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DOE OSTI2023

Deep learning integrates histopathology and proteogenomics at a pan-cancer level

We introduce a pioneering approach that integrates pathology imaging with transcriptomics and proteomics to identify predictive histology features associated with critical clinical outcomes in cancer. We utilize 2,755 H&E-stained histopathological slides from 657 patients across 6 cancer types from CPTAC. Our models effectively recapitulate distinctions readily made by human pathologists: tumor vs. normal (AUROC = 0.995) and tissue-of-origin (AUROC = 0.979). We further investigate predictive power on tasks not normally performed from H&E alone, including TP53 prediction and pathologic stage. Importantly, we describe predictive morphologies not previously utilized in a clinical setting. The incorporation of transcriptomics and proteomics identifies pathway-level signatures and cellular processes driving predictive histology features. Model generalizability and interpretability is confirmed using TCGA. We propose a classification system for these tasks, and suggest potential clinical applications for this integrated human and machine learning approach. A publicly available web-based platform implements these models.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Effects of surface undulations on asymmetric X-ray diffraction: a rocking-curve topography study

The results are reported of an X-ray diffraction study of an Si crystal designed and fabricated for very asymmetric diffraction from the 333 reflection for X-ray energies of 8.100 and 8.200 keV. A crystal with an asymmetry angle of 46 ± 0.1° between the surface and the (111) planes was studied. The grazing angles of incidence were near 1.08 and 0.33° for these two energies, respectively. Features arising from surface undulations were not observed at 8.100 keV, but were observed at 8.200 keV. The results at 8.100 keV allow an alternative explanation based on strain near the surface to be ruled out. Topographic images were obtained as a function of rocking angle, and in the case of 8.200 keV the surface morphology is evident. Finally, the results are found to be in agreement with dynamical X-ray diffraction calculations made with the Takagi–Taupin equations specialized to a surface having convex or concave features, as reported in the accompanying paper [Macrander (2020). J. Appl. Cryst. 53 , 793–799].

36 MATERIALS SCIENCE↗

DOE OSTI2025

Automated Scoring of Morphological Changes in Images of Pentaerythritol Tetranitrate

Recent advances in characterization techniques that generate large datasets of material microstructure images require robust, automated image-processing. We applied an unsupervised anomaly detection method called feature anomaly detection system (FADS) to automatically detect and quantify microstructure changes in images of the explosive pentaerythritol tetranitrate (PETN) aged at various temperatures. We demonstrated the FADS approach on two-dimensional images extracted from computed tomography scans, but the same technique can be readily applied to other imaging modalities. FADS calculates anomaly scores on the basis of differences in filter activations of nominal and test data in pretrained convolutional neural networks. The FADS scores successfully differentiated between pristine PETN and PETN aged at a temperature where material coarsening occurred. Morphological metric analysis of segmented images verified observed trends in FADS scores as a function of aging temperature and aging time, specifically by calculating volume fractions, specific boundary lengths, two-point correlation functions, and local thicknesses. Here, the FADS technique has two important advantages compared to traditional morphological analysis: First, it uses grayscale images as input, rather than images that are segmented to separate the appropriate phases; and second, FADS scores capture any type of changes among image sets, rather than requiring prior knowledge or selection of a relevant set of metrics.

Accelerated aging↗

DOE OSTI2020

Hierarchical morphologies in co-sputter deposited thin films

Co-depositions of immiscible alloy films at specific processing conditions have yielded hierarchical microstructures which consist of distinct features at multiple length scales, often agglomerates and concentration modulations on the sub-micrometer-scale and fine nanoprecipitates in a matrix on the nanoscale. The present work examined a series of immiscible alloy systems: Cu-Mo, Cu-Ag, Cu-Fe, Cu-Ta, Mo-Ag, Cu-Mo-Ag, to determine the kinetic conditions favorable for hierarchical organization and the formation mechanism of such structures. Thin films of six immiscible systems were sputter co-deposited over a range of deposition rates from 0.12 to 2 nm/s and various temperatures from 400 to 800°C. The resulting microstructures indicate that hierarchical structures form with sufficient disparity in kinetic energy between the constituent atoms, one species being highly mobile (A) and the other relatively immobile (B). This condition arises typically at elevated deposition temperatures and reduced deposition rates but is also alloy dependent. The hierarchical structures form during deposition via phase separation and self-organization processes across the multiple length scales. The adatoms diffuse on the film surface with the highly mobile species swiftly agglomerating into A-rich domains within which B-rich nanoprecipitates form, often self-organizing into periodic arrays. The smallest B-rich nanoprecipitates in the A-rich domains are found to be coherent and in a metastable crystal structure (B taking the structure of A), but coarser precipitates that exhibit the equilibrium structure of B element. The A-rich domains are surrounded by a B-rich matrix that phase-separates into a concentration modulated structure. In conclusion, the observations are interpreted via a model incorporating material properties and process parameters.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Evolution of LIBS technology to mobile instrumentation for expediting firearm-related investigations at the laboratory and the crime scene

