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The NASA Open Science Data Repository: Biomedical Data, Analysis Tools, and Informatic Collaborations

Increased biomedical risks and challenges associated with deep space missions require knowledge discovery, health countermeasures, and biomedical support capabilities. Maximally open-access and reusable data is needed by developers, scientists, and engineers to develop these systems. The NASA Open Science Data Repository (OSDR) is a maximally open access and FAIR database (ie., findable, accessible, interoperable, and reusable), and meets various scientific, technical, and operational needs. It offers users and submitters the ability to upload, download, search, share, analyze, cite, and visualize data across ‘omics, physiological, phenotypic, payload, hardware, behavioral, bioimaging, video, and environmental monitoring telemetry datasets. OSDR is an expanded database, based upon the successes of NASA GeneLab. OSDR has >460 studies with datasets covering model organisms to non-NASA human astronauts. There are ~12 datasets from the Inspiration 4 (I4) mission, spanning metagenomics, comprehensive metabolic panels, clonal hematopoiesis, spatial transcriptomics, proteomics, and cytokine panels. In the interest of data privacy, two I4 datasets with raw files relating to the epitranscriptome, and a new request feature is live in OSDR (with a backend review process established) developed from industry norms. OSDR is collecting and curating biomedical human data from a new sub-orbital research flight and is open to more space life science/biomedical submissions from the international and commercial sectors. OSDR also recently began a collaboration with the European Space Agency (ESA) to collect and curate >200 terabytes of human and model organism data. The OSDR submission portal is designed to ingest and curate ~25 ‘omics and ~50 physiological-phenotypic-imaging assay data types. Tools available for OSDR users include: 1) an Environmental Data Application to compare radiation, CO2, relative humidity, temperature, and other telemetry across missions and subjects, 2) the RadLab database, a collaboration between NASA, ESA, the German and Italian Space Agencies, and the Bulgarian Academy of Sciences, and 3) a Multi-study visualization tool which enables users to look across and combine ‘omics datasets. There are ~600 volunteer OSDR Analysis Working Group (AWG) members providing feedback on scientific data/metadata standards and collaborating to mine-reuse OSDR in research. OSDR/GeneLab has enabled ~60 publications reusing data as of October 2023.

space biology↗
NASA NTRS1992

Habituation and adaptation of the vestibuloocular reflex: a model of differential control by the vestibulocerebellum

We habituated the dominant time constant of the horizontal vestibuloocular reflex (VOR) of rhesus and cynomolgus monkeys by repeated testing with steps of velocity about a vertical axis and adapted the gain of the VOR by altering visual input with magnifying and reducing lenses. After baseline values were established, the nodulus and ventral uvula of the vestibulocerebellum were ablated in two monkeys, and the effects of nodulouvulectomy and flocculectomy on VOR gain adaptation and habituation were compared. The VOR time constant decreased with repeated testing, rapidly at first and more slowly thereafter. The gain of the VOR was unaffected. Massed trials were more effective than distributed trials in producing habituation. Regardless of the schedule of testing, the VOR time constant never fell below the time constant of the semicircular canals (approximately 5 s). This finding indicates that only the slow component of the vestibular response, the component produced by velocity storage, was habituated. In agreement with this, the time constant of optokinetic after-nystagmus (OKAN) was habituated concurrently with the VOR. Average values for VOR habituation were obtained on a per session basis for six animals. The VOR gain was adapted by natural head movements in partially habituated monkeys while they wore x 2.2 magnifying or x 0.5 reducing lenses. Adaptation occurred rapidly and reached about +/- 30%, similar to values obtained using forced rotation. VOR gain adaptation did not cause additional habituation of the time constant. When the VOR gain was reduced in animals with a long VOR time constant, there were overshoots in eye velocity that peaked at about 6-8 s after the onset or end of constant-velocity rotation. These overshoots occurred at times when the velocity storage integrator would have been maximally activated by semicircular canal input. Since the activity generated in the canals is not altered by visual adaptation, this finding indicates that the gain element that controls rapid changes in eye velocity in the VOR is separate from that which couples afferent input to velocity storage. Nodulouvulectomy caused a prompt and permanent loss of habituation, returning VOR time constants to initial values. VOR gain adaptation, which is lost after flocculectomy, was unaffected by nodulouvulectomy. Flocculectomy did not alter habituation of the VOR or of OKAN. Using a simplified model of the VOR, the decrease in the duration of vestibular nystagmus due to habituation was related to a decrement in the dominant time constant of the velocity storage integrator (1/h0).(ABSTRACT TRUNCATED AT 400 WORDS).

