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At least 433 records · Page 24

Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project

An important need exists to better understand and stratify kidney disease according to its underlying pathophysiology in order to develop more precise and effective therapeutic agents. National collaborative efforts such as the Kidney Precision Medicine Project are working towards this goal through the collection and integration of large, disparate clinical, biological and imaging data from patients with kidney disease. Ontologies are powerful tools that facilitate these efforts by enabling researchers to organize and make sense of different data elements and the relationships between them. Ontologies are critical to support the types of big data analysis necessary for kidney precision medicine, where heterogeneous clinical, imaging and biopsy data from diverse sources must be combined to define a patient’s phenotype. Here, the development of two new ontologies — the Kidney Tissue Atlas Ontology and the Ontology of Precision Medicine and Investigation — will support the creation of the Kidney Tissue Atlas, which aims to provide a comprehensive molecular, cellular and anatomical map of the kidney. These ontologies will improve the annotation of kidney-relevant data, and eventually lead to new definitions of kidney disease in support of precision medicine.

60 APPLIED LIFE SCIENCES↗

Role of kinetic energy on Nb 3 Sn thin films by low-temperature co-sputtering

Nb 3 Sn is a promising thin film material for superconducting radio frequency (SRF) applications. Although surface resistivity, critical temperature, and critical field are advantageous in comparison to pure Nb, currently the performance of Nb 3 Sn is lacking behind due to its complex defect structure and phase inhomogeneities. In this work, the influence of the kinetic energy of the deposited particles on the defect structure in Nb 3 Sn thin films synthesized at low temperatures is investigated. A combination of extended x-ray absorption fine structure analysis, x-ray absorption spectroscopy mapping, and transmission electron microscopy reveals an improved local order and elemental homogeneity of the Nb 3 Sn films induced by higher kinetic energies of the elemental species during deposition. Even more, these process conditions lead to suppressed local inhomogeneities at grain boundaries, which can be one of the causes of critically reduced superconducting properties of low temperature sputter-coated Nb 3 Sn thin films. Finally, we show that the magnetic field-induced reduction of critical currents across weak-links formed at grain boundaries can be eliminated by the suggested materials’ synthesis.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Rapid subsurface analysis of frequency-domain thermoreflectance images with K-means clustering

K-means clustering analysis is applied to frequency-domain thermoreflectance (FDTR) hyperspectral image data to rapidly screen the spatial distribution of thermophysical properties at material interfaces. Performing FDTR while raster scanning a sample consisting of 8.6 μm of doped-silicon (Si) bonded to a doped-Si substrate identifies spatial variation in the subsurface bond quality. Routine thermal analysis at select pixels quantifies this variation in bond quality and allows assignment of bonded, partially bonded, and unbonded regions. Performing this same routine thermal analysis across the entire map, however, becomes too computationally demanding for rapid screening of bond quality. To address this, K-means clustering was used to reduce the dimensionality of the dataset from more than 20 000 pixel spectra to just K = 3 component spectra. The three component spectra were then used to express every pixel in the image through a least-squares minimized linear combination providing continuous interpolation between the components across spatially varying features, e.g., bonded to unbonded transition regions. Fitting the component spectra to the thermal model, thermal properties for each K cluster are extracted and then distributed according to the weighting established by the regressed linear combination. Thermophysical property maps are then constructed and capture significant variation in bond quality over 25 μm length scales. The use of K-means clustering to achieve these thermal property maps results in a 74-fold speed improvement over explicit fitting of every pixel.

