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At least 1,225 records · Page 68
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Structure and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate

Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, cryoID , toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5′-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryo-EM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8α/8β TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryo-EM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37-amino-acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.

Methanosarcina acetivorans↗
NASA NTRS2007

Automated Recognition of 3D Features in GPIR Images

A method of automated recognition of three-dimensional (3D) features in images generated by ground-penetrating imaging radar (GPIR) is undergoing development. GPIR 3D images can be analyzed to detect and identify such subsurface features as pipes and other utility conduits. Until now, much of the analysis of GPIR images has been performed manually by expert operators who must visually identify and track each feature. The present method is intended to satisfy a need for more efficient and accurate analysis by means of algorithms that can automatically identify and track subsurface features, with minimal supervision by human operators. In this method, data from multiple sources (for example, data on different features extracted by different algorithms) are fused together for identifying subsurface objects. The algorithms of this method can be classified in several different ways. In one classification, the algorithms fall into three classes: (1) image-processing algorithms, (2) feature- extraction algorithms, and (3) a multiaxis data-fusion/pattern-recognition algorithm that includes a combination of machine-learning, pattern-recognition, and object-linking algorithms. The image-processing class includes preprocessing algorithms for reducing noise and enhancing target features for pattern recognition. The feature-extraction algorithms operate on preprocessed data to extract such specific features in images as two-dimensional (2D) slices of a pipe. Then the multiaxis data-fusion/ pattern-recognition algorithm identifies, classifies, and reconstructs 3D objects from the extracted features. In this process, multiple 2D features extracted by use of different algorithms and representing views along different directions are used to identify and reconstruct 3D objects. In object linking, which is an essential part of this process, features identified in successive 2D slices and located within a threshold radius of identical features in adjacent slices are linked in a directed-graph data structure. Relative to past approaches, this multiaxis approach offers the advantages of more reliable detections, better discrimination of objects, and provision of redundant information, which can be helpful in filling gaps in feature recognition by one of the component algorithms. The image-processing class also includes postprocessing algorithms that enhance identified features to prepare them for further scrutiny by human analysts (see figure). Enhancement of images as a postprocessing step is a significant departure from traditional practice, in which enhancement of images is a preprocessing step.

Park, Han↗
DOE OSTI2023

A plano–convex thick-lens velocity map imaging apparatus for direct, high resolution 3D momentum measurements of photoelectrons with ion time-of-flight coincidence

Since their inception, velocity map imaging (VMI) techniques have received continued interest in their expansion from 2D to 3D momentum measurements through either reconstructive or direct methods. Recently, much work has been devoted to the latter of these by relating electron time-of-flight (TOF) to the third momentum component. The challenge is having a timing resolution sufficient to resolve the structure in the narrow (<10 ns) electron TOF spread. Here, we build upon the work in VMI lens design and 3D VMI measurement by using a plano–convex thick-lens (PCTL) VMI in conjunction with an event-driven camera (TPX3CAM) providing TOF information for high resolution 3D electron momentum measurements. We perform simulations to show that, with the addition of a mesh electrode to the thick-lens geometry, the resulting plano–convex electrostatic field extends the detectable electron cutoff energy range while retaining the high resolution. This design also extends the electron TOF range, allowing for a better momentum resolution along this axis. We experimentally demonstrate these capabilities by examining above-threshold ionization in xenon, where the apparatus is shown to collect electrons of energy up to ∼7 eV with a TOF spread of ∼30 ns, both of which are improved compared to a previous work by factors of ∼1.4 and ∼3.75, respectively. Finally, the PCTL-VMI is equipped with a coincident ion TOF spectrometer, which is shown to effectively extract unique 3D momentum distributions for different ionic species in a gas mixture. These techniques have the potential to lend themselves to more advanced measurements involving systems where the electron momentum distributions possess non-trivial symmetries.

