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DOE OSTI2022

Identification of new marker genes from plant single‐cell RNA‐seq data using interpretable machine learning methods

Summary An essential step in the analysis of single‐cell RNA sequencing data is to classify cells into specific cell types using marker genes. In this study, we have developed a machine learning pipeline called single‐cell predictive marker (SPmarker) to identify novel cell‐type marker genes in the Arabidopsis root. Unlike traditional approaches, our method uses interpretable machine learning models to select marker genes. We have demonstrated that our method can: assign cell types based on cells that were labelled using published methods; project cell types identified by trajectory analysis from one data set to other data sets; and assign cell types based on internal GFP markers. Using SPmarker, we have identified hundreds of new marker genes that were not identified before. As compared to known marker genes, the new marker genes have more orthologous genes identifiable in the corresponding rice single‐cell clusters. The new root hair marker genes also include 172 genes with orthologs expressed in root hair cells in five non‐ Arabidopsis species, which expands the number of marker genes for this cell type by 35–154%. Our results represent a new approach to identifying cell‐type marker genes from scRNA‐seq data and pave the way for cross‐species mapping of scRNA‐seq data in plants.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Mushroom body input connections form independently of sensory activity in Drosophila melanogaster

Associative brain centers, such as the insect mushroom body, need to represent sensory information in an efficient manner. In Drosophila melanogaster, the Kenyon cells of the mushroom body integrate inputs from a random set of olfactory projection neurons, but some projection neurons—namely those activated by a few ethologically meaningful odors—connect to Kenyon cells more frequently than others. This biased and random connectivity pattern is conceivably advantageous, as it enables the mushroom body to represent a large number of odors as unique activity patterns while prioritizing the representation of a few specific odors. How this connectivity pattern is established remains largely unknown. Here, we test whether the mechanisms patterning the connections between Kenyon cells and projection neurons depend on sensory activity or whether they are hardwired. We mapped a large number of mushroom body input connections in partially anosmic flies—flies lacking the obligate odorant co-receptor Orco—and in wild-type flies. Statistical analyses of these datasets reveal that the random and biased connectivity pattern observed between Kenyon cells and projection neurons forms normally in the absence of most olfactory sensory activity. Finally, this finding supports the idea that even comparatively subtle, population-level patterns of neuronal connectivity can be encoded by fixed genetic programs and are likely to be the result of evolved prioritization of ecologically and ethologically salient stimuli.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1999

Antigen S1, encoded by the MIC1 gene, is characterized as an epitope of human CD59, enabling measurement of mutagen-induced intragenic deletions in the AL cell system

S1 cell membrane antigen is encoded by the MIC1 gene on human chromosome 11. This antigen has been widely used as a marker for studies in gene mapping or in analysis of mutagen-induced gene deletions/mutations, which utilized the human-hamster hybrid cell-line, AL-J1, carrying human chromosome 11. Evidence is presented here which identifies S1 as an epitope of CD59, a cell membrane complement inhibiting protein. E7.1 monoclonal antibody, specific for the S1 determinant, was found to react strongly with membrane CD59 in Western blotting, and to bind to purified, urinary form of CD59 in ELISAs. Cell membrane expression of S1 on various cell lines always correlated with that of CD59 when examined by immunofluorescent staining. In addition, E7.1 antibody inhibited the complement regulatory function of CD59. Identification of S1 protein as CD59 has increased the scope of the AL cell system by enabling analysis of intragenic mutations, and multiplex PCR analysis of mutated cells is described, showing variable loss of CD59 exons.

Non-NASA Center↗

NASA NTRS1977

A 'digital' technique for manual extraction of data from aerial photography

The interpretation procedure described uses a grid cell approach. In addition, a random point is located in each cell. The procedure required that the cell/point grid be established on a base map, and identical grids be made to precisely match the scale of the photographic frames. The grid is then positioned on the photography by visual alignment to obvious features. Several alignments on one frame are sometimes required to make a precise match of all points to be interpreted. This system inherently corrects for distortions in the photography. Interpretation is then done cell by cell. In order to meet the time constraints, first order interpretation should be maintained. The data is put onto coding forms, along with other appropriate data, if desired. This 'digital' manual interpretation technique has proven to be efficient, and time and cost effective, while meeting strict requirements for data format and accuracy.

