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At least 397 records · Page 22

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NASA NTRS2001

Compact Microscope Imaging System Developed

The Compact Microscope Imaging System (CMIS) is a diagnostic tool with intelligent controls for use in space, industrial, medical, and security applications. The CMIS can be used in situ with a minimum amount of user intervention. This system, which was developed at the NASA Glenn Research Center, can scan, find areas of interest, focus, and acquire images automatically. Large numbers of multiple cell experiments require microscopy for in situ observations; this is only feasible with compact microscope systems. CMIS is a miniature machine vision system that combines intelligent image processing with remote control capabilities. The software also has a user-friendly interface that can be used independently of the hardware for post-experiment analysis. CMIS has potential commercial uses in the automated online inspection of precision parts, medical imaging, security industry (examination of currency in automated teller machines and fingerprint identification in secure entry locks), environmental industry (automated examination of soil/water samples), biomedical field (automated blood/cell analysis), and microscopy community. CMIS will improve research in several ways: It will expand the capabilities of MSD experiments utilizing microscope technology. It may be used in lunar and Martian experiments (Rover Robot). Because of its reduced size, it will enable experiments that were not feasible previously. It may be incorporated into existing shuttle orbiter and space station experiments, including glove-box-sized experiments as well as ground-based experiments.

McDowell, Mark↗

NASA NTRS2005

Multipurpose Hyperspectral Imaging System

A hyperspectral imaging system of high spectral and spatial resolution that incorporates several innovative features has been developed to incorporate a focal plane scanner (U.S. Patent 6,166,373). This feature enables the system to be used for both airborne/spaceborne and laboratory hyperspectral imaging with or without relative movement of the imaging system, and it can be used to scan a target of any size as long as the target can be imaged at the focal plane; for example, automated inspection of food items and identification of single-celled organisms. The spectral resolution of this system is greater than that of prior terrestrial multispectral imaging systems. Moreover, unlike prior high-spectral resolution airborne and spaceborne hyperspectral imaging systems, this system does not rely on relative movement of the target and the imaging system to sweep an imaging line across a scene. This compact system (see figure) consists of a front objective mounted at a translation stage with a motorized actuator, and a line-slit imaging spectrograph mounted within a rotary assembly with a rear adaptor to a charged-coupled-device (CCD) camera. Push-broom scanning is carried out by the motorized actuator which can be controlled either manually by an operator or automatically by a computer to drive the line-slit across an image at a focal plane of the front objective. To reduce the cost, the system has been designed to integrate as many as possible off-the-shelf components including the CCD camera and spectrograph. The system has achieved high spectral and spatial resolutions by using a high-quality CCD camera, spectrograph, and front objective lens. Fixtures for attachment of the system to a microscope (U.S. Patent 6,495,818 B1) make it possible to acquire multispectral images of single cells and other microscopic objects.

Mao, Chengye↗

DOE OSTI2024

Developmental Ethanol Exposure Impacts Purkinje Cells but Not Microglia in the Young Adult Cerebellum

Fetal alcohol spectrum disorders (FASD) caused by developmental ethanol exposure lead to cerebellar impairments, including motor problems, decreased cerebellar weight, and cell death. Alterations in the sole output of the cerebellar cortex, Purkinje cells, and central nervous system immune cells, microglia, have been reported in animal models of FASD. To determine how developmental ethanol exposure affects adult cerebellar microglia and Purkinje cells, we used a human third-trimester binge exposure model in which mice received ethanol or saline from postnatal (P) days 4–9. In adolescence, cerebellar cranial windows were implanted and mice were aged to young adulthood for examination of microglia and Purkinje cells in vivo with two-photon imaging or in fixed tissue. Ethanol had no effect on microglia density, morphology, dynamics, or injury response. However, Purkinje cell linear frequency was reduced by ethanol. Microglia–Purkinje cell interactions in the Purkinje Cell Layer were altered in females compared to males. Overall, developmental ethanol exposure had few effects on cerebellar microglia in young adulthood and Purkinje cells appeared to be more susceptible to its effects.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Exploring filamentous fungi depolymerization of corn stover in the context bioenergy queuing operations

