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At least 631 records · Page 35

Combined computed tomography and position-resolved X-ray diffraction of an intact Roman-era Egyptian portrait mummy

Hawara Portrait Mummy 4, a Roman-era Egyptian portrait mummy, was studied with computed tomography (CT) and with CT-guided synchrotron X-ray diffraction mapping. These are the first X-ray diffraction results obtained non-invasively from objects within a mummy. The CT data showed human remains of a 5-year-old child, consistent with the female (but not the age) depicted on the portrait. Physical trauma was not evident in the skeleton. Diffraction at two different mummy-to-detector separations allowed volumetric mapping of features including wires and inclusions within the wrappings and the skull and femora. Additionally, the largest uncertainty in origin determination was approximately 1.5 mm along the X-ray beam direction, and diffraction- and CT-determined positions matched. Diffraction showed that the wires were a modern dual-phase steel and showed that the 7 × 5 × 3 mm inclusion ventral of the abdomen was calcite. Tracing the 00.2 and 00.4 carbonated apatite (bone's crystalline phase) reflections back to their origins produced cross-sectional maps of the skull and of femora; these maps agreed with transverse CT slices within approximately 1 mm. Coupling CT and position-resolved X-ray diffraction, therefore, offers considerable promise for non-invasive studies of mummies.

60 APPLIED LIFE SCIENCES↗

Fiber Bundle Morphisms as a Framework for Modeling Many-to-Many Maps

While it is not generally reflected in the `nice' datasets used for benchmarking machine learning algorithms, the real-world is full of processes that would be best described as many-to-many. That is, a single input can potentially yield many different outputs (whether due to noise, imperfect measurement, or intrinsic stochasticity in the process) and many different inputs can yield the same output (that is, the map is not injective). For example, imagine a sentiment analysis task where, due to linguistic ambiguity, a single statement can have a range of different sentiment interpretations while at the same time many distinct statements can represent the same sentiment. When modeling such a multivalued function $f: X \rightarrow Y$, it is frequently useful to be able to model the distribution on $f(x)$ for specific input $x$ as well as the distribution on fiber $f^{-1}(y)$ for specific output $y$. Such an analysis helps the user (i) better understand the variance intrinsic to the process they are studying and (ii) understand the range of specific input $x$ that can be used to achieve output $y$. Following existing work which used a fiber bundle framework to better model many-to-one processes we describe how morphisms of fiber bundles provide a template for building models which naturally capture the structure of many-to-many processes.

Coda, Elizabeth D.↗

LSM and CPT

We study a number of 1+1d lattice models with anti-unitary symmetries that simultaneously reflect space and reverse time. Some of these symmetries are anomalous, leading to Lieb-Schultz-Mattis-type constraints, thus excluding a trivially gapped phase. Examples include a mod 8 anomaly in the Majorana chain and various mod 2 anomalies in the spin chain. In some cases, there is an exact, non-anomalous lattice symmetry that flows in the continuum to CPT. In some other cases, the CPT symmetry of the continuum theory is emergent or absent. Depending on the model, the anomaly of the lattice model is matched in the continuum in different ways. In particular, it can be mapped to an emergent anomaly of an emanant symmetry.

Anomalies in Field and String Theories↗

The physics of desiccation cracks 1: Ductile fracturing and dependence on relative humidity

Ductile deformation is ubiquitously found in the shrinkage of geomaterials. The existence of ductility requires elastoplastic mechanics when analyzing the structure deformation under external stress. Here, in this work, we explore the physics of ductile fracturing based on the results from desiccation experiments and triaxial tests. By using the digital image correlation (DIC) method to generate the strain maps of samples undergoing desiccation cracking under different relative humidities, we obtain results showing the previously postulated Cnoidal Wave ductile failure patterns propagating under atmospheric condition-controlled crack velocities. We then correlate these observations with rate-dependent plasticity models calibrated through triaxial tests undergoing several unloading–reloading cycles and velocity stepping. This work demonstrates the necessity to consider ductility in soil cracking, indicating that the formation of crack patterns in soil desiccation is a slow and predictable process.

58 GEOSCIENCES↗

Mapping wall-to-wall fractional cover of Arctic tundra plant functional types in Alaska using 20-m spatial resolution satellite imagery and harmonized plot observations

Estimates of fractional cover (fCover) across given land surfaces are used to assess, and often model, vegetation composition and diversity, which are crucial for understanding the health and functioning of terrestrial ecosystems. Remote sensing provides a useful means for scaling local, plot-measured fCover estimates to regional scales. Leveraging a recently synthesized and harmonized plot database, this study generated wall-to-wall maps of fCover for six Alaskan-Arctic plant functional types (PFT), including non-vascular plants, forbs, graminoids, and deciduous and evergreen shrubs, using 20-m satellite data (Sentinel-1, Sentinel-2, ArcticDEM) using a machine learning regression approach, specifically the random forest (RF) algorithm, which is well-suited for handling nonlinear relationships and high-dimensional satellite datasets. This study additionally addressed the spatio-temporal inconsistencies e.g., sampling scale, plot size, and collection year in plot measured fCover by adopting a multivariate outlier detection approach—Cook’s distance—to identify high-quality plots for model training and validation. Our approach achieves high accuracy (R 2 = 0.59–0.93, root mean squared errors = 0.02–0.10 for all PFTs) between plot-observed and satellite-derived fCover when using high-quality plot samples. The mapped fCover characterizes the spatial patterns of different PFTs across the tundra biome at a 20-m resolution, providing key information needed for improved representation of Arctic tundra vegetation in terrestrial biosphere models to better understand climate-vegetation feedback across the Arctic tundra.

