measured in the wake of the model from -600 to 3600 m/s for flow enthalpies of 10.3 and 12.0 MJ/kg. Finally, the measured velocity distributions show good agreement when compared to computational fluid dynamics (CFD) modeling.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Utah FORGE 9-3664: Development of Tagged Proppant for Conductivity Enhancement and Reservoir Characterization - 2024 Annual Workshop Presentation

This is a presentation on the Development and Testing of Tagged Proppant for Fracture Conductivity Enhancement and Reservoir Characterization in EGS by The University of Oklahoma, presented by Ahmad Ghassemi. This slide presentation video discusses the development and testing of new proppants that can be used in geothermal conditions of at least 250 degrees C and at differential pressures of 35-70 MPa. This presentation was featured in the Utah FORGE R&D Annual Workshop on August 13-15, 2024.

15 GEOTHERMAL ENERGY↗
DOE OSTI2024

Data analysis in the ICARUS (SBN FD) Cosmic Ray Tagging system

When a cosmic ray particle collides with the upper atmosphere, it creates a shower of particles that transverse down to the Earth’s surface. These cosmogenic particles provide a challenging background in neutrino experiments. The Short Baseline Neutrino (SBN) Program is composed of three Liquid Argon Time Projection Chambers (LArTPCs) that will help us understand the elusive neutrino. Together with a Cosmic Ray Tagger (CRT) system, the ICARUS detector serves as the Far Detector in the SBN Program. The CRT surrounds the detector medium and tags incoming particles allowing us to combat the high flux of comic rays we experience at ICARUS. In this poster, I will show some of the first data analyses done with the fully commissioned CRT system, including studies using CRT timing information and CRT hit reconstruction.

43 PARTICLE ACCELERATORS↗
DOE OSTI2024

Fuel Performance Calculations of Tagged UO 2 MiniFuel Disks

Isotopic taggants are being considered as a novel form of forensic identifiers for nuclear fuels. As part of this effort, eighteen tagged MiniFuel disks were irradiated in the High Flux Isotope Reactor at Oak Ridge National Laboratory. In this work, the BISON fuel performance code was used to recreate the pellets and predict their behavior and their post-irradiation material properties. These predictions are to serve as a baseline to help investigators identify results of interest during post-irradiation examination of actual MiniFuel disks. The simulation methodology and models are described herein, along with the individual disk predictions. Several general trends were identified in this analysis. Based on the models, it is predicted that the pellets’ internal temperatures will rise over time, fission gas release will remain constant at around 1%, regardless of the burnup, and no grain growth will occur in any of the disks. The reasons for these predictions are discussed below. Probable shortcomings in the BISON predictions are addressed, and future work is proposed.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Neutron Tagging From Neutrino Interactions in DUNE-ND 2x2 Prototype

The Deep Underground Neutrino Experiment (DUNE) is a long-baseline neutrino oscillation experiment that aims to measure whether CP is violated in the leptonic sector (if violated, how much) and unambiguously determine the neutrino mass ordering. DUNE consists of near and far detectors that rely on liquid argon time projection chamber (LArTPC) technology to observe neutrino interactions. The near detector (ND) will be placed in Fermilab, near the neutrino source, while the far detector (FD) will be deployed in Sanford Lab, 1.5 km deep underground, which is 1300 km away from the source. LArTPCs provide excellent particle identification and calorimetry; however, detecting neutrons is challenging, as they do not leave direct ionization signals in LArTPCs. Neutrons can carry away up to 25% of the neutrino energy, introducing a significant uncertainty in DUNE measurements. The DUNE near detector (ND) features a novel modular LArTPC with pixelated charge readout, which enhances event recons truction. The modular design enables precise correlation between ionization signals and light signals in a high-rate environment, improving the identification of delayed energy depositions from neutrons in neutrino interactions. We introduce a neutron tagging technique using the 2x2 Demonstrator, a small-scale prototype of the DUNE ND LArTPC. The analysis utilizes Monte Carlo simulations and deep-learning techniques to identify neutron-induced energy depositions and reconstruct low-energy activity.

Kufatty, Georgette [Florida State U.]↗
DOE OSTI2022

Tagging Cosmic Ray Background in the Icarus Detector

ICARUS T-600 will be the Far Detector of the upcoming SBN program, for which it will leverage a ∼ 1ns response and a high resolution for neutrino event reconstruction. ICARUS will respond to the challenge of the cosmic flux at the surface thanks to its Cosmic Ray Tagging (CRT) system. The work conducted during the Summer Students at Fermilab program contributed to the calibration activities that are ongoing in view of the second physics run in late 2022: the timing of CRT and PMT signals was analysed, highlighting the need for corrections to the PMTs. The timing delay for the global trigger signal for a section of the side CRT. The possibility of calibrating the light yield of the side CRTs with run data was finally explored.