Instruments & Instrumentation↗
DOE OSTI2024

Optically multiplexed neutron time-of-flight technique for inertial confinement fusion

Neutron time-of-flight (nTOF) detectors are crucial in diagnosing the performance of inertial confinement fusion (ICF) experiments, which implode targets of deuterium–tritium fuel to achieve thermonuclear conditions. These detectors utilize the fusion neutron energy spectrum to extract key measurements, including the hotspot ion temperature and fuel areal density. Previous work [Danly et al., Rev. Sci. Instrum. 94, 043502 (2023)] has demonstrated adding 1D spatial resolution to an nTOF-like detector using a neutron aperture and streak camera to measure the ion temperature profile of an ICF implosion. By contrast, the study presented herein explores modifying the 1D detector to use a fast photomultiplier tube (PMT) to validate the design of a 2D spatially resolved instrument based on reconstruction from 1D profiles. The modification would collect time-of-flight traces from separate scintillators in an imaging array with one PMT using optical fibers of varying lengths to time-multiplex the signals. This technique has been demonstrated in ride-along experiments on the OMEGA laser with 20 fiber-coupled scintillator channels connected to a Photek PMT210. Results provide constraints on the fiber lengths and PMT gating requirements to promote pulse fidelity throughout all channels. Calibration of the detector to fixed nTOFs can provide a preliminary estimate of the instrument response function (IRF), although measurement of the IRF is currently under way. These results suggest that nTOF signals can potentially be time-multiplexed with fibers so long as the design is strategic to mitigate signal-to-noise reduction, modal dispersion, and charge build-up in the PMT, which has implications beyond ion temperature imaging.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Updates on MURAVES Project at Mt. Vesuvius

The MUon RAdiography of VESuvius (MURAVES) project aims to employ muography imaging techniques to investigate the internal structure of the summit of Mount Vesuvius, an active volcano located near Naples, Italy. This paper reports recent advancements in data analysis and simulation tools that significantly improve the quality and reliability of the experiment’s results. A new track selection method, referred to as the Golden Selection, has been developed to identify high-quality muon tracks by applying an improved χ 2 -based criterion. This method enhances the signal-to-background ratio and improves the resolution of the resulting muographic images. Moreover, the simulation framework has been upgraded through the integration of the MULDER (MUon simuLation for DEnsity Reconstruction) library, which consolidates the functionalities of previously used libraries into a single, unified platform. MULDER enables efficient and accurate modeling of muon flux variations induced by topographical features. A good agreement is observed between the simulated and measured muon flux maps, validating the effectiveness of the new analysis and simulation approaches.

Cosmic rays↗
DOE OSTI2021

Toward Discovering the Structure and Dynamics of the Sun-Interstellar Medium System (Los Alamos LDRD Report)

We have taken major steps toward developing the tools necessary to explore with unprecedented resolution the plasma structure and dynamics of the Sun-interstellar medium (ISM) interaction region, known as the heliosheath. We have applied a rigorous imaging technique known as Generalized Ridge Regression (GRR) to construct statistically robust sky maps of hydrogen energetic neutral atoms (ENAs) emanating from this region and detected by the Los Alamos-led IBEX-Hi ENA imager [1] on NASA’s Interstellar Boundary Explorer (IBEX) mission [2]. Our methods go far beyond the map reconstruction process currently applied by the IBEX Science Operations Center (ISOC), opening up the possibility of new discovery science with the IBEX data set and positioning LANL for a lead science role for the upcoming Interstellar Mapping and Acceleration Probe (IMAP) mission [3] for which LANL is providing two key experiments. We have successfully demonstrated that the new maps are higher resolution and are capable of revealing structures that are not presently resolveable in standard ISOC maps

58 GEOSCIENCES↗
NASA NTRS1975

Development of a spectroscopic photoelectric imaging Fabry-Perot interferometer preliminary observational results

In order to observe extended astronomical objects at high spatial and spectral resolution, a spectroscopic photoelectric imaging Fabry-Perot interferometer was constructed. Among the properties chosen for the instrument are an air-spaced, piezoelectrically scanned design allowing an accurately settable free spectral range and employing a single etalon of high finesse. Careful design of the etalon mountings and optical train preserves high ligh throughput. Spectra of single spatial elements with a photomultiplier were obtained, and an SEC vidicon detector was used to record a series of images through the interferometer while scanning the wavelength in discrete steps. The latter procedure yields sufficient information to reconstruct spectral features over the entire object, and for the conditions assumed, either series of observations requires only a small fraction of a rotational period for Jupiter or Saturn. An electronic control system was also constructed which permits rapid and flexible variation of the operational mode of the Fabry-Perot and its ancilliary devices so as to minimize loss of observational time.