Gunshot residue (GSR) is one of the few forensic disciplines that lack accurate screening techniques. This study proposes using a mobile LIBS instrument to detect inorganic GSR and compares performance to a previously validated laboratory instrument. The mobile LIBS is designed with advanced configurations specifically for on-site GSR analysis, including a CMOS detector and a sampling chamber that holds up to six typical GSR collection devices with separate gas flow ports to prevent cross-contamination. A significant novelty of the portable instrument is its image magnification, which allows quick searching and visualization of GSR particle morphology. The single-particle imaging and elemental composition capability is one of a kind and offers superior confirmatory features for GSR. The mobile LIBS performance was evaluated for residues collected from the hands of shooters (100 samples) and non-shooters (200 background samples), analyzed sequentially by the mobile instrument and then the laboratory instrument. Accuracies better than 98.8% were obtained by both instruments, demonstrating their suitability for trace IGSR detection from skin specimens. Implementation of this methodology is anticipated to drastically speed up response times (i.e., from several hours per sample by standard SEM-EDS practice to a few minutes by LIBS). The screening methods can be easily incorporated into workflows to improve decision-making processes at the crime scene and laboratory settings, reduce backlogs, and improve case management.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Harnessing peptide–cellulose interactions to tailor the performance of self-assembled, injectable hydrogels

Taking inspiration from natural systems, such as spider silk and mollusk nacre, that employ hierarchical assembly to attain robust material performance, we leveraged matrix–filler interactions within reinforced polymer–peptide hybrids to create self-assembled hydrogels with enhanced properties. Specifically, cellulose nanocrystals (CNCs) were incorporated into peptide–polyurea (PPU) hybrid matrices to tailor key hydrogel features through matrix–filler interactions. Herein, we examined the impact of peptide repeat length and CNC loading on hydrogelation, morphology, mechanics, and thermal behavior of PPU/CNC composite hydrogels. The addition of CNCs into PPU hydrogels resulted in increased gel stiffness; however, the extent of reinforcement of the nanocomposite gels upon nanofiller inclusion also was driven by PPU architecture. Temperature-promoted stiffening transitions observed in nanocomposite PPU hydrogels were dictated by peptide segment length. Analysis of the peptide secondary structure confirmed shifts in the conformation of peptidic domains (α-helices or β-sheets) upon CNC loading. Finally, PPU/CNC hydrogels were probed for their injectability characteristics, demonstrating that nanofiller–matrix interactions were shown to aid rapid network reformation (∼10 s) upon cessation of high shear forces. Overall, this research showcases the potential of modulating matrix–filler interactions within PPU/CNC hydrogels through strategic system design, enabling the tuning of functional hydrogel characteristics for diverse applications.

42 ENGINEERING↗

DOE OSTI2024

The influence of laser energy on deuterium emission characteristics from a Zircaloy-4 plasma