Istvan, L. B.↗

NASA NTRS1986

Continuous blood densitometry - Fluid shifts after graded hemorrhage in animals

Rapid fluid shifts in four pigs and two dogs subjected to graded hemorrhage are investigated. Arterial blood density (BD), mean arterial pressure (MAP), central venous pressure (CVP), arterial plasma density (PD), hematocrit (Hct) and erythrocyte density were measured. The apparatus and mechancial oscillator technique for measuring density are described. Fluid shifts between red blood cells and blood plasma and alterations in the whole-body-to-large vessel Hct, F(cell) are studied using two models. The bases of the model calculations are discussed. A decrease in MAP, CVP, and BP is detected at the beginning of hemorrhaging; continued bleeding results in further BD decrease correlating with volume displacement. The data reveal that at 15 ml/kg blood loss the mean PD and BD dropped by 0.99 + or - 0.15 and 2.42 + or 0.26 g/liter, respectively, and the Hct dropped by 2.40 + or 0.47 units. The data reveal that inward-shifted fluid has a higher density than normal ultrafiltrate and/or there is a rise in the F(cell) ratio. It is noted that rapid fluid replacement ranged from 5.8 + or - 0.8 to 10.6 + or - 2.0 percent of the initial plasma volume.

Hinghofer-Szalkay, H.↗

NASA NTRS2011

The 13 years of TRMM Lightning Imaging Sensor: From Individual Flash Characteristics to Decadal Tendencies

How often lightning strikes the Earth has been the object of interest and research for decades. Several authors estimated different global flash rates using ground-based instruments, but it has been the satellite era that enabled us to monitor lightning thunderstorm activity on the time and place that lightning exactly occurs. Launched into space as a component of NASA s Tropical Rainfall Measuring Mission (TRMM) satellite, in November 1997, the Lighting Imaging Sensor (LIS) is still operating. LIS detects total lightning (i.e., intracloud and cloud-to-ground) from space in a low-earth orbit (35deg orbit). LIS has collected lightning measurements for 13 years (1998-2010) and here we present a fully revised and current total lightning climatology over the tropics. Our analysis includes the individual flash characteristics (number of events and groups, total radiance, area footprint, etc.), composite climatological maps, and trends for the observed total lightning during these 13 years. We have identified differences in the energetics of the flashes and/or the optical scattering properties of the storms cells due to cell-relative variations in microphysics and kinematics (i.e., convective or stratiform rainfall). On the climatological total lightning maps we found a dependency on the scale of analysis (resolution) in identifying the lightning maximums in the tropics. The analysis of total lightning trends observed by LIS from 1998 to 2010 in different temporal (annual and seasonal) and spatial (large and regional) scales, showed no systematic trends in the median to lower-end of the distributions, but most places in the tropics presented a decrease in the highest total lightning flash rates (higher-end of the distributions).

Albrecht, R. I.↗

DOE OSTI2026

Super-moiré spin textures in twisted two-dimensional antiferromagnets

Stacking two-dimensional layered materials offers a platform to engineer electronic and magnetic states. In general, the resulting states—such as moiré magnetism—have a periodicity at the length scale of the moiré unit cell. Here we study magnetic order in twisted double-bilayer chromium triiodide by means of scanning nitrogen-vacancy microscopy. We observe long-range magnetic textures extending beyond the single moiré unit cell, which we dub a super-moiré magnetic state. At small twist angles, the size of the spontaneous magnetic texture increases with twist angle, opposite to the underlying moiré wavelength. The spin-texture size reaches a maximum of about 300 nm in 1.1° twisted devices, an order of magnitude larger than the underlying moiré wavelength, and vanishes at twist angles above 2°. The obtained magnetic field maps suggest the formation of antiferromagnetic Néel-type skyrmions spanning multiple moiré cells. The twist-angle-dependent study, combined with large-scale atomistic Monte Carlo simulations, suggests that the magnetic competition between the Dzyaloshinskii–Moriya interaction, magnetic anisotropy and exchange interactions—which all depend on the relative rotation of the layers—produces the topological textures that emerge in the super-moiré spin order.

