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At least 1,171 records · Page 65

A multimodal and integrated approach to interrogate human kidney biopsies with rigor and reproducibility: guidelines from the Kidney Precision Medicine Project

Comprehensive and spatially mapped molecular atlases of organs at a cellular level are a critical resource to gain insights into pathogenic mechanisms and personalized therapies for diseases. The Kidney Precision Medicine Project (KPMP) is an endeavor to generate three-dimensional (3-D) molecular atlases of healthy and diseased kidney biopsies by using multiple state-of-the-art omics and imaging technologies across several institutions. Obtaining rigorous and reproducible results from disparate methods and at different sites to interrogate biomolecules at a single-cell level or in 3-D space is a significant challenge that can be a futile exercise if not well controlled. Here we describe a “follow the tissue” pipeline for generating a reliable and authentic single-cell/region 3-D molecular atlas of human adult kidney. Our approach emphasizes quality assurance, quality control, validation, and harmonization across different omics and imaging technologies from sample procurement, processing, storage, shipping to data generation, analysis, and sharing. We established benchmarks for quality control, rigor, reproducibility, and feasibility across multiple technologies through a pilot experiment using common source tissue that was processed and analyzed at different institutions and different technologies. A peer review system was established to critically review quality control measures and the reproducibility of data generated by each technology before their being approved to interrogate clinical biopsy specimens. The process established economizes the use of valuable biopsy tissue for multiomics and imaging analysis with stringent quality control to ensure rigor and reproducibility of results and serves as a model for precision medicine projects across laboratories, institutions and consortia.

59 BASIC BIOLOGICAL SCIENCES↗

Investigating the Spatial and Temporal Limitations for Remote Sensing of Wildfire Smoke Using Satellite and Airborne Imagers During FIREX_AQ

Starting from point sources, wildfire smoke is important in the global aerosol system. The ability to characterize smoke near-source is key to modeling smoke dispersion and predicting air quality. With hemispheric views and 10-min refresh, imagers in Geostationary (GEO) orbit have advantages monitoring smoke over once-per-day sensors in low-earth orbit (LEO). However, both can be inadequate in capturing the characteristics of smoke plumes close to their sources due to too-coarse spatial resolution (both detector and product resolution), too-sparse temporal resolution (from LEO sensors), and too-conservative masking. In addition to satellite observations, the Fire Influence on Regional to Global Environments and Air Quality experiment offered sub-orbital enhanced-MODIS Airborne Simulator (eMAS) imagery at 50 m pixel resolution—including multiple eMAS flight tracks over individual fires in short time periods. It provided opportunity to explore smoke plume characterization at various spatial and temporal scales and quantify the limitations of space sensors for describing smoke magnitude near source as well as its temporal evolution. Here we applied modified aerosol algorithm to different imagers, relaxing its masking to estimate smoke's aerosol optical depth (AOD) as close as possible to its source. We found that GEO sensors with nominal 1 km spatial resolution can match the much finer resolution eMAS retrieved mean plume AOD, as long as the retrieval spatial resolution is finer than the width of the plumes. However, the plume's maximum AOD may be drastically underestimated by satellite products.

remote sensing↗

Improving and Assessing the Quality of Uncertainty Quantification in Deep Learning

Deep learning (DL) models have enjoyed increased attention in recent years because of their powerful predictive capabilities. While many successes have been achieved, standard deep learning methods suffer from a lack of uncertainty quantification (UQ). While the development of methods for producing UQ from DL models is an active area of current research, little attention has been given to the quality of the UQ produced by such methods. In order to deploy DL models to high-consequence applications, high-quality UQ is necessary. This report details the research and development conducted as part of a Laboratory Directed Research and Development (LDRD) project at Sandia National Laboratories. The focus of this project is to develop a framework of methods and metrics for the principled assessment of UQ quality in DL models. This report presents an overview of UQ quality assessment in traditional statistical modeling and describes why this approach is difficult to apply in DL contexts. An assessment on relatively simple simulated data is presented to demonstrate that UQ quality can differ greatly between DL models trained on the same data. A method for simulating image data that can then be used for UQ quality assessment is described. A general method for simulating realistic data for the purpose of assessing a model’s UQ quality is also presented. A Bayesian uncertainty framework for understanding uncertainty and existing metrics is described. Research that came out of collaborations with two university partners are discussed along with a software toolkit that is currently being developed to implement the UQ quality assessment framework as well as serve as a general guide to incorporating UQ into DL applications.