NASA Discipline Neuroscience↗
DOE OSTI2023

ChemoGraph: Interactive Visual Exploration of the Chemical Space

Exploratory analysis of the chemical space is an important task in the field of cheminformatics. For example, in drug discovery research, chemists investigate sets of thousands of chemical compounds in order to identify novel yet structurally similar synthetic compounds to replace natural products. Manually exploring the chemical space inhabited by all possible molecules and chemical compounds is impractical, and therefore presents a challenge. To fill this gap, we present ChemoGraph, a novel visual analytics technique for interactively exploring related chemicals. In ChemoGraph, we formalize a chemical space as a hypergraph and apply novel machine learning models to compute related chemical compounds. It uses a database to find related compounds from a known space and a machine learning model to generate new ones, which helps enlarge the known space. Moreover, ChemoGraph highlights interactive features that support users in viewing, comparing, and organizing computationally identified related chemicals. With a drug discovery usage scenario and initial expert feedback from a case study, we demonstrate the usefulness of ChemoGraph.

chemical space exploration↗
DOE OSTI2016

SU-F-J-88: Comparison of Two Deformable Image Registration Algorithms for CT-To-CT Contour Propagation

Purpose: To compare the contour propagation accuracy of two deformable image registration (DIR) algorithms in the Raystation treatment planning system – the “Hybrid” algorithm based on image intensities and anatomical information; and the “Biomechanical” algorithm based on linear anatomical elasticity and finite element modeling. Methods: Both DIR algorithms were used for CT-to-CT deformation for 20 lung radiation therapy patients that underwent treatment plan revisions. Deformation accuracy was evaluated using landmark tracking to measure the target registration error (TRE) and inverse consistency error (ICE). The deformed contours were also evaluated against physician drawn contours using Dice similarity coefficients (DSC). Contour propagation was qualitatively assessed using a visual quality score assigned by physicians, and a refinement quality score (0 0.9 for lungs, > 0.85 for heart, > 0.8 for liver) and similar qualitative assessments (VQS < 0.35, RQS > 0.75 for lungs). When anatomical structures were used to control the deformation, the DSC improved more significantly for the biomechanical DIR compared to the hybrid DIR, while the VQS and RQS improved only for the controlling structures. However, while the inclusion of controlling structures improved the TRE for the hybrid DIR, it increased the TRE for the biomechanical DIR. Conclusion: The hybrid DIR was found to perform slightly better than the biomechanical DIR based on lower TRE while the DSC, VQS, and RQS studies yielded comparable results for both. The use of controlling structures showed considerable improvement in the hybrid DIR results and is recommended for clinical use in contour propagation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Improved quasiparticle self-consistent electronic band structure and excitons in β – LiGaO 2

The band structure of β–LiGaO 2 is calculated using the quasiparticle self-consistent QSGWˆ method where the screened Coulomb interaction Wˆ is evaluated including electron-hole interaction ladder diagrams and G is the one-electron Green's function. Improved convergence compared to previous calculations leads to a significantly larger band gap of about 7.0 eV. However, exciton binding energies are found to be large and lead to an exciton gap of about 6.0 eV if also a zero-point-motion correction of about –0.4 eV is included. Furthermore, these results are in excellent agreement with recent experimental results on the onset of absorption. Besides the excitons observed thus far, the calculations indicate the existence of a Rydberg-like series of exciton excited states, which is however modified from the classical Wannier exciton model by the anisotropies of the material and the more complex mixing of Bloch states in the excitons resulting from the Bethe-Salpeter equation. The exciton fine structure and the exciton wave functions are visualized and analyzed in various ways.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Supplemental macronutrients and microbial fermentation products improve the uptake and transport of foliar applied zinc in sunflower ( Helianthus annuus L.) plants. Studies utilizing micro X-ray florescence