Wong, King Cho [Univ. of Stuttgart (Germany)] (ORC↗

NASA NTRS2000

Exploiting the Temperature Dependence of Magnetic Susceptibility to Control Convection in Fundamental Studies of Solidification Phenomena

It is well known that convection is a dominant mass transport mechanism when materials are solidified on Earth's surface. This convection is caused by gradients in density (and therefore gravitational force) that are brought about by gradients in temperature, composition or both. Diffusion of solute is therefore dwarfed by convection and the study of fundamental parameters, such as dendrite tip shape and growth velocity in the absence of convection is nearly impossible. Significant experimental work has therefore been carried out in orbiting laboratories with the intent of minimizing convection by minimizing gravity. One of the best known experiments of this kind is the Isothermal Dendritic Growth Experiment (IDGE), supported by NASA. Naturally such experiments are costly and one objective of the present investigation is to develop an experimental method whereby convection can be- halted, in solidification and other experiments, on the surface. A second objective is to use the method to minimize convection resulting from the residual accelerations suffered by experiments in microgravity. The method to be used to minimize convection relies on the dependence of the magnetic susceptibility of a fluid on temperature or composition (whichever is driving convection). All materials experience a force when placed in a magnetic field gradient. The direction and magnitude of that force depend on the magnetic susceptibility of the material. Consequently the force will vary if the susceptibility varies with temperature or composition. With a magnetic field gradient in the right direction (typically upward) and of the right magnitude, this variation in the magnetic force can be made to exactly cancel the variation in the gravitational force. Expressed another way, normal buoyancy is exactly countered by a "magnetic buoyancy". To demonstrate the principle, a solution of MnC12 in water has been used. First the variation of the susceptibility of this paramagnetic solution with temperature and concentration was measured. Then a "cell", containing this solution and 50mm long by 15mm high by 155mm wide, was placed in a superconducting magnet at Marshall Space Flight Center. The magnetic field was measured at various positions within the bore of the magnet using a Hall effect probe. In this way, a position was found where the magnetic field gradient was predominantly upward; the magnitude of the gradient could then be adjusted by adjusting the current of the magnet. The ends of the cell consisted of machined copper blocks maintained at controlled temperatures by circulating water from constant temperature baths. The walls of the cell were of rectangular section glass tubing so that the cell contents could be seen. Velocities arising from thermal gradients within the cell were measured by particle image velocimetry (PIV). Particles used for this purpose were silver-coated hollow glass spheres of micrometers diameter and nearly the same density as the solution. A central vertical plane of the cell was illuminated by a laser beam passing through a cylindrical lens. Digital images of the particles were captured on a CCD camera and fed to a computer so that frame-to-frame movements of particles traveling with the fluid were captured. These images were employed to compute velocity maps using commercial PIV software. In a typical experiment the cold end of the cell was maintained at 10C and the warm end at 30 C. With no current in the magnet, i.e.- with natural -convection allowed to occur, the fluid was observed to circulate with an average speed of approximately 0.3 millimeters per second. It was visually apparent that this circulation was diminished as the current was increased. At currents of approximately 20A the flow was halted, to within the precision of the PIV measurements. At yet higher currents the convection was reversed with the hotter solution sinking and the cooler solution rising. At 40A this reversed convection had speeds averaging 0.43 millimeters per second. The measurements of susceptibility and density allow an estimate of the field gradient necessary to halt convection in the experiment. That estimate was 7.8T (squared) per meter and the convection was observed to halt in the magnet at a current giving 7.21T (squared) per meter from the magnetic field measurements. Calculations of the flow have been carried out using the computational fluid dynamics software FLUENT and show good agreement with the measurements.

