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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Novel and Emerging Capabilities that Can Provide a Holistic Understanding of the Plant Root Microbiome

In recent years, the root microbiome (i.e., microorganisms growing inside, on, or in close proximity to plant roots) has been shown to play an important role in plant health and productivity. Despite its importance, the root microbiome is challenging to study because of its complexity, heterogeneity, and subterranean location. Fortunately, root microbiome research has seen a tremendous influx of novel technologies (e.g., imaging tools, robotics, and molecular analyses), experimental platforms (e.g., micro- and mesocosms), and data integration, modeling, and prediction tools in the past decade that have greatly increased our ability to dissect the complex network of interactions between above- and belowground environmental parameters, plants, bacteria, and fungi that dictate soil and broader ecosystem health. Herein, we discuss methods that are currently used in root microbiome research and that can be expanded to phytobiome research in general ranging from laboratory studies to mesocosm-scale studies and, finally, to field studies; evaluate their relevance to ecosystem studies; and discuss future root microbiome research directions.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1983

Balloon-borne diode-laser absorption spectrometer for measurements of stratospheric trace species

An instrument has been designed for the measurement of stratospheric trace species which utilizes tunable infrared diode lasers as sources for sensitive in situ absorption spectroscopy in selected wavelength regions. This instrument, the Balloon-Borne Laser In Situ Sensor (BLISS), is a high-resolution absorption spectrometer designed to provide measurements of the concentrations of stratospheric species and their diurnal variations. The instrument employs second-harmonic detection of the absorption of tunable diode laser (TDL) radiation (3-30 microns) in a 1 km path length defined by a retroreflector lowered 0.5 km below the BLISS gondola. Retroreflector tracking under microprocessor control is obtained using a He-Ne laser and coaligned TV camera with CID imaging. Simultaneous measurements of molecular species in the 20-40 km altitude range will be performed using four TDLs, with the predicted minimum-detectable mixing ratio at 30 km being typically less than or equal to 0.1 ppbv.

Menzies, R. T.↗
NASA NTRS2000

The Proton and Electron Aurora as Seen by Image-FUV and FAST

The Far Ultraviolet (FUV) instrument on IMAGE images the aurora in three different wavelength regions. The Wideband Imaging Camera (WIC) observes the molecular Lyman-Birge-Hopfield (LBH) and atomic Nitrogen emissions at 140-190 nm. The two channels of the Spectrographic Imager (SI) observe the Doppler shifted Lyman Alpha emission of precipitating protons at 121.8 nm (SI 12) and the mostly electron produced emission from oxygen OI at 135.6 nm (SI13). The major advantage of FUV compared to previously flown UV imagers is the simultaneous operation of all three imaging systems without the need for filter changes and the uncertainty of temporal changes of the aurora between exposures. The FAST satellite passes every two hours through FUV images during apogee operations. This enables a comparison between the remotely imaged particle precipitation and the in-situ measurements along the FAST track. The detailed analysis of images from all three systems together with a full simulation of auroral emissions based on in-situ measurements by FAST confirms the laboratory calibrations of FUV. The spatial resolution and image quality of WIC permits the observation of a good correspondence between in-situ and remote measurements of precipitation boundaries. The clear separation between the lower latitude proton precipitation and the more structured higher latitude electron precipitation is obtained with both SI-channels.

Gerard, J.-C.↗
NASA NTRS2001

Novel Diffusivity Measurement Technique

A common-path interferometer (CPI) system was developed to measure the diffusivity of liquid pairs. The CPI is an optical technique that can be used to measure changes in the gradient of the refraction index of transparent materials. This system uses a shearing interferometer that shares the same optical path from a laser light source to the final imaging plane. Hence, the molecular diffusion coefficient of liquids can be determined using the physical relations between changes in the optical path length and the liquid phase properties. The data obtained with this interferometer were compared with similar results from other techniques and demonstrated that the instrument is superior in measuring the diffusivity of miscible liquids while keeping the system very compact and robust. CPI can also be used for studies in interface dynamics and other diffusion-dominated-process applications.

Rashidnia, Nasser↗
NASA NTRS2001

Cancer Detection Using Neural Computing Methodology

This paper describes a novel learning methodology used to analyze bio-materials. The premise of this research is to help pathologists quickly identify anomalous cells in a cost efficient method. Skilled pathologists must methodically, efficiently and carefully analyze manually histopathologic materials for the presence, amount and degree of malignancy and/or other disease states. The prolonged attention required to accomplish this task induces fatigue that may result in a higher rate of diagnostic errors. In addition, automated image analysis systems to date lack a sufficiently intelligent means of identifying even the most general regions of interest in tissue based studies and this shortfall greatly limits their utility. An intelligent data understanding system that could quickly and accurately identify diseased tissues and/or could choose regions of interest would be expected to increase the accuracy of diagnosis and usher in truly automated tissue based image analysis.