36 MATERIALS SCIENCE↗

Smooth, homogeneous, high-purity Nb 3 Sn superconducting RF resonant cavity by seed-free electrochemical synthesis

Abstract Workbench-size particle accelerators, enabled by Nb 3 Sn-based superconducting radio-frequency (SRF) cavities, hold the potential of driving scientific discovery by offering a widely accessible and affordable source of high-energy electrons and x-rays. Thin-film Nb 3 Sn RF superconductors with high quality factors, high operation temperatures, and high-field potentials are critical for these devices. However, surface roughness, non-stoichiometry, and impurities in Nb 3 Sn deposited by conventional Sn-vapor diffusion prevent them from reaching their theoretical capabilities. Here we demonstrate a seed-free electrochemical synthesis that pushes the limit of chemical and physical properties in Nb 3 Sn. Utilization of electrochemical Sn pre-deposits reduces the roughness of converted Nb 3 Sn by five times compared to typical vapor-diffused Nb 3 Sn. Quantitative mappings using chemical and atomic probes confirm improved stoichiometry and minimized impurity concentrations in electrochemically synthesized Nb 3 Sn. We have successfully applied this Nb 3 Sn to the large-scale 1.3 GHz SRF cavity and demonstrated ultra-low BCS surface resistances at multiple operation temperatures, notably lower than vapor-diffused cavities. Our smooth, homogeneous, high-purity Nb 3 Sn provides the route toward high efficiency and high fields for SRF applications under helium-free cryogenic operations.

Physics↗

Investigating genomic prediction strategies for grain carotenoid traits in a tropical/subtropical maize panel

Abstract Vitamin A deficiency remains prevalent on a global scale, including in regions where maize constitutes a high percentage of human diets. One solution for alleviating this deficiency has been to increase grain concentrations of provitamin A carotenoids in maize (Zea mays ssp. mays L.)—an example of biofortification. The International Maize and Wheat Improvement Center (CIMMYT) developed a Carotenoid Association Mapping panel of 380 inbred lines adapted to tropical and subtropical environments that have varying grain concentrations of provitamin A and other health-beneficial carotenoids. Several major genes have been identified for these traits, 2 of which have particularly been leveraged in marker-assisted selection. This project assesses the predictive ability of several genomic prediction strategies for maize grain carotenoid traits within and between 4 environments in Mexico. Ridge Regression-Best Linear Unbiased Prediction, Elastic Net, and Reproducing Kernel Hilbert Spaces had high predictive abilities for all tested traits (β-carotene, β-cryptoxanthin, provitamin A, lutein, and zeaxanthin) and outperformed Least Absolute Shrinkage and Selection Operator. Furthermore, predictive abilities were higher when using genome-wide markers rather than only the markers proximal to 2 or 13 genes. These findings suggest that genomic prediction models using genome-wide markers (and assuming equal variance of marker effects) are worthwhile for these traits even though key genes have already been identified, especially if breeding for additional grain carotenoid traits alongside β-carotene. Predictive ability was maintained for all traits except lutein in between-environment prediction. The TASSEL (Trait Analysis by aSSociation, Evolution, and Linkage) Genomic Selection plugin performed as well as other more computationally intensive methods for within-environment prediction. The findings observed herein indicate the utility of genomic prediction methods for these traits and could inform their resource-efficient implementation in biofortification breeding programs.

59 BASIC BIOLOGICAL SCIENCES↗

Methods for Explainable Artificial Intelligence

We explored ways of quantifying information in a neural network. This can be used to determine the right size of a network or to infer the way in which a network is processing information. The first year and a half was somewhat exploratory while the last half of the project focused on approaches that seemed to show the most promise. The introduce a new way of computing explainable artificial intelligence (XAI) saliency maps that is several orders of magnitude faster than methods with similar fidelity We call it FastCAM. The method works be combining a Class Activation Map (CAM) method such as GradCAM with a forward activation map computed with a statistic we call SMOE Scale. The addition of the forward activation maps to CAM methods seems to always improve their fidelity. At the same time, computational overhead is not increased by very much. While Gradients with SmoothGrad scores better on some fidelity measures, it is overall not as good and requires more than 1500 times to compute. We demonstrate two completed applications of FastCAM on tasks outside of the LDRD at LLNL. The source code for FastCAM is currently being implanted into Captum, the official XAI toolkit for the popular deep learning toolkit PyTorch. The LDRD currently has 13 publications released to the public. 10 of them are journal length.