Seybert, C. D.↗

NASA NTRS2002

Alteration of gene expression profiles in skeletal muscle of rats exposed to microgravity during a spaceflight

To clarify the mechanism of skeletal muscle wasting during spaceflights, we investigated whether intramuscular gene expression profiles are affected, by using DNA microarray methods. Male rats sent on the 17-day NASA STS-90 Neurolab spaceflight were sacrificed 24 hours after return to earth (MG group). Ground control rats were maintained for 17 days in flight-simulated cages (CS group). Spaceflight induced a 19% and 23% loss of tibialis anterior and gastrocnemius muscle mass, respectively, as compared to ground controls. Muscle RNA was analyzed by the Clontech Atlas DNA expression array in four rats, with two MG/ CS pairs for the tibialis anterior, and one pair for the gastrocnemius. Alterations in gene expression were verified for selected genes by reverse-transcription PCR. In both muscles of MG rats, mRNAs for 12 genes were up-regulated by over 2-fold, and 38 were down-regulated compared to controls. There was inhibition of genes for cell proliferation and growth factor cascades, including cell cycle genes and signal transduction proteins, such as p21 Cip1, retinoblastoma (Rb), cyclins G1/S, -E and -D3, MAP kinase 3, MAD3, and ras related protein RAB2. These data indicate that following exposure to microgravity, there is downregulation of genes involved in regulation of muscle satellite cell replication.

NASA Program Fundamental Space Biology↗

NASA NTRS2002

Temporal gradients in shear stimulate osteoblastic proliferation via ERK1/2 and retinoblastoma protein

Bone cells are subject to interstitial fluid flow (IFF) driven by venous pressure and mechanical loading. Rapid dynamic changes in mechanical loading cause transient gradients in IFF. The effects of pulsatile flow (temporal gradients in fluid shear) on rat UMR106 cells and rat primary osteoblastic cells were studied. Pulsatile flow induced a 95% increase in S-phase UMR106 cells compared with static controls. In contrast, ramped steady flow stimulated only a 3% increase. Similar patterns of S-phase induction were also observed in rat primary osteoblastic cells. Pulsatile flow significantly increased relative UMR106 cell number by 37 and 62% at 1.5 and 24 h, respectively. Pulsatile flow also significantly increased extracellular signal-regulated kinase (ERK1/2) phosphorylation by 418%, whereas ramped steady flow reduced ERK1/2 activation to 17% of control. Correspondingly, retinoblastoma protein was significantly phosphorylated by pulsatile fluid flow. Inhibition of mitogen-activated protein (MAP)/ERK kinase (MEK)1/2 by U0126 (a specific MEK1/2 inhibitor) reduced shear-induced ERK1/2 phosphorylation and cell proliferation. These findings suggest that temporal gradients in fluid shear stress are potent stimuli of bone cell proliferation.

NASA Discipline Cell Biology↗

DOE OSTI2021

Charge order textures induced by non-linear couplings in a half-doped manganite

Abstract The self-organization of strongly interacting electrons into superlattice structures underlies the properties of many quantum materials. How these electrons arrange within the superlattice dictates what symmetries are broken and what ground states are stabilized. Here we show that cryogenic scanning transmission electron microscopy (cryo-STEM) enables direct mapping of local symmetries and order at the intra-unit-cell level in the model charge-ordered system Nd 1/2 Sr 1/2 MnO 3 . In addition to imaging the prototypical site-centered charge order, we discover the nanoscale coexistence of an exotic intermediate state which mixes site and bond order and breaks inversion symmetry. We further show that nonlinear coupling of distinct lattice modes controls the selection between competing ground states. The results demonstrate the importance of lattice coupling for understanding and manipulating the character of electronic self-organization and that cryo-STEM can reveal local order in strongly correlated systems at the atomic scale.