97 MATHEMATICS AND COMPUTING↗

Validation of Ocean Color Remote Sensing Reflectance Using Autonomous Floats

The use of autonomous proling oats for observational estimates of radiometric quantities in the ocean is explored, and the use of this platform for validation of satellite-based estimates of remote sensing reectance in the ocean is examined. This effort includes comparing quantities estimated from oat and satellite data at nominal wavelengths of 412, 443, 488, and 555 nm, and examining sources and magnitudes of uncertainty in the oat estimates. This study had 65 occurrences of coincident high-quality observations from oats and MODIS Aqua and 15 occurrences of coincident high-quality observations oats and Visible Infrared Imaging Radi-ometer Suite (VIIRS). The oat estimates of remote sensing reectance are similar to the satellite estimates, with disagreement of a few percent in most wavelengths. The variability of the oatsatellite comparisons is similar to the variability of in situsatellite comparisons using a validation dataset from the Marine Optical Buoy (MOBY). This, combined with the agreement of oat-based and satellite-based quantities, suggests that oats are likely a good platform for validation of satellite-based estimates of remote sensing reectance.

In Situ Oceanic Observations↗

Inverse Compton X-ray emission from the superluminal quasar 3C 345

In quasars with strong radio cores, the inverse-Compton process is believed to be the dominant source X-ray emission. For objects with parsec-scale radio jets, simple models have predicted that components in the jet emerging from the quasar nucleus generate the observed X-ray emission. We have tested this hypothesis in detail for the quasar 3C 345 using a ROSAT X-ray observation in 1990 July, together with quasi-simultaneous very long base interferometry (VLBI) imaging of the parsec-scale jet at five frequencies. The ROSAT spectrum is well fitted by a power law with index alpha = -0.96 +/- -0.13, consistent with models in which the X-ray emission results from inverse-Compton scattering of radio radiation from high-energy electrons in compact components. We show that the radio properties of brightest `knot' in the jet (`C5') can be fitted with a homogeneous sphere model whose parameters require bulk relativistic motion of the emitting material; otherwise the predicted model whose parameters require bulk relativistic motion of the emitting material; otherwise the predicted inverse-Compton X-ray emission exceeds the observed flux. If C5 is the origin of the X-ray emission, then it has a Doppler factor delta = 7.5((sup +3 sub -2)). If the nucleus or other components contribute to the X-ray emission, then this becomes a firm lower limit to delta. The inhomogeneous jet model of Koenigl is a good fit both to the barely resolved (less than 1 pc) flat-spectrum nucleus in the radio, and also to the ROSAT X-ray spectrum. The synchrotron and inverse-Compton emitting fluid moves down a narrow cone (opening angle 2 phi approximately 5 deg) nucleus relativistically, with delta approximately 4.6. Doppler factors for the nucleus and C5, derived from our ROSAT observation, provide evidence for bulk relativistic motion in the jet. By combining these constraints with well-known superluminal motion of jet components, we can deduce geometry. For epoch 1990.5 we infer the Lorentz factor gamma = 7.5 ((sup +1.0 sub -1.5)) and angle to the line of sight theta = 8((sup +2 deg sub -3 deg)) for H(sub 0) = 100 km/s/Mpc. These values are the most reliable yet derived using this method, because of the near-simultaneity of our X-ray and VLBI observations and the quality of the multifrequency of VLBI images and component radio spectra.

Unwin, S. C.↗

How Low Can You Go? Using Synthetic 3D Imagery to Drastically Reduce Real-World Training Data for Object Detection

Deep convolutional neural networks (DCNNs) currently provide state-of-the-art performance on image classification and object detection tasks, and there are many global security mission areas where such models could be extremely useful. Crucially, the success of these models is driven in large part by the widespread availability of high-quality open source data sets such as Image Net, Common Objects in Context (COCO), and KITTI, which contain millions of images with thousands of unique labels. However, global security relevant objects-of-interest can be difficult to obtain: relevant events are low frequency and high consequence; the content of relevant images is sensitive; and adversaries and proliferators seek to obscure their activities. For these cases where exemplar data is hard to come-by, even fine-tuning an existing model with available data can be effectively impossible. Recent work demonstrated that models can be trained using a combination of real-world and synthetic images generated from 3D representations; that such models can exceed the performance of models trained using real-world data alone; and that the generated images need not be perfectly realistic (Tremblay, et al., 2018). However, this approach still required hundreds to thousands of real-world images for training and fine tuning, which for sparse, global security-relevant datasets can be an unrealistic hurdle. In this research, we validate the performance and behavior of DCNN models as we drive the number of real-world images used for training object detection tasks down to a minimal set. We perform multiple experiments to identify the best approach to train DCNNs from an extremely small set of real-world images. In doing so, we: Develop state-of-the-art, parameterized 3D models based on real-world images and sample from their parameters to increase the variance in synthetic image training data; Use machine learning explainability techniques to highlight and correct through targeted training the biases that result from training using completely synthetic images; and Validate our results by comparing the performance of the models trained on synthetic data to one another, and to a control model created by fine-tuning an existing ImageNet-trained model with a limited number (hundreds) of real-world images.