97 MATHEMATICS AND COMPUTING↗

Developing socially and economically generative, resilient PV-energy systems for low- and moderate-income communities: Applications for Puerto Rico (Final Technical Report)

The nexus of energy and poverty is one of the most significant long-term challenges facing the energy and electricity sectors, with negative feedback loops between energy-related costs, risks, and insecurities, on the one hand, and diverse other social and economic insecurities, on the other, helping to undermine health, wellbeing, and resilience in low- and moderate-income communities around the US and the world (Biswas et al. 2022). The transition of energy systems to clean energy alternatives offers a potential opportunity to redesign future energy arrangements in ways that, instead, create beneficial social value for communities, reverses the energy-poverty nexus, and enhances community wellbeing (Biswas et al. 2020; Miller et al. 2018). The promise of clean energy transitions to address the energy-poverty nexus is especially significant when designed using principles of just energy transitions. To leverage just clean energy transitions to accomplish a reversal of the energy-poverty nexus requires improvement in three capabilities: (1) Understanding and mapping the community-scale dynamics and variability of the energy-poverty nexus, which vary considerably from community to community; (2) Evaluating the technical, social, and economic potential for different clean energy system designs to deliver social value to specific communities; and (3) Working collaboratively with communities to imagine and design clean energy systems solutions that meet their needs, fit their capabilities and contexts, and deliver multiple forms of community-desired social value/benefits that help reverse key facets of the energy-poverty nexus. This project developed a portfolio of novel tools, methodological approaches, and collaborative partnerships with four communities in Puerto Rico that further the objective of building these three capabilities.

14 SOLAR ENERGY↗

Full-sky Models of Galactic Microwave Emission and Polarization at Subarcminute Scales for the Python Sky Model

Polarized foreground emission from the Galaxy is one of the biggest challenges facing current and upcoming cosmic microwave background (CMB) polarization experiments. We develop new models of polarized Galactic dust and synchrotron emission at CMB frequencies that draw on the latest observational constraints; that employ the “polarization fraction tensor” framework to couple intensity and polarization in a physically motivated way; and that allow for stochastic realizations of small-scale structure at subarcminute angular scales currently unconstrained by full-sky data. We implement these models into the publicly available Python Sky Model (PySM) software and additionally provide PySM interfaces to select models of dust and CO emission from the literature. We characterize the behavior of each model by quantitatively comparing it to observational constraints in both maps and power spectra, demonstrating an overall improvement over previous PySM models. Finally, we synthesize models of the various Galactic foreground components into a coherent suite of three plausible microwave skies that span a range of astrophysical complexity allowed by current data. Author contributions to this paper can be found at the end of this work.

Group, The Pan-Experiment Galactic Science↗

Reinterpretations of the northern Nectaris Basin, part F

Photogeologic analysis was attempted on a strip of Apollo 16 metric photographs; the superior quality and stereographic properties of the photography permitted this reevaluation. Geologic contacts, as redrawn closely resemble those of earlier maps, but some differences resulted because of improved photographic quality and a conscious attempt to test fully the impact hypothesis. All or most of the nonmare material of the region of the northern Nectaris Basin rim can be explained by the formation of impact basins. This interpretation seems strained only for some irregular and clustered craters north of Mare Nectaris and for the southern facies of the Descartes material. If the latter material is shown to have been sampled and to be of impact origin, then extensive hill and crater-forming volcanic material of Imbrian or younger age probably does not exist on the lunar terra.

Wilhelms, D. E.↗

Applications of ERTS-1 imagery to terrestrial and marine environmental analyses in Alaska

ERTS-1 imagery provides a means of distinguishing and monitoring estuarine surface water circulation patterns and changes in the relative sediment load of discharging rivers on a regional basis. It also will aid local fishing industries by augmenting currently available hydrologic and navigation charts. The interpretation of geologic and vegetation features resulted in preparation of improved surficial geology, vegetation and permafrost terrain maps at a scale of 1:1 million utilizing ERTS-1 band 7 imagery. This information will be further utilized in a route and site selection study for the Nome to Kobuk Road in central Alaska. Large river icings along the proposed Alaska pipeline route have been monitored. Sea ice deformation and drift northeast of Point Barrow, Alaska has been measured and shorefast ice accumulation and ablation along the west coast of Alaska is being mapped for the spring and early summer seasons. These data will be used for route and site selection, regional environmental analysis, identification and inventory of natural resources, land use planning, and in land use regulation and management.