42 ENGINEERING↗

DOE OSTI2025

Deep learning of structural morphology imaged by scanning X-ray diffraction microscopy

Scanning X-ray nanodiffraction microscopy is a powerful technique for spatially resolving nanoscale structural morphologies by diffraction contrast. One of the critical challenges in experimental nanodiffraction data analysis is posed by the convergence angle of nanoscale focusing optics which creates simultaneous dependency of the far-field scattering data on three independent components of the local strain tensor-corresponding to dilation and two potential rigid body rotations of the unit cell. All three components are in principle resolvable through a spatially mapped sample tilt series; however, traditional data analysis is computationally expensive and prone to artifacts. In this study, we implement NanobeamNN, a convolutional neural network specifically tailored to the analysis of scanning probe X-ray microscopy data. NanobeamNN learns lattice strain and rotation angles from simulated diffraction of a focused X-ray nanobeam by an epitaxial thin film and can directly make reasonable predictions on experimental data without the need for additional fine-tuning. We demonstrate that this approach represents a significant advancement in computational speed over conventional methods, as well as a potential improvement in accuracy over the current standard.

Luo, Aileen [Cornell Univ., Ithaca, NY (United Sta↗

DOE OSTI2020

Quantitative temporally and spatially resolved X-ray fluorescence microprobe characterization of the manganese dissolution-deposition mechanism in aqueous Zn/α-MnO 2 batteries

Rechargeable aqueous Zn/α-MnO 2 batteries are a possible alternative to lithium ion batteries for scalable stationary energy storage applications due to their low cost, safety and environmentally benign components. A critical need for advancement of this battery system is a full understanding of the electrochemical reaction mechanisms, which remain unclear. In this report, operando , spatiotemporal resolved synchrotron X-ray fluorescence mapping measurements on a custom aqueous Zn/α-MnO 2 cell provided direct evidence of a Mn dissolution-deposition faradaic mechanism that governs the electrochemistry. Simultaneous visualization and quantification of the Mn distribution in the electrolyte revealed the formation of aqueous Mn species during discharge and depletion on charge. The findings are supported by ex situ transmission electron microscopy (TEM), X-ray diffraction, Mn K-edge X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) measurements. The elucidated mechanism is fundamentally different from the previously proposed Zn 2+ insertion or conversion reactions. These findings provide a foundation for developing dissolution- deposition chemistries suitable for scalable stationary energy storage with aqueous electrolyte.

25 ENERGY STORAGE↗

DOE OSTI2024

Observation of Skewed Electromagnetic Wakefields in an Asymmetric Structure Driven by Flat Electron Bunches

Relativistic charged -particle beams that generate intense longitudinal fields in accelerating structures also inherently couple to transverse modes. The effects of this coupling may lead to beam breakup instability and thus must be countered to preserve beam quality in applications such as linear colliders. Beams with highly asymmetric transverse sizes (flat beams) have been shown to suppress the initial instability in slab -symmetric structures. However, as the coupling to transverse modes remains, this solution serves only to delay instability. In order to understand the hazards of transverse coupling in such a case, we describe here an experiment characterizing the transverse effects on a flat beam, traversing near a planar dielectric lined structure. Further, the measurements reveal the emergence of a previously unobserved skew-quadrupolelike interaction when the beam is canted transversely, which is not present when the flat beam travels parallel to the dielectric surface. We deploy a multipole field fitting algorithm to reconstruct the projected transverse wakefields from the data. We generate the effective kick vector map using a simple two -particle theoretical model, with particle -in -cell simulations used to provide further insight for realistic particle distributions.