Laser-produced plasma coupled with optical emission spectroscopy (OES) is a promising technique for detecting certain isotopes, with unique capabilities such as standoff and rapid detection and minimal to no sample preparation requirements. The key figure-of-merit for isotopic analysis using optical spectroscopy tools is the linewidth relative to the isotope shift. Although the isotopes of hydrogen (1H, 2H, and 3H) possess large isotopic shifts (1H–2H ≈ 180 pm, 1H–3H ≈ 240 pm), being a light element, the H transitions are susceptible to various broadening mechanisms in the plasma environment. One of the critical parameters that influence the linewidth of a transition in an LPP is the incident laser energy. In the present study, we evaluated the role of laser energy on plume expansion dynamics, deuterium emission intensity, and linewidth in a nanosecond laser-produced Zircaloy-4 plasma. The changes in 2Hα emission intensity and linewidth were investigated for varying laser fluence and time after plasma onset. Spatially resolved and spatially integrated OES were performed and compared to investigate the emission spectral features and linewidth of 2Hα. Monochromatic two-dimensional time-resolved imaging was also performed to understand the morphology of the deuterium and protium emission relative to all species in the plume. Our results showed that 1Hα and 2Hα emissions predominantly occur closer to the target. Measurements of 2Hα linewidth approached similar values at later times of plasma evolution regardless of the laser energy. The linewidths of the 2Hα transition showed insignificant differences between spatially resolved and spatially integrated measurements.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Topological magnetic hysteresis in single crystals of CeAgSb 2 ferromagnet

Closed-topology magnetic domains are usually observed in thin films and in an applied magnetic field. In this work, we report the observation of rectangular cross-section tubular ferromagnetic domains in thick single crystals of CeAgSb 2 in zero applied field. Relatively low exchange energy, small net magnetic moment, and anisotropic in-plane crystal electric fields lower the domain wall energy and allow for the formation of the closed-topology patterns. The tubular domain structure irreversibly transforms into a dendritic pattern upon cycling the magnetic field. This transition between closed and open topologies results in a ‘topological magnetic hysteresis’— the actual hysteresis in magnetization, not due to the imperfections and pinning, but due to the difference in the pattern morphology. Similar physics was suggested before in pure type-I superconductors and is believed to be a generic feature of other nonlinear single (present case), or two-phase (type-I superconductor) systems where the effects similar to demagnetization (shape-dependent macroscopic variation of properties) lead to pattern formation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Metalorganic chemical vapor deposition of ZnGeN 2 films on GaN: effects of cation stoichiometry on surface morphology and crystallinity

Novel optoelectronic device designs based on the heterostructures of III-N and II-IV-N 2 are promising to advance device performance significantly. For example, by utilizing InGaN-ZnGeN 2 quantum well (QW) structures instead of pure InGaN, the band structure engineering in the QW active region can lead to improved electron-hole wavefunction overlap, and thus enhance the radiative efficiency for photon generation. These novel heterostructures have great potential to address the current challenge of low quantum efficiency in InGaN QW based light emitting diodes emitting in green and beyond. The materials development of ZnGeN 2 is still at an early stage as compared to the much matured GaN material system. In an ideal octet rule preserving ordered structure of ZnGeN 2 , every N atom is coordinated by exactly two Zn and two Ge atoms. However, local violation of octet rule can be caused by non-ideal coordination of N by the cations. The disordered structure is thermodynamically less favorable but can still be achieved, for example, in kinetics-limited growth regime. The ordered ZnGeN 2 has a bandgap very close to that of GaN (~3.4 eV) and a lattice mismatch of <0.1% with GaN. Interestingly, the valence band of ZnGeN 2 has been predicted to be ~1 eV above that of GaN, which has inspired novel designs for high efficiency light emitters. In this work, we investigated the metalorganic chemical vapor deposition (MOCVD) of ZnGeN 2 films on GaN/c-sapphire templates. Diethylzinc (DEZn), germane (GeH4) and ammonia were used as the precursors for Zn, Ge and N, respectively. A systematic study was conducted to investigate the cation stoichiometry as a function of growth temperature (TG), total reactor pressure (P) and DEZn/GeH 4 molar flow rate ratio (RII/IV). Under the investigated growth window, the Zn/(Zn+Ge) composition in the films, determined from energy dispersive X-ray spectroscopy, decreased monotonically with increase in TG but increased with increase in P and RII/IV. Atom probe tomography data did not indicate the presence of any secondary phases such as Zn 3 N 2 or Ge 3 N 4 . The surface morphology and crystallinity of the grown films had strong correlation with the Zn/(Zn+Ge) composition. The scanning electron microscopy images showed that the near-stoichiometric films have planar surfaces whereas Zn-rich films had crystallites on their surface and the Zn-poor films had faceted surface. Scanning transmission electron microscopy (STEM) imaging revealed that the Zn-rich and Zn-poor films have columnar and filament-like morphology, respectively, whereas the near-stoichiometric films have continuous film-like cross-sectional morphology. TEM nano-diffraction patterns as well as X-ray diffraction 2θ-ω scan profiles indicate that the near stoichiometric films are single crystalline. Nano-diffraction pattern of the stoichiometric films resembled that of a disordered ZnGeN 2 structure. Room temperature Raman spectra of near-stoichiometric films showed only the phonon density of states like features of a cation disordered ZnGeN 2 . Cathodoluminescence and photoluminescence spectra measured at different temperatures had similar features with peak emission wavelength at ~ 2 eV. In conclusion, the stoichiometry of ZnGeN 2 films can be widely tuned by tuning the MOCVD growth parameters. The surface morphology and the crystallinity of the films were found to have strong correlation with the Zn/(Zn+Ge) composition. The stoichiometric ZnGeN 2 films grown on GaN were demonstrated with uniform surface morphology and high crystalline quality. The results from this work will provide pathway to implement ZnGeN 2 in device structures.