Recalcitrance of lignocellulosic feedstocks to depolymerization is a significant barrier for bioenergy production approaches that require conversion of monomeric carbohydrates to renewable energy sources. This study assesses how low-cost modifications in the feedstock supply chain can be transformed into targeted pretreatments in the context of the entire bioenergy supply chain. The aim of this research is to overcome the physiochemical barriers in corn stover that necessitate increased severity in conversion in terms of chemical loading, temperature, and residence time. Corn stover samples were inoculated with a selective (Ceriporiopsis subvermispora) and non-selective (Phaenarochaete chrysosporium) lignin degrading filamentous fungal strains, then stored aerobically to determine the working envelope for fungal pretreatment to achieve lignin degradation. Dry matter loss and gross chemical makeup of corn stover varied by the length of treatment (2 and 4 weeks) and by the moisture content of the treated corn stover samples (40 and 60%, wet basis). Dry matter loss in P. chrysosporium inoculated biomass was elevated compared to the C. subvermispora inoculated biomass; however, treatment also induced additional chemical composition changes suggestive of depolymerization. Scanning electron microscope images reveal hyphae attached within cell lumen and suggest structural changes within P. chrysosporium treated corn stover after 60% moisture storage. These results highlight that fungal treatment approaches must balance loss of convertible material with the potential for reduction in recalcitrance. Techno-economic assessment (TEA) of fungal pretreatment in a short-term queuing system indicated the viability of this approach compared to conventional queuing operations. The total queuing system cost was estimated at $\$$1.65/tonne of biomass stored. After applying the credit of $\$$1.48/tonne from energy savings in the conversion phase using fungal pretreated biomass, the total system cost was $0.80 lower than traditional biomass queueing approach. While the TEA results suggested that treating biomass with C. subvermispora is the most economically viable storage method in the designed fungal-assisted queuing system, future research should focus on additional fungal depolymerization such as those observed in the P. chrysosporium inoculated biomass.

09 BIOMASS FUELS↗

DOE OSTI2020

τ-SIMPLE Algorithm for the closure problem in homogenization of stokes flows

Estimation of the permeability tensor is crucial for many natural and industrial porous media applications. Homogenization provides a rigorous framework to calculate effective parameters from pore-scale images of a representative unit cell of the porous medium by solving a boundary value problem, also known as closure problem, subject to global constraints. However, the latter are hard to satisfy for arbitrarily complex geometries. We have developed a novel computational algorithm to calculate rigorously the permeability tensor. The approach, here referred to as τ-SIMPLE, is based on introducing an artificial time scale τ to satisfy the global constraint within the SIMPLE iteration. Here, we show that the proposed algorithm has high accuracy for both two-dimensional and three-dimensional periodically arranged geometries.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Listeria monocytogenes loss of cultivability on carrot is associated with the formation of mesosome-like structures

Raw carrot is known to have antimicrobial activity against Listeria monocytogenes, but the mechanism of action has not been fully elucidated. In this study, we examined carrot antilisterial activity against several strains of Listeria species (including L. grayi, L. innocua, L. seeligeri, and L. welshimeri) and L. monocytogenes. A representative strain of L. monocytogenes was subsequently used for further characterizing carrot antilisterial activity. Exposure to fresh-cut carrot for 15 min resulted in a similar loss of cultivability, ranging from 2.5 to 4.7 log units, across all Listeria strains evaluated. L. monocytogenes recovered from the fresh-cut surface of different raw carrots was 1.6 to 4.1 log lower than levels obtained from paired boiled carrot samples with abolished antilisterial activity. L. monocytogenes levels recovered from fresh-cut carrot were 2.8 to 3.1 log lower when enumerated by culture-dependent methods than by the culture-independent method of PMAxx-qPCR, a qPCR assay that is performed using DNA pre-treated to selectively sequester DNA from cells with injured membranes. These results suggested that L. monocytogenes loss of cultivability on fresh-cut carrot was not associated with a loss of L. monocytogenes cell membrane integrity and putative cell viability. Transmission electron microscopy imaging revealed that L. monocytogenes rapidly formed mesosome-like structures upon exposure to carrot fresh-cut surface but not upon exposure to boiled carrot surface, suggesting there may be an association between the formation of these mesosome-like structures and a loss of cultivability in L. monocytogenes. As a result, further research is necessary to conclude the causality of this association.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Predicting Dexter Energy Transfer Interactions from Molecular Orbital Overlaps