Smith, W. H.↗
NASA NTRS1976

Spectroscopic photoelectric imaging Fabry-Perot interferometer - Its development and preliminary observational results

In order to observe extended astronomical objects at high spatial and spectral resolution, we have constructed a spectroscopic photoelectric imaging Fabry-Perot interferometer (SPIFI). Among the properties chosen for the instrument are an air-spaced, piezoelectrically scanned design allowing an accurately settable free spectral range and employing a single etalon of high finesse. Careful design of the etalon mountings and optical train preserves high light throughput. We either obtain spectra of single spatial elements with a photomultiplier or use an SEC vidicon detector to record a series of images through the interferometer while scanning the wavelength in discrete steps. The latter procedure yields sufficient information to reconstruct spectral features over the entire object. For the conditions assumed, either series of observations requires only a small fraction of a rotational period for Jupiter or Saturn, for example.

Smith, W. H.↗
NASA NTRS1992

Characterization of Martian near-subsurface materials by determination of cohesion and angle of internal friction

Back-analysis (reconstruction) of the stability of thirty avalanche chutes was performed in the very limited areas where high resolution imaging overlapped with available 1:500 K topographic map coverage. A new technique was developed to incorporate the third dimension (width) of an avalanche chute in stability back-analysis in order to yield unambiguous values of cohesion and angle of internal friction. The procedure is based upon extending the ordinary method of slices to three dimensions, in order to construct avalanche chute cross-sections whose widths and depths vary as a function of gradient, gravity, density of material, and phi and c. Applying the technique to the well documented slide at Lodalen, Norway as a test produces excellent correspondence with reality. Generally, the technique reveals that the width:depth ratio of any avalanche chute decreases with increasing contrast between the average slope angle and the angle of internal friction. Applying this technique to the martian avalanche chute yields results consistent with indications from earlier work, but with greater certainty. Values of cohesion and angle of internal friction identify the materials at the time of failure as moderately cohesive debris. If Sharp's identification of these features as avalanche chutes is correct, then the results here imply that weathering processes have had a significant effect to depths of tens of meters (where failure has occured) below the martian surface. It is also implied that on relatively steep slopes within Valles Marineris, sizable, unaltered, unmantled bedrock exposures for high resolution spectral and spatial scanning by Mars Observer may be scarce.

Sullivan, R. J.↗
NASA NTRS1995

Gravity Sensors and the Role of 3-D Visualization and Simulation in Biomedical Research

Ross 3.0 software was developed in the Biocomputation Center for semi-automated reconstruction of objects from serial thin sections. Data are captured directly from a transmission electron microscope via a video camera to a graphics workstation where the sections are mosaicked and contours are traced, registered and displayed by semi-automated methods. For the first time, macular type II cells are described completely for their innervation patterns. The purposes are to learn more about the fundamental circuitry of the macula and to demonstrate whether the terminals are altered morphologically by space flight. Current examples, from the medial part of the macula, are from maculas collected in-flight on the Space Life Sciences-2 mission, 4.5 hrs post-flight, and from a ground control. Results show that the typical type 11 cell receives processes from up to six nearby calyces or afferents. Nearly all the processes are elongated; some have bouton-like swellings and numerous vesicles. Multiple (2 to 4) processes from a single calyx to a type II cell are common, and approx. 1/3 of the processes innervate 2 type II cells of a neighboring cluster of 3 cells. About 2% of type II cells resemble type I cells morphologically and are surrounded by demicalyces. Differences in size or shape of the terminals under flight conditions could not be determined because the sample size is still too small; but it is clear that reconstruction methods provide insights into macular circuitry not obtainable by other techniques. The results demonstrate a morphological basis for interactions between adjacent receptive fields, through feedback-feedforward connections, during preprocessing of linear acceleratory information by the maculas. While the methods are currently being tested using vestibular maculas as the model system, it is clear that the technology is applicable to any tissue that can be physically or optically sectioned. ROSS software has already been implemented for reconstructing objects from tissues studied by confocal and by transmitted light microscopy, and research into magnetic resonance imaging-computational tomography combined visualization are underway.

Ross, Muriel D.↗
NASA NTRS2013

Chromatin Folding, Fragile Sites, and Chromosome Aberrations Induced by Low- and High- LET Radiation

We previously demonstrated non-random distributions of breaks involved in chromosome aberrations induced by low- and high-LET radiation. To investigate the factors contributing to the break point distribution in radiation-induced chromosome aberrations, human epithelial cells were fixed in G1 phase. Interphase chromosomes were hybridized with a multicolor banding in situ hybridization (mBAND) probe for chromosome 3 which distinguishes six regions of the chromosome in separate colors. After the images were captured with a laser scanning confocal microscope, the 3-dimensional structure of interphase chromosome 3 was reconstructed at multimega base pair scale. Specific locations of the chromosome, in interphase, were also analyzed with bacterial artificial chromosome (BAC) probes. Both mBAND and BAC studies revealed non-random folding of chromatin in interphase, and suggested association of interphase chromatin folding to the radiation-induced chromosome aberration hotspots. We further investigated the distribution of genes, as well as the distribution of breaks found in tumor cells. Comparisons of these distributions to the radiation hotspots showed that some of the radiation hotspots coincide with the frequent breaks found in solid tumors and with the fragile sites for other environmental toxins. Our results suggest that multiple factors, including the chromatin structure and the gene distribution, can contribute to radiation-induced chromosome aberrations.