Karim, Md Rezaul↗

DOE OSTI2023

Anatomy of an agricultural antagonist: Feeding complex structure and function of three xylem sap‐feeding insects illuminated with synchrotron‐based 3D imaging

Abstract Many insects feed on xylem or phloem sap of vascular plants. Although physical damage to the plant is minimal, the process of insect feeding can transmit lethal viruses and bacterial pathogens. Disparities between insect‐mediated pathogen transmission efficiency have been identified among xylem sap‐feeding insects; however, the mechanistic drivers of these trends are unclear. Identifying and understanding the structural factors and associated integrated functional components that may ultimately determine these disparities are critical for managing plant diseases. Here, we applied synchrotron‐based X‐ray microcomputed tomography to digitally reconstruct the morphology of three xylem sap‐feeding insect vectors of plant pathogens: Graphocephala atropunctata (blue‐green sharpshooter; Hemiptera, Cicadellidae) and Homalodisca vitripennis (glassy‐winged sharpshooter; Hemiptera, Cicadellidae), and the spittlebug Philaenus spumarius (meadow spittlebug; Hemiptera, Aphrophoridae). The application of this technique revealed previously undescribed anatomical features of these organisms, such as key components of the salivary complex. The visualization of the 3D structure of the precibarial valve led to new insights into the mechanism of how this structure functions. Morphological disparities with functional implications between taxa were highlighted as well, including the morphology and volume of the cibarial dilator musculature responsible for extracting xylem sap, which has implications for force application capabilities. These morphological insights will be used to target analyses illuminating functional differences in feeding behavior.

3D imaging↗

DOE OSTI2022

The Wormholes Within: A Study of 1, 3, 5–Triamino–2, 4, 6–Trinitrobenzene Crystal Morphology by Micro and Nano–Scale X–Ray Computed Tomography and its Effects Upon the Shock Sensitivity of Detonation

We report that we understand heterogeneous-explosive detonation only to the extent that we can first measure the salient chemical and microstructural features. Barring an inordinate amount of trial and error, we can tailor the detonation properties of our HE formulations only to the extent that we understand (at least qualitatively) the same effects. As an insensitive high explosive, 1, 3, 5-triamino-2, 4, 6-trinitrobenzene (TATB) burns more heterogeneously than conventional high explosives, making its detonation properties sensitive to microstructure. The Benziger route can produce various grain morphologies depending on the amount of water used in the amination step. So-called dry-aminated (DA) TATB crystals are riddled with a void structure called wormholes, which are washed out ammonium chloride (NH4Cl) inclusions that form during synthesis. So-called wet-aminated (WA) TATB crystals do not contain NH 4 Cl inclusions but possess a very convoluted external structure. Using both micro and nano-scale CT, we explore three DA-TATB lots that reflect evolutionary processing changes, plus one WA-TATB material. Micro CT imaged crystal collections show the exterior grain structure, revealing its roughness and providing a crude particle size measurement. The DA-TATB lots that test most sensitively in the LANL ECOT corner-turning test are roughest, having the appearance of being “corroded”. Nano-scale CT reveals both internal NH 4 Cl inclusions and void structures. The DA-TATB lots that tested intermediate and high sensitivity in ECOT exhibited similar wormhole structures, which were more extensive than that of the low-sensitivity lot. The least sensitive DA-TATB lot also retained more NH 4 Cl, consistent with reduced connectivity of voids to the surface.