liquid crystal tunable filters↗
NASA NTRS2011

Massive Young Stellar Objects in the Galactic Center: Spectroscopic Identification from Spitzer/IRS Observations - 1

We present results from our spectroscopic study, using the Infrared Spectrograph (IRS) onboard the Spitzer Space Telescope, designed to identify massive young stellar objects (YSOs) in the Galactic Center (GC). Our sample of 107 YSO candidates was selected based on IRAC colors from the high spatial resolution, high sensitivity Spitzer/IRAC images in the Central Molecular Zone (CMZ), which spans the central approximately 300 pc region of the Milky Way Galaxy. We obtained IRS spectra over 5 micron to 35 micron using both high- and low-resolution IRS modules. We spectroscopically identify massive YSOs by the presence of a 15.4 micron shoulder on the absorption profile of 15 micron CO2 ice, suggestive of CO2 ice mixed with CH30H ice on grains. This 15.4 micron shoulder is clearly observed in 16 sources and possibly observed in an additional 19 sources. We show that 9 massive YSOs also reveal molecular gas-phase absorption from C02, C2H2, and/or HCN, which traces warm and dense gas in YSOs. Our results provide the first spectroscopic census of the massive YSO population in the GC. We fit YSO models to the observed spectral energy distributions and find YSO masses of 8 - 23 solar Mass, which generally agree with the masses derived from observed radio continuum emission. We find that about 50% of photometrically identified YSOs are confirmed with our spectroscopic study. This implies a preliminary star formation rate of approximately 0.07 solar mass/yr at the GC.

An, Deokkeun↗
NASA NTRS1989

The Viking biology results

A brief review of the purposes and the results from the Viking Biology experiments is presented, in the expectation that the lessons learned from this mission will be useful in planning future approaches to the biological exploration of Mars. Since so little was then known about potential micro-environments on Mars, three different experiments were included in the Viking mission, each one based on different assumptions about what Martian organisms might be like. In addition to the Viking Biology Instrument (VBI), important corollary information was obtained from the Viking lander imaging system and from the molecular analysis experiments that were conducted using the gas chromatograph-mass spectrometer (GCMS) instrument. No biological objects were noted by the lander imaging instrument. The GCMS did not detect any organic compounds. A description of the tests conducted by the Gas Exchange Experiment, the Labeled Release experiment, and the Pyrolytic Release experiment is given. Results are discussed. Taken as a whole, the Viking data yielded no unequivocal evidence for a Martian biota at either landing site. The results also revealed the presence of one or more reactive oxidants in the surface material and these need to be further characterized, as does the range of micro-environments, before embarking upon future searches for extant life on Mars.

Klein, Harold P.↗
DOE OSTI2022

Data for "In vitro and in vivo NIR Fluorescence Lifetime Imaging with a time-gated SPAD camera"

Near-infrared (NIR) fluorescence lifetime imaging (FLI) provides a unique contrast mechanism to monitor biological parameters and molecular events in vivo. Single-photon avalanche diode (SPAD) cameras have been recently demonstrated in FLI microscopy (FLIM) applications, but their suitability for in vivo macroscopic FLI (MFLI) in deep tissues remains to be demonstrated. Herein, we report in vivo NIR MFLI measurement with SwissSPAD2, a large time-gated SPAD camera. We first benchmark its performance in well-controlled in vitro experiments, ranging from monitoring environmental effects on fluorescence lifetime, to quantifying Förster resonant energy transfer (FRET) between dyes. Next, we use it for in vivo studies of target-drug engagement in live and intact tumor xenografts using FRET. Information obtained with SwissSPAD2 was successfully compared to that obtained with a gated intensified charge-coupled device (ICCD) camera, using two different approaches. Our results demonstrate that SPAD cameras offer a powerful technology for in vivo preclinical applications in the NIR window.

2DG↗
DOE OSTI2026

Imaging from Macro to Nanoscale: Multimodal Advances in Chemical and Biomedical Imaging

Imaging increasingly serves as a multiscale framework for linking molecular mechanisms to cellular behavior, tissue architecture, and organ phenotypes in biology and unraveling fundamental processes in chemistry, physics and materials science. This Perspective highlights recent advances in chemical and biomedical imaging across macro-, micro-, and nanoscales, using representative examples published in Chemical and Biomedical Imaging (CBMI). At the macroscale, we discuss chemically selective MRI, including endogenous and exogenous CEST strategies, together with photoacoustic imaging as a hybrid modality with functional and chemical contrast. At the microscale, we consider fluorescence, label-free optical and vibrational imaging, and selected X-ray approaches that expand sensitivity, specificity, and temporal resolution in biological and materials systems. At the nanoscale, we highlight super-resolution fluorescence microscopy, single-molecule methods, tip-enhanced Raman spectroscopy, and correlative imaging strategies that resolve local heterogeneity and molecular organization. Across scales, a common theme emerges that advances in probes, contrast mechanisms, instrumentation, and sample handling are enabling chemically informed imaging that connects molecular specificity with biological context.