Zhang, Ye↗
NASA NTRS2015

Interphase Chromosome Conformation and Chromatin-Chromatin Interactions in Human Epithelial Cells Cultured Under Different Gravity Conditions

Microgravity has been shown to alter global gene expression patterns and protein levels both in cultured cells and animal models. It has been suggested that the packaging of chromatin fibers in the interphase nucleus is closely related to genome function, and the changes in transcriptional activity are tightly correlated with changes in chromatin folding. This study explores the changes of chromatin conformation and chromatin-chromatin interactions in the simulated microgravity environment, and investigates their correlation to the expression of genes located at different regions of the chromosome. To investigate the folding of chromatin in interphase under various culture conditions, human epithelial cells, fibroblasts, and lymphocytes were fixed in the G1 phase. Interphase chromosomes were hybridized with a multicolor banding in situ hybridization (mBAND) probe for chromosome 3 which distinguishes six regions of the chromosome as separate colors. After images were captured with a laser scanning confocal microscope, the 3-dimensional structure of interphase chromosome 3 was reconstructed at multi-mega base pair scale. In order to determine the effects of microgravity on chromosome conformation and orientation, measures such as distance between homologous pairs, relative orientation of chromosome arms about a shared midpoint, and orientation of arms within individual chromosomes were all considered as potentially impacted by simulated microgravity conditions. The studies revealed non-random folding of chromatin in interphase, and suggested an association of interphase chromatin folding with radiation-induced chromosome aberration hotspots. Interestingly, the distributions of genes with expression changes over chromosome 3 in cells cultured under microgravity environment are apparently clustered on specific loci and chromosomes. This data provides important insights into how mammalian cells respond to microgravity at molecular level.

International Space Station↗
DOE OSTI2023

AdjointBackMapV2: Precise reconstruction of arbitrary CNN unit’s activation via adjoint operators

Adjoint operators have been found to be effective in the exploration of CNN’s inner workings (Wan and Choe, 2022). However, the previous no-bias assumption restricted its generalization. We overcome the restriction via embedding input images into an extended normed space that includes bias in all CNN layers as part of the extended space and propose an adjoint-operator-based algorithm that maps high-level weights back to the extended input space for reconstructing an effective hypersurface. Such hypersurface can be computed for an arbitrary unit in the CNN, and here we prove that this reconstructed hypersurface, when multiplied by the original input (through an inner product), will precisely replicate the output value of each unit. We show experimental results based on the CIFAR-10 and CIFAR-100 data sets where the proposed approach achieves near 0 activation value reconstruction error.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Determinants of synapse diversity revealed by super-resolution quantal transmission and active zone imaging

Neural circuit function depends on the pattern of synaptic connections between neurons and the strength of those connections. Synaptic strength is determined by both postsynaptic sensitivity to neurotransmitter and the presynaptic probability of action potential evoked transmitter release (P r ). Whereas morphology and neurotransmitter receptor number indicate postsynaptic sensitivity, presynaptic indicators and the mechanism that sets P r remain to be defined. To address this, we developed QuaSOR, a super-resolution method for determining P r from quantal synaptic transmission imaging at hundreds of glutamatergic synapses at a time. We mapped the P r onto super-resolution 3D molecular reconstructions of the presynaptic active zones (AZs) of the same synapses at the Drosophila larval neuromuscular junction (NMJ). We find that P r varies greatly between synapses made by a single axon, quantify the contribution of key AZ proteins to P r diversity and find that one of these, Complexin, suppresses spontaneous and evoked transmission differentially, thereby generating a spatial and quantitative mismatch between release modes. Transmission is thus regulated by the balance and nanoscale distribution of release-enhancing and suppressing presynaptic proteins to generate high signal-to-noise evoked transmission.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Three-dimensional hard X-ray ptychographic reflectometry imaging on extended mesoscopic surface structures