97 MATHEMATICS AND COMPUTING↗

Development of an information data base for watershed monitoring

Landsat multispectral scanner data, Defense Mapping Agency digital terrain data, conventional maps, and ground data were integrated to create a comprehensive information data base (the Image Based Information System), to monitor the water quality of the Lake Tahoe Basin. Landsat imagery was used as the planimetric base to which all other data were registered. A georeference image plane, which provided an interface between all data planes for the Lake Tahoe Basin data base, was created from the drainage basin map. The data base was used to extract each drainage basin for separate display. The Defense Mapping Agency-created elevation image was processed with VICAR software to produce a component representing slope magnitude, which was cross-tabulated with the drainage basin georeference table. Future applications of the data base include the development of precipitation modeling, surface runoff models, and classification of drainage basin cover types.

Smith, A. Y.↗

Computational Ghost Imaging for Remote Sensing

This work relates to the generic problem of remote active imaging; that is, a source illuminates a target of interest and a receiver collects the scattered light off the target to obtain an image. Conventional imaging systems consist of an imaging lens and a high-resolution detector array [e.g., a CCD (charge coupled device) array] to register the image. However, conventional imaging systems for remote sensing require high-quality optics and need to support large detector arrays and associated electronics. This results in suboptimal size, weight, and power consumption. Computational ghost imaging (CGI) is a computational alternative to this traditional imaging concept that has a very simple receiver structure. In CGI, the transmitter illuminates the target with a modulated light source. A single-pixel (bucket) detector collects the scattered light. Then, via computation (i.e., postprocessing), the receiver can reconstruct the image using the knowledge of the modulation that was projected onto the target by the transmitter. This way, one can construct a very simple receiver that, in principle, requires no lens to image a target. Ghost imaging is a transverse imaging modality that has been receiving much attention owing to a rich interconnection of novel physical characteristics and novel signal processing algorithms suitable for active computational imaging. The original ghost imaging experiments consisted of two correlated optical beams traversing distinct paths and impinging on two spatially-separated photodetectors: one beam interacts with the target and then illuminates on a single-pixel (bucket) detector that provides no spatial resolution, whereas the other beam traverses an independent path and impinges on a high-resolution camera without any interaction with the target. The term ghost imaging was coined soon after the initial experiments were reported, to emphasize the fact that by cross-correlating two photocurrents, one generates an image of the target. In CGI, the measurement obtained from the reference arm (with the high-resolution detector) is replaced by a computational derivation of the measurement-plane intensity profile of the reference-arm beam. The algorithms applied to computational ghost imaging have diversified beyond simple correlation measurements, and now include modern reconstruction algorithms based on compressive sensing.

Erkmen, Baris I.↗

The Penn State astronomical image processing system

The needs of modern astronomy for image processing set demanding standards in simultaneously requiring fast computation speed, high-quality graphic display, large data storage, and interactive response. An innovative image processing system was designed, integrated, and used; it is based on a supermicro architecture which is tailored specifically for astronomy, which provides a highly cost-effective alternative to the traditional minicomputer installation. The paper describes the design rationale, equipment selection, and software developed to allow other astronomers with similar needs to benefit from the present experience.