multiscale imaging↗
DOE OSTI2023

Molecular homing and retention of muscle membrane stabilizing copolymers by non-invasive optical imaging in vivo

First-in-class membrane stabilizer Poloxamer 188 (P188) has been shown to confer membrane protection in an extensive range of clinical conditions; however, elements of the systemic distribution and localization of P188 at the organ, tissue, and muscle fiber levels in vivo have not yet been elucidated. Here we used non-invasive fluorescence imaging to directly visualize and track the distribution and localization of P188 in vivo. The results demonstrated that the Alx647 probe did not alter the fundamental properties of P188 to protect biological membranes. Distribution kinetics in mdx mice demonstrated that Alx647 did not interface with muscle membranes and had fast clearance kinetics. In contrast, the distribution kinetics for P188-Alx647 was significantly slower, indicating a dramatic depot and retention effect of P188. Results further demonstrated the significant retention of P188-Alx647 in the skeletal muscle of mdx mice, showing a significant genotype effect with a higher fluorescence signal in the mdx muscles over BL10 mice. High-resolution optical imaging provided direct evidence of P188 surrounding the sarcolemma of skeletal and cardiac muscle cells. Taken together, these findings provide direct evidence of muscle-disease-dependent molecular homing and retention of synthetic copolymers in striated muscles thereby facilitating advanced studies of copolymer-membrane association in health and disease.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1990

A search for pre-main sequence stars in the high-latitude molecular clouds. II - A survey of the Einstein database

The preliminary results are reported of a survey of every EINSTEIN image which overlaps any high-latitude molecular cloud in a search for X-ray emitting pre-main sequence stars. This survey, together with complementary KPNO and IRAS data, will allow the determination of how prevalent low mass star formation is in these clouds in general and, particularly, in the translucent molecular clouds.

Caillault, Jean-Pierre↗
DOE OSTI2020

Chemical and steric effects in simulating noncontact atomic force microscopy images of organic molecules on a Cu (111) substrate

Noncontact mode of atomic force microscopy (nc-AFM) employing a CO-functionalized tip is a very powerful tool for studying molecular structures. However, interpreting nc-AFM images for nonplanar molecules can sometimes be problematic. To illustrate and resolve the nature of such problematic systems, we employ real-space pseudopotentials constructed within density functional theory to simulate nc-AFM images. In this work, we focus on several representative nonplanar organic molecules (pentacene, naphthanthrone, olympicene, and 6-phenylhexa-1,3,5-triynybenzene (PHTB)) on a typical substrate: the Cu (111) surface. This substrate results in significant distortions in the molecular geometries of pentacene and naphthanthrone. Including these distortions in simulated nc-AFM imaging notably improves the agreement between the simulated and measured images. In naphthanthrone, the relatively large interaction between the O atom and the Cu substrate offers a straightforward explanation for the absence of the C = O bond in the measured image. Nonplanar features such as tilting or twisting are also apparent in olympicene and PHTB. A “triangular” bright feature associated with the –CH 2 group in olympicene appears in simulated and measured nc-AFM images. This feature is directly related to the tilting angle of the molecule with respect to the Cu substrate. The “defective” benzene ring feature and the faint ellipsoidal C ≡ C feature in PHTB can be ascribed to its twisted nature. The ability to simulate such subatomic images in nc-AFM reflects the accuracy and efficiency of calculating quantum forces in real space.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

SAXS-guided unbiased coarse-grained Monte Carlo simulation for identification of self-assembly nanostructures and dimensions

Recent studies have shown that solvated amphiphiles can form nanostructured self-assemblies called dynamic binary complexes (DBCs) in the presence of ions. Since the nanostructures of DBCs are directly related to their viscoelastic properties, it is important to understand how the nanostructures change under different solution conditions. However, it is challenging to obtain a three-dimensional molecular description of these nanostructures by utilizing conventional experimental characterization techniques or thermodynamic models. To this end, we combined the structural data from small angle X-ray scattering (SAXS) experiments and thermodynamic knowledge from coarse-grained Monte Carlo (CGMC) simulations to identify the detailed three-dimensional nanostructure of DBCs. Specifically, unbiased CGMC simulations are performed with SAXS-guided initial conditions, which aids us to sample accurate nanostructures in a computationally efficient fashion. As a result, an elliptical bilayer nanostructure is obtained as the most probable nanostructure of DBCs whose dimensions are validated by scanning electron microscope (SEM) images. Then, utilizing the obtained molecular model of DBCs, here we could also explain the pH tunability of the system. Overall, our results from SAXS-guided unbiased CGMC simulations highlight that using potential energy combined with SAXS data, we can distinguish otherwise degenerate nanostructures resulting from the inherent ambiguity of SAXS patterns.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Molecular qubits based on photogenerated spin-correlated radical pairs for quantum sensing