Dexter energy transfer (DET), also known as spin forbidden energy transfer (e.g., 3 D 1 A → 1 D 3 A), is undergoing renewed interest because of its utility in energy science, photocatalysis, and biomedical imaging. The DET reactions enable exciton fission and fusion and have been recently used to facilitate nanoscale imaging of protein assemblies on cell surfaces. While DET and Förster energy transfer rates are often well described using Fermi’s golden rule, the donor–acceptor couplings for DET may be bridge-state-mediated and depend on the electronic structure of and interactions among the donor, bridge, and acceptor. We provide a simple approach to approximate DET couplings using a product of molecular orbital overlap factors. This approach may be used to guide the design of DET systems with targeted energy-transfer kinetics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Structural basis for ring-opening fluorescence by the RhoBAST RNA aptamer

Abstract Tagging RNAs with fluorogenic aptamers has enabled imaging of transcripts in living cells, revealing novel aspects of RNA metabolism and dynamics. While a diverse set of fluorogenic aptamers has been developed, a new generation of aptamers uses the ring-opening of spirocyclic rhodamine dyes to achieve robust performance in live mammalian cells. These fluorophores have two chemical states: a cell-permeable spirocyclic state and a fluorescent zwitterionic state. The SpyRho555 dye is mostly non-fluorescent in solution and becomes fluorescent in complex with the RhoBAST aptamer. To understand the basis for RhoBAST-SpyRho555 fluorogenicity, we have determined crystal structures of RhoBAST in complex with 5-carboxytetramethylrhodamine and a SpyRho555 analogue, MaP555. RhoBAST is organized by a perfect four-way junction that positions two loops to form the dye-binding pocket. The core of the ligand resides between a tri-adenine floor and a single guanine base, largely driven by π-stacking interactions. Importantly, the unpaired guanine interacts with the 3-position group of MaP555 to stabilize the open conformation, supported by mutagenesis data, and may play an active role in promoting the open conformation of the dye. This work has implications for the development of new fluorogenic aptamers with improved properties using structure-guided design approaches.

Biochemistry & Molecular Biology↗

DOE OSTI2022

In situ x-ray diffraction study of dynamically compressed α -cristobalite using a dynamic diamond anvil cell

Here we present results of the dynamic compression of α -cristobalite up to a pressure of 106 GPa with the use of the dynamic diamond anvil cell. X-ray diffraction images were recorded at different ramp compression and decompression rates to investigate in situ the high-pressure phase transitions of α -cristobalite. Our results suggest that the pressure onset of the phase transformation of α -cristobalite to cristobalite II, cristobalite X-I, and ultimately to seifertite ( α – PbO 2 type SiO 2 ) is dependent on the applied compression rates and stress conditions of the experiment. Increasing compression rates in general shift the studied phase transitions to higher pressures. Furthermore, our results indicate for single crystals under hydrostatic conditions a suppression of a phase transition from cristobalite X-I to seifertite at pressures of up to 82 GPa.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism

Abstract Background Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse CPR bacteria and grow in sulfide-rich springs to investigate microbial controls on biogeochemical cycling. Results Sulfide springs biofilms were investigated using bulk geochemical analysis, genome-resolved metagenomics, and scanning transmission X-ray microscopy (STXM) at room temperature and 87 K. Chemolithotrophic sulfur-oxidizing bacteria, including Thiothrix and Beggiatoa , dominate the biofilms, which also contain CPR Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, and Parcubacteria. STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts. STXM and NEXAFS spectroscopy at carbon K and sulfur L 2,3 edges show that filamentous bacteria contain protein-encapsulated spherical elemental sulfur granules, indicating that they are sulfur oxidizers, likely Thiothrix . Berkelbacteria and Moranbacteria in the same biofilm sample are predicted to have a novel electron bifurcating group 3b [NiFe]-hydrogenase, putatively a sulfhydrogenase, potentially linked to sulfur metabolism via redox cofactors. This complex could potentially contribute to symbioses, for example, with sulfur-oxidizing bacteria such as Thiothrix that is based on cryptic sulfur cycling. One Doudnabacteria genome encodes adjacent sulfur dioxygenase and rhodanese genes that may convert thiosulfate to sulfite. We find similar conserved genomic architecture associated with CPR bacteria from other sulfur-rich subsurface ecosystems. Conclusions Our combined metagenomic, geochemical, spectromicroscopic, and structural bioinformatics analyses of biofilms growing in sulfide-rich springs revealed consortia that contain CPR bacteria and sulfur-oxidizing Proteobacteria, including Thiothrix , and bacteria from a new family within Beggiatoales. We infer roles for CPR bacteria in sulfur and hydrogen cycling.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Self-driving thin film laboratory: autonomous epitaxial atomic-layer synthesis via real-time computer vision analysis of electron diffraction