Anderson, D. M.↗

The cartographic application of ERTS/RBV imagery in polar regions

The author has identified the following significant results. A 1.1,000,000 scale sketch map has been prepared from ERTS imagery of the Prince Olav Coast, Antarctica. This is the first such mapping of the extent of the ice tongues of the Shtrase and Fietta Bay glaciers. Shtrase is of particular interest because the ERTS imagery shows the tongue extending out into the Lutzom-Holm Bay approximately 32 miles further than ever depicted on existing maps. This sketch map and others in work covering coastal areas of the Antarctic continent show many coastal changes when compared to what is believed to be the most current published maps. These sketch maps along with the accompanying mosaics will be a bench mark for future revision to existing maps and charts and also an invaluable source for mew mapping. ERTS imagery is now available over Mt. Siple, Antarctica, and it is expected to provide a source to position Mt. Siple correctly in relation to the Executive Committee Range. A mosaic at 1:500,000 scale is also being compiled that will serve as a source for future revision of 1:250,000 scale maps of the Ellsworth Mountains, change and improve the shape and size of the islands within the Ronne Ice Shelf, and redefine the ice front of the Ronne and Filchner Shelves.

Macdonald, W. R.↗

Investigation of Antarctic crust and upper mantle using MAGSAT and other geophysical data

Plans to create an improved version of the MAGSAT magnetic anomaly map by more carefully scrutinizing the accepted data for field-aligned current effects are discussed. Data are continued to a 300 km surface for the compilation of a final map. Based on this set of data, vector anomaly maps over Antarctica are planned. A high-pass anomaly map with a cut-off wavelength of approximately 1500 km is also envisioned. It is suspected that longer-wavelength features have their origin outside the crust.

Bentley, C. R.↗

Landsat Thematic Mapper studies of land cover spatial variability related to hydrology

Past accomplishments involving remote sensing based land-cover analysis for hydrologic applications are reviewed. Ongoing research in exploiting the increased spatial, radiometric, and spectral capabilities afforded by the TM on Landsats 4 and 5 is considered. Specific studies to compare MSS and TM for urbanizing watersheds, wetlands, and floodplain mapping situations show that only a modest improvement in classification accuracy is achieved via statistical per pixel multispectral classifiers. The limitations of current approaches to multispectral classification are illustrated. The objectives, background, and progress in the development of an alternative analysis approach for defining inputs to urban hydrologic models using TM are discussed.

Wharton, S.↗

X-rays from the radio halo of Virgo A = M87

The purpose of this study is to investigate in more detail the associated X-ray and radio emission in the Virgo A halo discovered by SGF. Improved Einstein HRI data and new radio maps obtained with the Very Large Array are described and the relation between the X-ray and radio structures is carefully examined. Several possible explanations are presented for the X-ray emission. The inverse compton model is found to be viable only if the magnetic field is variable and substantially weaker than the equipartition value. The principal alternative is excess thermal X-rays due to compression of the intracluster medium by the radio lobe. In either case, the association of such prominent radio and X-ray structures is unique among known radio galaxies.

Source record↗

An improved version of NCOREL: A computer program for 3-D nonlinear supersonic potential flow computations

A computer code called NCOREL (for Nonconical Relaxation) has been developed to solve for supersonic full potential flows over complex geometries. The method first solves for the conical at the apex and then marches downstream in a spherical coordinate system. Implicit relaxation techniques are used to numerically solve the full potential equation at each subsequent crossflow plane. Many improvements have been made to the original code including more reliable numerics for computing wing-body flows with multiple embedded shocks, inlet flow through simulation, wake model and entropy corrections. Line relaxation or approximate factorization schemes are optionally available. Improved internal grid generation using analytic conformal mappings, supported by a simple geometric Harris wave drag input that was originally developed for panel methods and internal geometry package are some of the new features.