Truax, Ryland J.↗

Monitoring and Assuring the Quality of Digital Aerial Data

This viewgraph presentation explains the USGS plan for monitoring and assuring the quality of digital aerial data. The contents include: 1) History of USGS Aerial Imaging Involvement; 2) USGS Research and Results; 3) Outline of USGS Quality Assurance Plan; 4) Other areas of Interest; and 5) Summary

Christopherson, Jon↗

Dimorphic Mechanisms of Fragility in Diabetes Mellitus: the Role of Reduced Collagen Fibril Deformation

ABSTRACT Diabetes mellitus (DM) is an emerging metabolic disease, and the management of diabetic bone disease poses a serious challenge worldwide. Understanding the underlying mechanisms leading to high fracture risk in DM is hence of particular interest and urgently needed to allow for diagnosis and treatment optimization. In a case–control postmortem study, the whole 12th thoracic vertebra and cortical bone from the mid-diaphysis of the femur from male individuals with type 1 diabetes mellitus (T1DM) (n = 6; 61.3 ± 14.6 years), type 2 diabetes mellitus (T2DM) (n = 11; 74.3 ± 7.9 years), and nondiabetic controls (n = 18; 69.3 ± 11.5) were analyzed with clinical and ex situ imaging techniques to explore various bone quality indices. Cortical collagen fibril deformation was measured in a synchrotron setup to assess changes at the nanoscale during tensile testing until failure. In addition, matrix composition was analyzed including determination of cross-linking and non-crosslinking advanced glycation end-products like pentosidine and carboxymethyl-lysine. In T1DM, lower fibril deformation was accompanied by lower mineralization and more mature crystalline apatite. In T2DM, lower fibril deformation concurred with a lower elastic modulus and tendency to higher accumulation of non-crosslinking advanced glycation end-products. The observed lower collagen fibril deformation in diabetic bone may be linked to altered patterns mineral characteristics in T1DM and higher advanced glycation end-product accumulation in T2DM. © 2022 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).

59 BASIC BIOLOGICAL SCIENCES↗

Accommodating a hexagonal ζ- phase Mn 2 N film on a cubic MgO (001) substrate

The thin films of c -plane dominated hexagonal ζ- phase Mn 2 N were successfully grown on a cubic MgO (001) substrate directly using plasma-assisted molecular beam epitaxy. The surface was comprehensively studied through experimental and theoretical approaches. Reflection high energy electron diffraction revealed two pseudo-cubic domains along [100] MgO and [110] MgO , and one hexagonal domain, which is 30° apart from the [100] MgO direction. Scanning tunneling microscopy was used to image and resolve the high-quality surface, revealing a distorted hexagonal surface structure. Furthermore, atomic resolution of the hexagonal domain with a 2 × 2 reconstructed surface is presented. For c-plane surface, theoretical investigations were carried out using first principles studies to determine the surface formation energy for various reconstructed surfaces. The theoretical study shows that the nitrogen terminated 2 × 2 structure with a manganese adatom on the surface as the most stable reconstruction that reproduces the experimental results. A corresponding simulated scanning tunneling microscopy model is also presented, providing strong support for the experimentally observed in-plane lattice structures. Furthermore, the manganese: nitrogen stoichiometry within the bulk and surface is in good agreement with the expected ratio of 2:1.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Machine learning-assisted upscaling analysis of reservoir rock core properties based on micro-computed tomography imagery

Optimum solutions for geologic modeling and reservoir simulation in industries such as oil and gas recovery and carbon capture and storage require accurate characterization of reservoir properties, which are often heterogeneous. In this study, high-quality micro-computed tomography (CT) images (1.475-μm/pixel resolution) of a sandstone core acquired from the Bell Creek oil field, USA, were used to provide nondestructive analysis of pore- and core-scale heterogeneity across measurement scales of 94–566 μm. In addition to characterizing the as-received sample, the core sample was flooded with brine to evaluate the capacity of the core sample to receive injected fluids. The micro-CT images were systematically segmented into pore spaces and grains via machine learning (ML) steps including image preprocessing, label creation using a traditional ML method based on limited manual image annotation, and finally U-Net segmentation. The segmented image stacks were reconstructed into digital cubes of various scales of voxel lengths. The 3D porosity values were calculated for all the digital cubes, and the fractal dimensions of the cubes were estimated using a box-counting method. The results showed that smaller cubes had greater heterogeneity and that the porosity values could be accurately estimated by fractal dimension and voxel lengths using ML models. For the core sample with brine flooding, the ratio of pores filled by brine to the total pore space was related to the porosity and could also be accurately estimated by porosity, fractal dimension, and voxel lengths using ML models. In conclusion, the results of this study demonstrate that the concept of fractal dimension can be a useful vector to perform upscaling analysis of sandstone rock heterogeneity from the pore to core scale and that fractal dimensions can be used to estimate porosity values and pore space-filling capacity across those scales.