Emerging materials science platforms with the ability to make autonomous decisions on the fly are fundamentally changing the outlook and protocols for materials optimization and discovery. Because AI-driven self-navigating schemes can effectively reduce the total number of iterations needed to arrive at the "answer" (i.e. the best stochiometric composition for a desired physical property, optimum materials processing parameters, etc.) by significant margins, they have the potential to revolutionize materials and chemical manufacturing processes at large in research laboratory settings as well as in industrial plants. Here, we demonstrate a successful implementation of real-time closed-loop autonomous navigation of a multi-dimensional materials synthesis parameter space for fabricating phase-pure epitaxial films of a metastable phase of a functional oxide in a combinatorial pulsed laser deposition chamber. Sequential epitaxial growth iterations in search of the optimized recipe to stabilize the desired crystal phase were performed using frame-by-frame quantitative computer vision analysis of reflection high-energy electron diffraction (RHEED) images of the unit-cell level film being deposited. The autonomous scheme regularly resulted in > 30-fold reduction in the number of required experiments compared to a comprehensive mapping of the parameter space. The real-time workflow developed here can be readily extended to a variety of thin film synthesis platforms opening the door for self-driving atomic-level materials design as well as autonomous optimization of semiconductor manufacturing.

36 MATERIALS SCIENCE↗

NASA NTRS1982

Effect of Fluid Flow on Zinc Electrodeposits from Acid Chloride Electrolytes

Zinc was deposited potentiostatically from acid chloride baths. Once bath chemistry and electrochemistry were controlled, the study was focused on convective mass transfer at horizontal electrodes and its effect on cell performance. A laser schlieren imaging technique allowed in situ observations of flow patterns and their correlation with current transients. Convection was turbulent and mass transfer as a function of Rayleigh number was well correlated by: Sh = 0.14 R to the 1/3 power. Similarly, convection initiation time was correlated by DT/d squared = 38 Ra to the -2/3 power. Time scale of fluctuations was about half the initiation time. Taking the boundary layer thickness as a characteristic length, a critical Rayleigh number for the onset of convection was deduced: Ra sub CR = 5000. Placing the anode on the top of the cathode completely changed the flow pattern but kept the I-t curves identical whereas the use of a cathode grid doubled the limiting current. A well defined plateau in the current voltage curves suggested that hydrogen evolution has been successfully inhibited. Finally, long time deposition showed that convection at horizontal electrodes increased the induction time for dentrite growth by at least a factor of 2 with respect to a vertical wire.

Abdelmassir, A. A.↗

NASA NTRS2002

Biomolecular Effects of Cold Plasma Exposure

The effects of cold plasma exposure on Deinococcus radiodurans, plasmid DNA and model proteins were assessed using microbiological, spectrometric and biochemical techniques. Exposure of D. radiodurans, an extremely radiation resistant microbe, to O2 plasma (less than or equal to 25 W, approx. 45 mTorr, 90 min) yielded a approx. 99.999 % sterilization and the sterilization rate was increased approx. 10-fold at 100 W and 500 mTorr. AFM images shows that the exposed cells are significantly deformed and possess 50-70 nm concavities. IR analysis indicates the chemical degradation of lipids, proteins and carotenoids of the cell wall and membrane. Intracellular damage was indicated by major absorbance loss at 1245, 1651 and 1538/cm corresponding to degradation of DNA and proteins, respectively. Biochemical experiments demonstrate that plasmas induce strand scissions and crosslinking of plasmid DNA, and reduction of enzyme activity; the degradation is power dependent with total sample loss occurring in 60 s at 200 W and 500 mTorr. Emission spectroscopy shows that D. radiodurans is volatilized into CO2, CO, N2 and H2O confirming the removal of biological matter from contaminated surfaces. The O2 plasma impacts several cellular components predominantly through chemical degradation by atomic oxygen. A CO2, plasma, however, was not effective at degrading D. radiodurans, revealing the importance of plasma composition, which has implications for planetary protection and the contamination of Mars.