1, 3, 5-triamino-2,4↗

DOE OSTI2023

GaAs solar cells grown on acoustically spalled GaAs substrates with 27% efficiency

Acoustic spalling presents a potentially low-cost reuse pathway for III–V epitaxial growth substrates via exfoliation of device layers with recovery and reuse of the substrate. However, surface features formed during spalling can reduce the performance of subsequently grown devices. Here, we develop an understanding of how the surface morphology of acoustically spalled substrates affects GaAs solar cell performance and develop strategies to mitigate these impacts. We demonstrate that minor planarization of the surface by wet chemical etching and/or epitaxial growth, or the redesign of the device structure to thicken critical layers, prevents performance degradation. Using these strategies, we demonstrate a 0.25 cm 2 single-junction GaAs device with 26.9% ± 0.2% photovoltaic conversion efficiency under the AM1.5G spectrum grown on an acoustically spalled substrate. These results enable the growth of high-performance III–V devices on non-traditional substrates with the potential for significantly reduced device costs.

14 SOLAR ENERGY↗

DOE OSTI2022

Hierarchically structured metal carbides as conductive fillers in thermo-responsive polymer nanocomposites for battery safety

Integrating thermo-responsive polymer switching materials (TRPS) into lithium-ion batteries (LIBs) has been recognized as one of the most effective strategies to prevent thermal runaway under various abuse scenarios. However, the current methods to obtain TRPS cannot satisfy different practical applications. Herein, we develop a versatile strategy for the preparation of various metal carbides (e.g., tungsten carbide, molybdenum carbide) with controllable hierarchical structure that is featured with surface protrusion structure, which is critical for high conductivity and rapid thermal response. Systematic studies of the phase and morphology evolutions by advanced characterizations illustrate that the reducing agent and reduction rate are critical for developing the specific morphology. In conclusion, by using the above-mentioned carbides as the conductive fillers of TRPS, the resulting TRPS with a specially controlled shape exhibits over 5 order of conductivity improvement compared with common carbides with particulate morphology, in addition to reversible shutdown performance and effective thermal abuse protections toward safe LIB operation.

25 ENERGY STORAGE↗

DOE OSTI2023

Automated Quantification of Wind Turbine Blade Leading Edge Erosion from Field Images

Wind turbine blade leading edge erosion is a major source of power production loss and early detection benefits optimization of repair strategies. Two machine learning (ML) models are developed and evaluated for automated quantification of the areal extent, morphology and nature (deep, shallow) of damage from field images. The supervised ML model employs convolutional neural networks (CNN) and learns features (specific types of damage) present in an annotated set of training images. The unsupervised approach aggregates pixel intensity thresholding with calculation of pixel-by-pixel shadow ratio (PTS) to independently identify features within images. The models are developed and tested using a dataset of 140 field images. The images sample across a range of blade orientation, aspect ratio, lighting and resolution. Each model (CNN v PTS) is applied to quantify the percent area of the visible blade that is damaged and classifies the damage into deep or shallow using only the images as input. Both models successfully identify approximately 65% of total damage area in the independent images, and both perform better at quantifying deep damage. The CNN is more successful at identifying shallow damage and exhibits better performance when applied to the images after they are preprocessed to a common blade orientation.

Aird, Jeanie A.↗

DOE OSTI2025

Faceted NiO(111) nanosheets: morphological and catalytic evolution for the oxygen evolution reaction

The renaissance of the energy system through the use of green hydrogen by water electrolysis lies behind the development of abundant, active, and scalable catalysts for the oxygen evolution reaction (OER). A fundumental understanding of the surface properties for these materials is of vital importance in producing viable heterogenous catalysts. In this feature article, we summarize several years of collaborative work on a uniquely faceted NiO(111) nanosheet possessing hexagonal holes with a focus on understanding how the evolution of the catalyst surface and bulk composition effects OER performance. The importance of surface faceting, morphological evolution, and metal combination by different doping strategies are all analyzed and summarized to further improve the material's performance. Furthermore, microwave and supercritical synthesis processes are utilized to understand how varying wet-chemical techniques effect the formation of the NiO(111) nanosheet and activity of the material. We discuss our chosen strategies and the difficulties encountered with optimizing a catalyst surface for the OER.