58 GEOSCIENCES↗

Forecasting Battery Electrode Performance via Electrochemical Fluorescence Microscopy and Machine-Learning

Predicting lithium-ion battery performance is hindered by microscale electrode heterogeneities invisible to conventional diagnostics. Here, we combine electrochemical fluorescence microscopy (EFM), which maps electronic connectivity by visualizing an electrofluorophore reaction distribution, with a multitask ElasticNet regression to forecast discharge capacity from spatial heterogeneity. Analyzing 196 images from six pilot-scale LiNi 0.5 Mn 0.3 Co 0.2 O 2 cathodes with varying carbon loadings, we extract 62 descriptors that capture morphology and texture. A compact five-feature model predicts capacity across eight discharge rates, achieving a per-target R 2 of up to 0.63 and an overall R 2 of 0.92, with a mean absolute percentage error of less than 2%. This performance rivals impedance-based approaches while avoiding their reliance on postformation data and incomplete electronic network information. Our facile and rapid, image-driven method may enable electrode quality control upstream of costly cell assembly to offer a transformative tool for data-driven battery research and manufacturing.

battery electrodes↗

Storage Conditions of Human Kidney Tissue Sections Affect Spatial Lipidomics Analysis Reproducibility

Lipids often are labile, unstable, and tend to degrade overtime, so it is of the upmost importance to study these molecules in their most native state. In this study, we sought to understand the optimal storage conditions for spatial lipidomic analysis of human kidney tissue sections. Specifically, we evaluated human kidney tissue sections on several different days throughout the span of a week using our established protocol for elucidating lipids using high mass resolution matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). We studied kidney tissue sections stored under five different conditions: open stored at –80 °C, vacuumed sealed and stored at –80 °C, with matrix preapplied before storage at –80 °C, under a nitrogen atmosphere and stored at –80 °C, and at room temperature in a desiccator. Results were compared to data obtained from kidney tissue sections that were prepared and analyzed immediately after cryosectioning. Data was processed using METASPACE. After a week of storage, the sections stored at room temperature showed the largest amount of lipid degradation, while sections stored under nitrogen and at –80 °C retained the greatest number of overlapping annotations in relation to freshly cut tissue. Overall, we found that molecular degradation of the tissue sections was unavoidable over time, regardless of storage conditions, but storing tissue sections in an inert gas at low temperatures can curtail molecular degradation within tissue sections.

60 APPLIED LIFE SCIENCES↗

Computed Tomography (CT) Analysis of 3D Printed Lattice Structures

LATTICE structures are increasingly used in product design across different industries, including the Department of Energy (DOE), due to their high strength and lightweight properties. These structures possess qualities such as high stiffness, energy absorption, large surface area, and structural support. To ensure lattice structures' quality and symmetry, it is crucial to have defect-free structures. However, in some cases, traditional non-destructive evaluation methods may not be practical due to encasing lattice structures in material. To analyze the lattice structures' quality, this project will employ CT imaging to gain access to the encased structures and perform a detailed analysis of each section. Three 3D printed complex lattice cubes were created, with two exposed and one encased in material, for this project. The CT X-ray cabinet will be used to scan all three cubes, and the data collected will be reconstructed and evaluated using complex interpretation software. This analysis will allow for a detailed examination of the structure's porosity, inclusions, cracks, wall thickness, and symmetry in each section.

36 MATERIALS SCIENCE↗

Feasibility study for automatic reduction of phase change imagery

The feasibility of automatically reducing a form of pictorial aerodynamic heating data is discussed. The imagery, depicting the melting history of a thin coat of fusible temperature indicator painted on an aerodynamically heated model, was previously reduced by manual methods. Careful examination of various lighting theories and approaches led to an experimentally verified illumination concept capable of yielding high-quality imagery. Both digital and video image processing techniques were applied to reduction of the data, and it was demonstrated that either method can be used to develop superimposed contours. Mathematical techniques were developed to find the model-to-image and the inverse image-to-model transformation using six conjugate points, and methods were developed using these transformations to determine heating rates on the model surface. A video system was designed which is able to reduce the imagery rapidly, economically and accurately. Costs for this system were estimated. A study plan was outlined whereby the mathematical transformation techniques developed to produce model coordinate heating data could be applied to operational software, and methods were discussed and costs estimated for obtaining the digital information necessary for this software.

Nossaman, G. O.↗