Mogul, Rakesh↗

NASA NTRS2009

Stereo Vision Based Terrain Mapping for Off-Road Autonomous Navigation

Successful off-road autonomous navigation by an unmanned ground vehicle (UGV) requires reliable perception and representation of natural terrain. While perception algorithms are used to detect driving hazards, terrain mapping algorithms are used to represent the detected hazards in a world model a UGV can use to plan safe paths. There are two primary ways to detect driving hazards with perception sensors mounted to a UGV: binary obstacle detection and traversability cost analysis. Binary obstacle detectors label terrain as either traversable or non-traversable, whereas, traversability cost analysis assigns a cost to driving over a discrete patch of terrain. In uncluttered environments where the non-obstacle terrain is equally traversable, binary obstacle detection is sufficient. However, in cluttered environments, some form of traversability cost analysis is necessary. The Jet Propulsion Laboratory (JPL) has explored both approaches using stereo vision systems. A set of binary detectors has been implemented that detect positive obstacles, negative obstacles, tree trunks, tree lines, excessive slope, low overhangs, and water bodies. A compact terrain map is built from each frame of stereo images. The mapping algorithm labels cells that contain obstacles as no-go regions, and encodes terrain elevation, terrain classification, terrain roughness, traversability cost, and a confidence value. The single frame maps are merged into a world map where temporal filtering is applied. In previous papers, we have described our perception algorithms that perform binary obstacle detection. In this paper, we summarize the terrain mapping capabilities that JPL has implemented during several UGV programs over the last decade and discuss some challenges to building terrain maps with stereo range data.

passive perception↗

DOE OSTI2024

Non-destructive Post-Transient Examination Results of the MOXTOP-1 Experiment

The MOXTOP-1 experiment has been assembled and irradiated in INL’s HFEF and TREAT facilities followed by disassembly of the experiment to enable initial post-transient examination. Results of neutron radiography of the fuel pin still in the THOR capsule were somewhat inconclusive due to the additional scatter and attenuation from the iron heat sink included in the design. Nonetheless, no obvious failure or fuel relocation could be identified in the radiography. Following disassembly of the fuel pin from the capsule, initial visual inspections were performed, and documented via images obtained through the hot cell window. No obvious signs of fuel failure were identified, indicating that the fuel pin remained intact during the transient. Some discoloration was observed near the middle of the fuel pin, likely corresponding to the fueled zone indicating that that region may have reached a relatively high temperature. Pre-transient, and post-transient profilometry of the fuel pin were performed and compared. Some additional strain displacement in the bottom portion of the fuel zone is identified, but remains well below 1%.

Mixed Oxide↗

DOE OSTI2021

Fusing Quantitative-Phase Imaging with Airy Light- Sheet Microscopy

We report the integration of quantitative-phase imaging (QPI) with light-sheet (LS) fluorescent microscopy on to a standard inverted microscope that retains compatibility with microfluidics. QPI enables label-free imaging and number-density quantification of single cells and their organelles. Conversely, LS yields considerable speed and phototoxicity gains in quantifying the 4D dynamics of gene-encoded fluorescent biomarkers. We will detail the system design that relied on spatial light interferometry for QPI and an accelerating Airy- beam light-sheet for fluorescence, its performance, as well as results of a representative multivariate imaging analysis of single-cell metabolism.

imaging, lattice light sheet, Yarrowia lipolytica,↗

NASA NTRS1994

Monolithic in-based III-V compound semiconductor focal plane array cell with single stage CCD output

A monolithic semiconductor imager includes an indium-based III-V compound semiconductor monolithic active layer of a first conductivity type, an array of plural focal plane cells on the active layer, each of the focal plane cells including a photogate over a top surface of the active layer, a readout circuit dedicated to the focal plane cell including plural transistors formed monolithically with the monolithic active layer and a single-stage charge coupled device formed monolithically with the active layer between the photogate and the readout circuit for transferring photo-generated charge accumulated beneath the photogate during an integration period to the readout circuit. The photogate includes thin epitaxial semiconductor layer of a second conductivity type overlying the active layer and an aperture electrode overlying a peripheral portion of the thin epitaxial semiconductor layer, the aperture electrode being connectable to a photogate bias voltage.

Fossum, Eric R.↗

NASA NTRS1995

Monolithic in-based III-V compound semiconductor focal plane array cell with single stage CCD output

Fossum, Eric R.↗