47 OTHER INSTRUMENTATION↗
DOE OSTI2026

Low-latency Jet Tagging for HL-LHC Using Transformer Architectures

Transformers are the state-of-the-art model architectures and widely used in application areas of machine learning. However the performance of such architectures is less well explored in the ultra-low latency domains where deployment on FPGAs or ASICs is required. Such domains include the trigger and data acquisition systems of the LHC experiments. We present a transformer-based algorithm for jet tagging built with the HGQ2 framework, which is able to produce a model with heterogeneous bitwidths for fast inference on FPGAs, as required in the trigger systems at the LHC experiments. The bitwidths are acquired during training by minimizing the total bit operations as an additional parameter. By allowing a bitwidth of zero, the model is pruned in-situ during training. Using this quantization-aware approach, our algorithm achieves state-of-the-art performance while also retaining permutation invariance which is a key property for particle physics applications. Due to the strength of transformers in representation learning, our work also serves as a stepping stone for the development of a larger foundation model for trigger applications.

Laatu, Lauri [Imperial Coll., London]↗
DOE OSTI2024

Hypersonic Wake Velocity Measurements Using Acetone Molecular Tagging Velocimetry

A non-intrusive laser diagnostic known as molecular tagging velocimetry was used to find quantitative off-body velocity measurements in the wake of a sphere in the Mach 7 Ludwieg Tube Wind Tunnel located at The University of Texas at San Antonio. Acetone gas seeded in the flow was excited using the 4th harmonic of a pulse-burst Nd:YAG laser. The experimental results were used to validate and compare to simulations using a continuous Galerkin flow solver. Both the experimental and simulated results agreed on negative velocities in the viscous shear layer. Near the centerline of the sphere, average velocities of -200 m/s were observed due to reverse flow in the recirculation region. Outside of the shear layer, velocities of 800 m/s were observed in both the experimental and simulated results. The overall average uncertainty for the strut-mounted and free-flight case was estimated to be ±27 m/s. The flow features of the wake were visualized using schlieren imaging, and the experimental results agreed well with the simulated results.

Shoemake, Lawton↗
DOE OSTI2021

Resin Assisted Capture Coupled with Isobaric Tandem Mass Tag Labeling for Multiplexed Quantification of Protein Thiol Oxidation

Reversible oxidative modifications on protein thiols have recently emerged as important mediators of cellular function. Herein we describe the detailed procedure of a quantitative redox proteomics method that utilizes resin-assisted capture (RAC) in combination with tandem mass tag (TMT) isobaric labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to allow multiplexed stochiometric quantification of oxidized protein thiols at the proteome level. The site-specific quantitative information on oxidized cysteine residues provides additional insight into the functional impacts of such modifications. The workflow is adaptable across many sample types including cultured cells (e.g. mammalian, prokaryotic) and whole tissues (e.g. heart, lung, muscle) which are initially lysed/homogenized with free thiols being alkylated to prevent artificial oxidation. The oxidized protein thiols are then reduced and captured by a thiol affinity resin which streamlines and simplifies the workflow steps by allowing the proceeding digestion, labeling, and washing procedures to be performed without additional transfer of proteins/peptides. Finally, labeled peptides are eluted and analyzed by LC-MS/MS to reveal comprehensive stoichiometric changes related to thiol oxidation across the entire proteome. This method greatly improves our understanding of the role of redox dependent regulation under physiological and pathophysiological states related to protein thiol oxidation.

RAC, TMT, thiol redox proteomics, cysteine, PTM st↗
DOE OSTI2024

TRAC Time Tags of individual particle samples collected for microscopy analysis at RMBL [AMF2] from June 2023 to August 2023

The dataset presents the time tags of individual particle samples collected on microscopy substrates during the Surface Atmosphere Integrated Field Laboratory (SAIL) campaign in Gothic, CO. A Time Resolved Aerosol Collector was deployed at the Rocky Mountain Biological Laboratory, 200 m north of AMF2 to collect ambient particles. The instrument inlet was placed 5 m above ground level. Particles are deposited on 400 mesh copper carbon-B film TEM grids (Ted Pella 01814-F). Samples are sealed and currently stored at Purdue University. A subset of the samples can be shared. Please contact dataset authors for more information. The dataset reports the sample start times in UTC and MST along with the sample ID, used to guide its location and retrieval from the storage plate. TRAC sampling started on June 17, 2023, and ended on July 31, 2023.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1969

Tagged arithmetic

Tagged arithmetic system for use with FORTRAN programs

Armstead, B. J.↗