Enhancing nutrient uptake and the subsequent elemental transport from the sites of application to sites of utilization is of great importance to the science and practical field application of foliar fertilizers. The aim of this study was to investigate the mobility of various foliar applied zinc (Zn) formulations in sunflower ( Helianthus annuus L.) and to evaluate the effects of the addition of an organic biostimulant on phloem loading and elemental mobility. This was achieved by application of foliar formulations to the blade of sunflower ( H. annuus L.) and high-resolution elemental imaging with micro X-ray fluorescence (μ-XRF) to visualize Zn within the vascular system of the leaf petiole. Although no significant increase of total Zn in petioles was determined by inductively-coupled plasma mass-spectrometer, μ-XRF elemental imaging showed a clear enrichment of Zn in the vascular tissues within the sunflower petioles treated with foliar fertilizers containing Zn. The concentration of Zn in the vascular of sunflower petioles was increased when Zn was applied with other microelements with EDTA (commercial product Kick-Off) as compared with an equimolar concentration of ZnSO₄ alone. The addition of macronutrients N, P, K (commercial product CleanStart) to the Kick-Off Zn fertilizer, further increased vascular system Zn concentrations while the addition of the microbially derived organic biostimulant “GroZyme” resulted in a remarkable enhancement of Zn concentrations in the petiole vascular system. The study provides direct visualized evidence for phloem transport of foliar applied Zn out of sites of application in plants by using μ-XRF technique, and suggests that the formulation of the foliar applied Zn and the addition of the organic biostimulant GroZyme increases the mobility of Zn following its absorption by the leaf of sunflower.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

SU-E-I-51: Use of Blade Sequences in Cervical Spine MR Imaging for Eliminating Motion, Truncation and Flow Artifacts

Purpose: To assess the efficacy of the BLADE technique to eliminate motion, truncation, flow and other artifacts in Cervical Spine MRI compared to the conventional technique. To study the ability of the examined sequences to reduce the indetention and wrap artifacts, which have been reported in BLADE sagittal sequences. Methods: Forty consecutive subjects, who had been routinely scanned for cervical spine examination using four different image acquisition techniques, were analyzed. More specifically, the following pairs of sequences were compared: a) T2 TSE SAG vs. T2 TSE SAG BLADE and b) T2 TIRM SAG vs. T2 TIRM SAG BLADE. A quantitative analysis was performed using the signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR) and relative contrast (ReCon) measures. A qualitative analysis was also performed by two radiologists, who graded seven image characteristics on a 5-point scale (0:non-visualization; 1:poor; 2:average; 3:good; 4:excellent). The observers also evaluated the presence of image artifacts (motion, truncation, flow, indentation). Results: Based on the findings of the quantitative analysis, the ReCON values of the CSF (cerebrospinal fluid)/SC (spinal cord) between TIRM SAG and TIRM SAG BLADE were found to present statistical significant differences (p<0.001). Regarding motion and truncation artifacts, the T2 TSE SAG BLADE was superior compared to the T2 TSE SAG and the T2 TIRM SAG BLADE was superior compared to the T2 TIRM SAG. Regarding flow artifacts, T2 TIRM SAG BLADE eliminated more artifacts compared to the T2 TIRM SAG. Conclusion: The use of BLADE sequences in cervical spine MR examinations appears to be capable of potentially eliminating motion, pulsatile flow and trancation artifacts. Furthermore, BLADE sequences are proposed to be used in the standard examination protocols based on the fact that a significantly improved image quality could be achieved.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Model-based CT performance assessment and optimization for iodinated and noniodinated imaging tasks as a function of kVp and body size