08 HYDROGEN↗

DOE OSTI2020

Expansion dynamics and chemistry evolution in ultrafast laser filament produced plasmas

Laser ablation in conjunction with optical emission spectroscopy is a potential non-contact, standoff detection method for all elements in the periodic table and certain isotopes such as radionuclides. Currently, significant development efforts are on-going to use ultrafast laser filaments for remote sensing. The application of filaments is of particular interest in extending the range of stand-off capability associated with elemental and isotopic detection via laser-induced breakdown spectroscopy. In this study, we characterize the expansion dynamics and chemical evolution of filament-produced uranium (U) plasmas. Laser filaments are generated in the laboratory by loosely focusing 35 femtosecond (fs), 6 milli Joule (mJ) pulses in air. Two-dimensional spectrally-integrated and time-resolved imaging was performed to study hydrodynamics and evolution of U atomic and UO molecular emission in filament-produced U plasmas. Our results highlight that filament ablation of U plasmas gives a cylindrical plasma plume morphology with an appearance of plume splitting into slow and fast moving components at later times of its evolution. Emission from the slow-moving region shows no distinct spectral features (i.e. broadband-like) and is contributed in part by nanoparticles generated during ultrafast laser ablation. Additionally, we find U atoms and U oxide molecules (i.e. UO, UxOy) co-exist in the filament produced plasma, which can be attributed to the generation of low-temperature plasma conditions during filament ablation

(140.3440) Laser-induced breakdown, (280.5395) Pla↗

DOE OSTI2026

Characterizing microscale signatures in uranium ore concentrates using electron probe microanalyzer

Impurities in uranium ore concentrates (UOCs) serve as forensic signatures of processing history and origin. Here, this study utilizes Electron Probe Microanalyzer (EPMA) to characterize microscale compositional and textural features in individual UOC particles from both commercial and bench-scale production. At the particle scale, multiple internal phases with distinct morphologies, chemical signatures, and stoichiometries are documented. Our data shows that chemical impurities are heterogeneously distributed within single particles and among particles within a sample. These microscale heterogeneities correlate with known processing histories, indicating that microscale signatures of early fuel cycle materials can provide valuable information for nuclear forensic material analysis.

organic↗

DOE OSTI2020

Growth, total lipid, and omega-3 fatty acid production by Nannochloropsis spp. cultivated with raw plant substrate

Improving productivity and lipid concentration in microalgae is important for the economic success of both biofuel and microalgae coproducts production. Nannochloropsis spp. are marine microalgae currently being grown at large-scale for the production of biofuel and lipid coproducts. In this work, we demonstrate improvements of growth and omega-3 production in Nannochloropsis gaditana CCMP526 and Nannochloropsis oceanica CCAP849/10 with plant substrate addition, a potentially economical option for increasing microalgal productivity. Furthermore, we examine growth in the presence of corn stover, switchgrass, sugarcane bagasse, and yard waste. By examining the microbial ecology of N. gaditana cultures with and without plant substrate and with and without antibiotics, we discovered a potential bacterial interaction in these cultures, but its presence is not necessary for algal growth improvements in the presence of plant substrate. Analysis of plant substrate morphology by scanning electron microscopy (SEM) after cultivation in media with and without N. gaditana shows a degradation of specific plant structural features and a colonization of the plant phloem by N. gaditana. An examination of N. gaditana in a Congo red plate assay indicates potential cellulolytic activity, but a preliminary examination of the potential cellulase transcripts does not reveal differential expression of a candidate in the presence of plant. This evidence demonstrates potential raw plant utilization by a marine microalga for increased productivity and provides a potentially economical option for increasing coproduct concentration at industrial scale without genetic engineering.

59 BASIC BIOLOGICAL SCIENCES↗