Siclari, Michael J.↗

Optical alignment and testing of the Diffuse IR Background Experiment IR cryogenic telescope

Diffuse Infrared Background Experiment (DIRBE) optical alignment and testing methods are discussed. Using strobe videography, vibration and performance testing of a 32 hz tuning-fork chopper was carried out. The Cosmic Background explorer satellite provides improved microwave and IR all-sky maps of the cosmic background radiation from a polar orbit. A liquid helium cryostat houses the DIRBE and the Far IR Absolute Spectrophotometer (FIRAS) instruments at a temperature of 2 K. Differential MicRowave Radiometers (DMRs) provide large scale maps of anisotropy of the 3 K background at wavelengths of 3.3, 5.7, and 9.6 mm. The DIRBE telescope is an IR photometric instrument with 10 wavelength bands between 1 and 300 microns, designed to measure radiation from the epoch of galaxy formation. Stringent stray light requirements mean that the DIRBE flight instrument has to be built and tested in a class 100 environment.

Wood, H. John↗

Preliminary results of imaging spectroscopy of the Humorum Basin region of the moon

Imaging spectroscopy of the lunar surface was carried out using a CCD spectrograph employed as an imaging spectrometer at the University of Hawaii 2.24-m telescope at Mauna Kea Observatory. A portion of the Humorum multiringed impact basin was observed, yielding an imaging spectroscopic dataset consisting of approximately 400,000 spectra covering the wavelength region 0.7-0.98 microns at a spectral resolution of 200 (lambda/Delta-lambda). Results of this analysis included (1) identifying craters and other explosures of highland material within the bounds of Mare Humorum, (2) identifying craters in the highlands adjacents to Mare Humorum that excavate buried mare basalt, and (3) identifying two spectral units in the highlands that likely represent compositional units. The region is shown to be extremely diverse spectrally and demonstrates the ability of imaging spectroscopy to enable a qualitative improvement in the ability to identify and map compositional units.

Lucey, P. G.↗

Non-intrusive measurements in a rocket engine combustor

In recent years analytical tools to characterize combustor flow have been developed in order to support design. To facilitate anchoring of combustion related physical models and the CFD codes in which they are incorporated, considerable development and application of non-intrusive combustion diagnostic capabilities has occurred. Raman spectroscopy can be used to simultaneously detect all polyatomic molecules present in significant concentrations and to determine gas temperature. This is because all molecules possess a distinct temperature dependent Raman spectrum. A multi-point diagnostic system for non-intrusive temperature and species profiling in rocket engines has been developed at Rocketdyne. In the present effort, the system has been undergoing validation for application to rocket engine component testing. A 4 inch diameter windowed combustor with a coaxial gas-gas injector was chosen for this series of validation experiments. Initially an excimer-pumped tunable dye laser and later a solid state Nd-Yag laser served as excitation sources. The Raman signal was dispersed by a monochromator and detected by a gated, intensified Charged Coupled Device (CCD) array. Experiments were carried out prior to each series of hot fire tests to ensure that the Raman signal detected was due to a spontaneous rather than a stimulated Raman emission process. Over sixty hot fire tests were conducted during the first series of tests with the excimer/dye laser. All hot fire testing was at a mixture ratio of 0.5 and chamber pressures of approximately 100 and approximately 300 psia. The Raman spectra of hydrogen, water vapor and oxygen recorded during single element hot fire tests were reduced and analyzed. A significant achievement was the attainment of single shot Raman spectra in cold flow tests. Unfortunately, the single shot signal-to-noise ratio deteriorated to an unacceptable level during the hot fire testing. Attempts to obtain temperature data from the hydrogen Q1-branch profiles obtained in hot fire tests suggest that potentially complicating factors may render the approach of averaging data on the photodiode array invalid. A second series of hot fire tests was conducted with a 4 element coaxial injector using the Nd-Yag laser. A very compact and portable diagnostics set up was assembled for ease of alignment, relocation and flexibility. Measurements were made at several regions in the chamber in order to map concentration profiles. High spatial resolution and improved signal to noise characteristics were demonstrated.

Farhangi, S.↗