Purpose: The goal of this study was to assess the comparative performance of iterative reconstruction in space (IRIS) and filtered back projection (FBP) reconstruction algorithms in terms of image quality and dose across kVps and phantom sizes. Methods: The ACR CT phantom (model 464) was supplemented with the addition of an iodinated spherical capsule (1.5 mm diameter, 3.4 mg iodine per ml) to simulate the contrast filled structures and with an additional circular attachment consisting of an array of 500 um brass beads for spatial resolution measurements. A larger sized phantom was also created by wrapping the original phantom with additional tissue equivalent material of 4 cm thickness. The phantoms were imaged on a 64 detector array multidetector computed tomography scanner (Somatom Definition, Siemens, Germany) using clinically applicable protocols (0.5 s rotation time; 80, 100, 120, and 140 kVp; 64 to 640 mA; 220 to 250 mm field of view). Images were reconstructed using the FBP and the IRIS algorithms. Combining measurements of image noise and spatial resolution with a task function, a figure of merit (FOM) for image quality was generated taking into account the type of visualization required from the image for the detection of either large or small image features with and without iodine content. The FOM was further reported in terms of area under the receiver operating characteristic (ROC) curve (A{sub Z}) to predict the comparative diagnostic performance of the two algorithms at different dose levels. Results: For a given dose level, the predicted A{sub Z} for IRIS consistently outperformed that of FBP. At comparative A{sub Z}, depending on protocol and task, the dose requirement for the optimal technique (optimized kVp with IRIS) was 2-3 times lower than that for standard technique (120 kVp with FBP). The potential for dose reduction was found to be higher when performing small feature detection tasks in comparison to larger feature detection tasks. The optimal kVp was from 80 to 100 kVp for the small phantom, 100 to 120 kVp for the larger phantom. Conclusions: Overall, greater dose reduction may be achieved with IRIS compared to FBP, with enhanced advantage at thinner slice reconstructions. The results highlight how IRIS may offer a superior balance between image quality and dose across a range of imaging tasks, thus enabling dose reduction at constant quality or image quality improvement at constant dose. The prediction of the investigation can be used toward effective design of subsequent clinical studies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Argon broad ion beam sectioning and high resolution scanning electron microscopy imaging of hydrated alite

Highlights: • The native fibrous outer and dense inner C-S-H structure are preserved by using low energy argon broad ion beam sectioning. • Possible artefacts of the preparation and imaging of hydrated alite are shown and discussed. • An approach for a semi automated pore analysis of the obtained high resolution images is demonstrated. Scanning electron microscopy (SEM) imaging is able to visualize micro- to nano-structures of cement and concrete. A prerequisite is that the sample preparation preserves the native structure of the specimen. In this study, argon broad ion beam (BIB) sectioning is compared to state-of-the-art sample preparation (resin embedding, polishing) for hydrated alite. Additionally, it is investigated if during BIB, sample cooling is beneficial to avoid deterioration of cement hydrates. The aim is to quantitatively measure pore size distributions in hardened alite pastes. Therefore, not only optimized sample preparation but also optimized imaging conditions are investigated. Finally, it is demonstrated that by image analysis pores down to a diameter of 5 nm in hydrated alite pastes can be quantitatively analysed.

36 MATERIALS SCIENCE↗
DOE OSTI2020

High-Resolution Comonomer Sequencing of Blocky Brominated Syndiotactic Polystyrene Copolymers Using 13C NMR Spectroscopy and Computer Simulations

This work demonstrates the first high-resolution comonomer sequencing of Blocky brominated syndiotactic polystyrene (sPS-co-sPS-Br) copolymers based on pentad assign- ments of the quaternary carbon region of the nuclear magnetic resonance spectrum. Copolymers containing p-bromostyrene (Br-Sty) units were prepared in matched sets using postpolymerization bromination methods carried out in the heterogeneous gel state (Blocky) and homogeneous solution state (Random). Quantitative information from the quaternary carbon spectra, heteronuclear multiple bond correlation spectroscopy, electronic structure calculations, and simulated statistically random copolymers was correlated to confirm the carbon resonance assignments for all 20 possible pentad comonomer sequences. Using the experimental pentad sequence prevalences, a computer code was developed to simulate chains with microstructures typical of each sample as a means to visually represent the copolymer blockiness with quantitative precision. Based on the microstructure and distribution of run lengths in these chains, the simulations revealed that the Blocky copolymers contain a high degree of blockiness. By comparing the run lengths in the simulated chains to the average number of styrene units in a crystalline segment of sPS (found by small-angle X-ray scattering), copolymer crystallizability was predicted. For the simulated Blocky B-21% (21 mol % Br-Sty) chain, the probability of randomly selecting a styrene unit in a crystallizable block was 25.8%, while that in the simulated Random R-18% was zero, in excellent agreement with the experimental crystallization behavior measured by differential scanning calorimetry. Additionally, these predictions confirmed that the simulated chains accurately represent the ensemble of chains in their respective copolymer samples. Furthermore, each simulated Blocky chain contained one or more long sPS blocks that paralleled the measured 38-40 styrene units spanning a crystalline segment within the sPS/CCl4 gel. This finding affirmed that the long sPS segments originated from the precise lamellar structure within the heterogeneous gel morphology (i.e., block length is correlated with lamellar thickness). Overall, the ability to tailor the copolymer microstructure through control of the semicrystalline gel morphology opens the door to synthesizing ordered copolymers by postpolymerization functionalization processes with unprecedented levels of compositional control.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Assessment of Commercial Building Lighting as a Frequency Regulation Resource