Photogenerated spin-correlated radical pairs (SCRPs) in electron donor–bridge–acceptor (D–B–A) molecules can act as molecular qubits and inherently spin qubit pairs. SCRPs can take singlet and triplet spin states, comprising the quantum superposition state. Their synthetic accessibility and well-defined structures, together with their ability to be prepared in an initially pure, entangled spin state and optical addressability, make them one of the promising avenues for advancing quantum information science. Coherence between two spin states and spin selective electron transfer reactions form the foundation of using SCRPs as qubits for sensing. We can exploit the unique sensitivity of the spin dynamics of SCRPs to external magnetic fields for sensing applications including resolution-enhanced imaging, magnetometers, and magnetic switch. Molecular quantum sensors, if realized, can provide new technological developments beyond what is possible with classical counterparts. While the community of spin chemistry has actively investigated magnetic field effects on chemical reactions via SCRPs for several decades, we have not yet fully exploited the synthetic tunability of molecular systems to our advantage. This review offers an introduction to the photogenerated SCRPs-based molecular qubits for quantum sensing, aiming to lay the foundation for researchers new to the field and provide a basic reference for researchers active in the field. We focus on the basic principles necessary to construct molecular qubits based on SCRPs and the examples in quantum sensing explored to date from the perspective of the experimentalist.

Mani, Tomoyasu (ORCID:0000000241255195)↗
DOE OSTI2020

Hyperspectral X-ray Imaging with TES Detectors for Nanoscale Chemical Speciation Mapping

We are developing an imaging capability (“Hyperspectral X-ray Imaging”) for mapping chemical information (molecular formula, phase, oxidation state, hydration) that is based on ultra-high-resolution X-ray emission spectroscopy with large transition-edge sensor microcalorimeter arrays in the scanning electron microscope. By combining microcalorimeter arrays with hundreds of pixels, high-bandwidth microwave frequency-division multiplexing, and fast digital electronics for near real-time data processing, our goal is to enable measurements using laboratory-scale instrumentation rather than synchrotron beamlines. Our application focus here is on mapping the chemical form of uranium compounds on the nanoscale. Furthermore, we will present our approach to developing the Hyperspectral X-ray Imaging capability, progress toward a 128-pixel microwave multiplexed X-ray fluorescence instrument at LANL, and the path to high-throughput nanoscale chemical mapping.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Converting tabular data into images for deep learning with convolutional neural networks

Abstract Convolutional neural networks (CNNs) have been successfully used in many applications where important information about data is embedded in the order of features, such as speech and imaging. However, most tabular data do not assume a spatial relationship between features, and thus are unsuitable for modeling using CNNs. To meet this challenge, we develop a novel algorithm, image generator for tabular data (IGTD), to transform tabular data into images by assigning features to pixel positions so that similar features are close to each other in the image. The algorithm searches for an optimized assignment by minimizing the difference between the ranking of distances between features and the ranking of distances between their assigned pixels in the image. We apply IGTD to transform gene expression profiles of cancer cell lines (CCLs) and molecular descriptors of drugs into their respective image representations. Compared with existing transformation methods, IGTD generates compact image representations with better preservation of feature neighborhood structure. Evaluated on benchmark drug screening datasets, CNNs trained on IGTD image representations of CCLs and drugs exhibit a better performance of predicting anti-cancer drug response than both CNNs trained on alternative image representations and prediction models trained on the original tabular data.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1992

Near-infrared images and color maps of Arp 220

Near-infrared images (1.3-3.7 microns) are presented for the nuclear region of Arp 220. Color maps in J - H and H - K reveal steep gradients, and the two nuclei previously detected at 20 cm and 2.2 microns appear on the J - H image as peaks separated by 1 arcsec. Hot dust emission (T about 1000 K) at 3.7 microns and extremely red J - H and H - K colors are found for both nuclei. The increasingly red color approaching the center of the galaxy are explained most naturally by a mixture of extinction and emission by increasing amounts of hot dust. The near-infrared emission is consistent with a circumnuclear starburst extending to a radius of about 1.5 kpc from the nuclei; further from the center the colors are consistent with a normal late-type stellar population. Inside a radius of 1 kpc the color maps show a NE-SW elongation that aligns with the concentration of molecular gas seen in CO images. The observed 3.7-micron luminosity, when corrected for nuclear extinction determined by 10-micron silicate absorption measurements and normalized by the bolometric luminosity, is consistent with UV-excess quasars and is about 10 times greater than that found in infrared luminous starburst galaxies.

Mazzarella, J. M.↗