Many nanodevices and quantum devices, with their sizes often spanning from millimeters down to sub-nanometer, have intricate low-dimensional, non-uniform, or hierarchical structures on surfaces and interfaces. Since their functionalities are dependent on these structures, high-resolution surface-sensitive characterization becomes imperative to gain a comprehensive understanding of the function–structure relationship. We thus developed hard x-ray ptychographic reflectometry imaging, a new technique that merges the high-resolution two-dimensional imaging capabilities of hard x-ray ptychography for extended objects, with the high-resolution depth profiling capabilities of x-ray reflectivity for layered structures. The synergy of these two methods fully leverages both amplitude and phase information from ptychography reconstruction to not only reveal surface topography and localized structures, such as shapes and electron densities, but also yields statistical details, such as interfacial roughness that is not readily accessible through coherent imaging solely. The hard x-ray ptychographic reflectometry imaging is well-suited for three-dimensional imaging of mesoscopic samples, particularly those comprising planar or layered nanostructures on opaque supports, and could also offer a high-resolution surface metrology and defect analysis on semiconductor devices, such as integrated nanocircuits and lithographic photomasks for microchip fabrications.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Application of recoil-imaging time projection chambers to directional neutron background measurements in the SuperKEKB accelerator tunnel

Gaseous time projection chambers (TPCs) with high readout segmentation are capable of reconstructing detailed 3D ionization distributions of nuclear recoils resulting from elastic neutron scattering. Here, using a system of six compact TPCs with pixel ASIC readout, filled with a 70:30 mixture of He:CO 2 gas, we analyze the first directional measurements of beam-induced neutron backgrounds in the tunnel regions surrounding the Belle II detector at the SuperKEKB e + e – collider. With the use of 3D recoil tracking, we show that these TPCs are capable of maintaining nearly 100% nuclear recoil purity to reconstructed ionization energies (E reco ) as low as 5 keV ee . Using a large sample of Monte-Carlo (MC)-simulated 4 He, 12 C, and 16 O recoil tracks, we find consistency between predicted and measured recoil energy spectra in five of the six TPCs, providing useful validation of the neutron production mechanisms modeled in simulation. Restricting this sample to 4 He recoil tracks with E reco > 40 keV ee , we further demonstrate axial angular resolutions within 8° and we introduce a procedure that under suitable conditions, correctly assigns the vector direction to 91% of these simulated 4 He recoils. Applying this procedure to assign vector directions to measured 4 He recoil tracks, we observe consistency between the angular distributions of observed and simulated recoils, providing first experimental evidence of localized neutron “hotspots” in the accelerator tunnel. Observed rates of nuclear recoils in these TPCs suggest that simulation overestimates the neutron flux from these hotspots. Despite this, we estimate these hotspots to produce the majority of neutron backgrounds in the accelerator tunnel at SuperKEKB’s target luminosity of 6.3 x 10 35 cm –2 s –1 , making them important regions to continue to monitor.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

A Method of Ground-Based Cloud Motion Predict: CCLSTM + SR-Net

Ground-based cloud images can provide information on weather and cloud conditions, which play an important role in cloud cover monitoring and photovoltaic power generation forecasting. However, the cloud motion prediction of ground-based cloud images still lacks advanced and complete methods, and traditional technologies based on image processing and motion vector calculation are difficult to predict cloud morphological changes. In this paper, we propose a cloud motion prediction method based on Cascade Causal Long Short-Term Memory (CCLSTM) and Super-Resolution Network (SR-Net). Firstly, CCLSTM is used to estimate the shape and speed of cloud motion. Secondly, the Super-Resolution Network is built based on perceptual losses to reconstruct the result of CCLSTM and, finally, make it clearer. We tested our method on Atmospheric Radiation Measurement (ARM) Climate Research Facility TSI (total sky imager) images. The experiments showed that the method is able to predict the sky cloud changes in the next few steps.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Deep Learning for Pion Identification and Energy Calibration with the ATLAS Detector

Separating charged and neutral pions as well as calibrating the pion energy response is a core component of reconstruction in the ATLAS calorimeter. This note presents an investigation of deep learning techniques for these tasks, representing the signal in the ATLAS calorimeter layers as pixelated images. Deep learning approaches outperform the classification applied in the baseline local hadronic calibration and are able to improve the energy resolution for a wide range in particle momenta, especially for low energy pions. This work demonstrates the potential of deep-learning-based low-level hadronic calibrations to significantly improve the quality of particle reconstruction in the ATLAS calorimeter.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