This paper evaluates the potential for automated lighting control as a resource for frequency regulation of the electric grid system in the context of current energy policies, economic incentives, and technological trends. The growing prevalence of renewable energy has increased the need for ancillary services to maintain grid frequency and stability. While demand side resources like heating, ventilating, and air-conditioning systems, as well as water treatment plants are already evaluated as regulation service providers, the potential application to electrical lighting systems has largely been ignored. Yet, aggregations of lighting systems that are retrofitted with intelligent controls could conceivably contribute to frequency regulation services with little impact on user comfort. To further explore the feasibility of lighting potential, this paper explores (1) how lighting control systems are limited by visual comfort perception and acceptability, (2) how such limitations impact the performance of the lighting system as an frequency regulation resource, and (3) how the market potential of lighting systems as demand side resources compares in different regional transmission organizations. Finally, the impact of developing technologies on the application of lighting systems for frequency regulation is discussed.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
NASA NTRS1973

Experiment M-131 - Human vestibular function.

The purpose of the M-131 experiment is to measure responses in astronauts throughout orbital flight that reflect vestibular function and compare them with measurements made before and after flight. Three subtasks require measurement of (1) susceptibility to motion sickness, (2) thresholds of response to stimulation of the semicircular canals, and (3) space perception, viz, visual and nonvisual localization, using external spacecraft and internal morphological frames of reference. Four astronauts will be available for all measurements in Skylab 2 and 3 and two additional astronauts for only the 'static' measurements during the flights.

Miller, E. F., II↗
NASA NTRS1974

Sensor performance evaluation of the Skylab multispectral photographic facility

Results of resolution tests for multispectral imagery from Skylabs 2, 3, and 4 are presented. Methods employed were visual edge matching and edge slope analysis, and resolution was evaluated as a function of spectral band, EREP pass, target orientation, field of view, exposure, and contrast. Preflight and postflight image quality data were compared. The multispectral image quality has equaled or slightly exceeded design predictions.

Corbett, F. J.↗
NASA NTRS1981

Natural sunlight accelerated weathering of photovoltaic modules

Photovoltaic modules are exposed to the equivalent of ten years of sunlight aging in an accelerated exposure testing and evaluation program, the objective being to determine the long-term durability characteristics of flat plate modules in comparatively short periods of time. The modules are illuminated with concentrated sunlight in a large, sun-tracking, Fresnel-reflecting solar concentrator. The effects of the accelerated exposure are assessed by performing periodic visual inspections and electrical measurements. It is found that field-experienced failure modes are duplicated, that acceleration factors of 6x to 8x are readily attainable, and that the test method is feasible as a predictive tool for photovoltaic module lifetime durability.

Zerlaut, G. A.↗
NASA NTRS1983

Detection and recognition of simple spatial forms

A model of human visual sensitivity to spatial patterns is constructed. The model predicts the visibility and discriminability of arbitrary two-dimensional monochrome images. The image is analyzed by a large array of linear feature sensors, which differ in spatial frequency, phase, orientation, and position in the visual field. All sensors have one octave frequency bandwidths, and increase in size linearly with eccentricity. Sensor responses are processed by an ideal Bayesian classifier, subject to uncertainty. The performance of the model is compared to that of the human observer in detecting and discriminating some simple images.