43 PARTICLE ACCELERATORS↗

DOE OSTI2019

Modeling Present and Future Permafrost Distribution at Seward Peninsula, Alaska: Modeling Archive

This dataset contains results from two GIPL runs for RCP4.5 and RCP8.5 across the Seward Peninsula. The model was run on 500 m by 500 m resolution for the period 1901-2100. Meteo variables include forcing air temperature and precipitation as well as modeled maxim and average snow height. This dataset also includes ground temperature at 10 different depths for every grid cell, active layer depth and talik thickness. Auxillary variables include ecotype map and projected latitude and longitude. Ground temperature borehole data that is used for model calibration and validation of GIPL2 for Seward Peninsula 500 m resolution model runs for 1901-2100 time period. Dataset also includes calibrated model parameters for future use. The main purpose of this dataset is the reproducibility of research. Data were produced for regional permafrost distribution assessment for present and future, in addition, model parameters can be used for future model runs on adjacent territories. This dataset contains *.pdf, *.txt, *.csv, and *.nc. files. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1987

Efficiency of a model human image code

Hypothetical schemes for neural representation of visual information can be expressed as explicit image codes. Here, a code modeled on the simple cells of the primate striate cortex is explored. The Cortex transform maps a digital image into a set of subimages (layers) that are bandpass in spatial frequency and orientation. The layers are sampled so as to minimize the number of samples and still avoid aliasing. Samples are quantized in a manner that exploits the bandpass contrast-masking properties of human vision. The entropy of the samples is computed to provide a lower bound on the code size. Finally, the image is reconstructed from the code. Psychophysical methods are derived for comparing the original and reconstructed images to evaluate the sufficiency of the code. When each resolution is coded at the threshold for detection artifacts, the image-code size is about 1 bit/pixel.

Watson, Andrew B.↗

NASA NTRS1990

Magellan to Venus

This video presents cell animation of the Magellan approach to Venus, orbit insertion, and mapping sequence.

Source record↗

NASA NTRS1993

Ionospheric convection response to slow, strong variations in a Northward interplanetary magnetic field: A case study for January 14, 1988

We analyze ionospheric convection patterns over the polar regions during the passage of an interplanetary magnetic cloud on January 14, 1988, when the interplanetary magnetic field (IMF) rotated slowly in direction and had a large amplitude. Using the assimilative mapping of ionospheric electrodynamics (AMIE) procedure, we combine simultaneous observations of ionspheric drifts and magnetic perturbations from many different instruments into consistent patterns of high-latitude electrodynamics, focusing on the period of northward IMF. By combining satellite data with ground-based observations, we have generated one of the most comprehensive data sets yet assembled and used it to produce convection maps for both hemispheres. We present evidence that a lobe convection cell was embedded within normal merging convection during a period when the IMF B(sub y) and B(sub z) components were large and positive. As the IMF became predominantly northward, a strong reversed convection pattern (afternoon-to-morning potential drop of around 100 kV) appeared in the southern (summer) polar cap, while convection in the northern (winter) hemisphere became weak and disordered with a dawn-to-dust potential drop of the order of 30 kV. These patterns persisted for about 3 hours, until the IMF rotated significantly toward the west. We interpret this behavior in terms of a recently proposed merging model for northward IMF under solstice conditions, for which lobe field lines from the hemisphere tilted toward the Sun (summer hemisphere) drape over the dayside magnetosphere, producing reverse convection in the summer hemisphere and impeding direct contact between the solar wind and field lines connected to the winter polar cap. The positive IMF B(sub x) component present at this time could have contributed to the observed hemispheric asymmetry. Reverse convection in the summer hemisphere broke down rapidly after the ratio absolute value of B(sub y)/B(sub z) exceeded unity, while convection in the winter hemisphere strengthened. A dominant dawn-to-dusk potential drop was established in both hemispheres when the magnitude of B(sub y) exceeded that of B(sub z) with potential drops of the order of 100 kV, even while B(sub z) remained northward. The latter transition to southward B(sub z) produced a gradual intensification of the convection, but a greater qualitative change occurred at the transition through absolute value of B(sub y)/B(sub z) = 1 than at at the transition through B(sub z) = 0. The various convection patterns we derive under northward IMF conditions illustrate all possibilities previously discussed in the literature: nearly single-cell and multicell, distorted and symmetric, ordered and unordered, and sunward and antisunward.

Knipp, D. J.↗