Watson, A. B.↗
NASA NTRS1991

Investigations into the damage for various types of unprotected carbon fibre composites with a variety of lightning arc attachments

Very little quantitative information exists on the extent and nature of damage caused to unprotected carbon fiber composites (CFC's) due to lightning arc attachment. An initial investigation into the arc damage to three different types and various thickness of CFC's from A and C component type lightning discharges is described. The difference in damage which the two types of waveform produced and the way the area of damage varies with different levels of action integral and charge transfer is compared. In some cases, the temperature rise at the rear of the panels was recorded for various levels of action integral and charge transfer. A comparison was made of the area of damage from visual inspection and soft x ray photography, using a suitable penetrant in the damage area. It is concluded there is a need for a more detailed analysis of the damage.

Reid, G. W.↗
NASA NTRS1993

Multicolor photometry of x ray selected Abell clusters

Strong evidence of evolution in cluster of galaxies at relatively low redshift has been indicated by recent x-ray studies. We are conducting a comprehensive optical study of a sample of Abell clusters that are strong x-ray emitters in order to test the x-ray evolution scenarios that have been proposed. The initial observations consist of three-color (B, R, I) imaging of low-redshift (0.025 less than z less than 0.25) Abell clusters using the T2KA CCD on the 0.9m telescope at KPNO the large field (23 ft. x 23 ft., approx. 1 Mpc at z = 0.025 and approx. 7 Mpc at z = 0.25) gives the unprecedented ability to sample most of the extent of the field of low-redshift clusters using a CCD. Given the advantages of CCDs over photographic plates, we expect to improve on many of the previous studies. A list of x-ray selected cluster of galaxies provides a homogeneous sample of true clusters that cannot be mistaken from apparent over-densities due to projection effects of field galaxies. Some optical indicators of cluster evolution are the population of ratios of cluster galaxies and their spatial distribution, a regular spiral-poor cluster is expected to be more evolved than an irregular spiral-rich cluster. Also regular spiral-poor clusters present high central concentrations while irregular spiral-rich are less concentrated. Variations in the Luminosity Function (LF) can indicate evolution. But in order to build reliable LFs it is necessary to determine the Hubble types of the cluster galaxies. In the past the classifications of cluster galaxies have been done by visual inspection on photographic material, this technique is very limited and can lead to errors when the galaxies are faint. The Hubble types of cluster galaxies can be determined in an objective manner by comparing colors and profiles from surface photometry. To show that this approach is feasible, I have presented preliminary results from the photometric analysis of the Abell-cluster A1213. Colors and profiles of the surface brightness distribution were compared to determine the Hubble types of the cluster galaxies.

Lopez-Cruz, Omar↗
NASA NTRS1961

Effects of Mach Number, Leading-Edge Bluntness, and Sweep on Boundary-Layer Transition on a Flat Plate

The effects of leading-edge bluntness and sweep on boundary-layer transition on flat plate models were investigated at Mach numbers of 2.00, 2.50, 3.00, and 4.00. The effect of sweep on transition was also determined on a flat plate model equipped with an elliptical nose at a Mach number of 0.27. Models used for the supersonic investigation had leading-edge radii varying from 0.0005 to 0.040 inch. The free-stream unit Reynolds number was held constant at 15 million per foot for the supersonic tests and the angle of attack was 0 deg. Surface flow conditions were determined by visual observation and recorded photographically. The sublimation technique was used to indicate transition, and the fluorescent-oil technique was used to indicate flow separation. Measured Mach number and sweep effects on transition are compared with those predicted from shock-loss considerations as described in NACA Rep. 1312. For the models with the blunter leading edges, the transition Reynolds number (based on free-stream flow conditions) was approximately doubled by an increase in Mach number from 2.50 to 4.00; and nearly the same result was predicted from shock-loss considerations. At all super- sonic Mach numbers, increases in sweep reduced the transition Reynolds number and the amount of reduction increased with increases in bluntness. The shock-loss method considerably underestimated- the sweep effects, possibly because of the existence of crossflow instability associated with swept wings. At a Mach number of 0.27, no reduction in the transition Reynolds number with sweep was measured (as would be expected with no shock loss) until the sweep angle was attained where crossflow instability appeared.

Jillie, Don W.↗