Arctic tundra↗

Fe Oxidation and Species Distribution at the Rock–Fluid Interface of Marcellus Shale Reacted with Hydraulic Fracturing Fluid

Hydraulic fracturing of shale reservoirs resulted in significant opportunity for increased oil and gas production in the United States. Rock-fluid interactions can cause mineral dissolution and precipitation reactions that lead to permeability changes in the shale matrix, which ultimately may affect transport pathways and hydrocarbon production. Understanding the distribution of secondary precipitates, such as barite and Fe(III) (hydro)oxides, and cation leaching at the rock-fluid interface is an important step to further investigate how these geochemical processes can change permeability and transport pathways. In this study, thin sections of the fracture-matrix interface were made from reacted Marcellus shale cores. The thin sections were characterized using synchrotron X-ray fluorescence imaging and synchrotron X-ray absorption spectroscopy. Fe species with different oxidation states were identified in the maps, together with barite and Ca distribution. The results show that ferrihydrite, as newly formed Fe(III)-bearing precipitates, aligned well with the border of the Ca (e.g., calcite) leaching region in the reaction front. Some Fe-containing clay also dissolved, but the dissolution region for the clay was not as deep as the calcite. Further, the reaction front is about three times deeper in the direction parallel to the shale bedding than that perpendicular to the bedding. The Ca leaching region can be an index for reaction front detection for Marcellus shale. Reactive transport modeling was conducted and the predicted Ca leaching boarder align well with ferrihydrite precipitation, consistent with the experimental observation. The carbonate mineral dissolution can be crucial to promote fluid access into the shale matrix. Together with our previous study on the shale reactive surface, this follow-up study showed similar Ca leaching region and Fe(III) precipitates distribution in the reaction front regardless of barite precipitation on the surface, indicating that the barite coatings on the surface may not pose a significant impact on reactive transport at the shale-fluid interface.

04 OIL SHALES AND TAR SANDS↗

The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior

Lipid membranes are central to cellular life. Complementing experiments, computational modeling has been essential in unraveling complex lipid-biomolecule interactions, crucial in both academia and industry. The Martini model, a coarse-grained force field for efficient molecular dynamics simulations, is widely used to study membrane phenomena but has faced limitations, particularly in capturing realistic lipid phase behavior. Here, we present refined Martini 3 lipid models with a mapping scheme that distinguishes lipid tails that differ by just two carbon atoms, enhancing the structural resolution and thermodynamic accuracy of model membrane systems including ternary mixtures. The expanded Martini lipid library includes thousands of models, enabling simulations of complex and biologically relevant systems. These advancements establish Martini as a robust platform for lipid-based simulations across diverse fields.

Lipids↗

Measurement of atom resolvability in cryo-EM maps with Q-scores

Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q-score. Q-scores can be calculated for atoms in proteins, nucleic acids, water, ligands and other solvent atoms, using models fitted to or derived from cryo-EM maps. Q-scores can also be averaged to represent larger features such as entire residues and nucleotides. Averaged over entire models, Q-scores correlate very well with the estimated resolution of cryo-EM maps for both protein and RNA. Here, assuming the models they are calculated from are well fitted to the map, Q-scores can be used as a measure of resolvability in cryo-EM maps at various scales, from entire macromolecules down to individual atoms. Q-score analysis of multiple cryo-EM maps of the same proteins derived from different laboratories confirms the reproducibility of structural features from side chains down to water and ion atoms.

59 BASIC BIOLOGICAL SCIENCES↗

Kelvin probe force microscopy under ambient conditions

Kelvin probe force microscopy (KPFM) is a technique derived from atomic force microscopy that provides maps of surface potential or work function differences across material systems, with nanometre-scale resolution. KPFM is a useful tool for investigating electrical phenomena such as dipole orientation, interfacial charge transfer, charge accumulation, band bending and doping levels. This Primer aims to provide an overview of typical ambient-condition KPFM measurements, covering their underlying principles, experimental implementations and wide-ranging applications. Key KPFM variants, including amplitude and frequency modulation, heterodyne detection schemes and innovative open loop and pulsed force techniques, are discussed, with practical guidance on optimizing signal acquisition and reducing errors. Specialized approaches, such as time-resolved KPFM and multimodal KPFM, are discussed for their ability to capture dynamic charge processes and chemical information, respectively. Here, we highlight recent advances in KPFM applications, spanning metal alloys, soft matter, ferroelectrics, photovoltaics and 2D materials, showcasing its versatility across research domains. By addressing current limitations and identifying future opportunities, this Primer underscores the transformative potential of KPFM in advancing the understanding of nanoscale electrical phenomena.

Zahmatkeshsaredorahi, Amirhossein [Lehigh Univ., B↗

Low-temperature trapping of N 2 reduction reaction intermediates in nitrogenase MoFe protein–CdS quantum dot complexes

The biological reduction of N 2 to ammonia requires the ATP-dependent, sequential delivery of electrons from the Fe protein to the MoFe protein of nitrogenase. It has been demonstrated that CdS nanocrystals can replace the Fe protein to deliver photoexcited electrons to the MoFe protein. Herein, light-activated electron delivery within the CdS:MoFe protein complex was achieved in the frozen state, revealing that all the electron paramagnetic resonance (EPR) active E-state intermediates in the catalytic cycle can be trapped and characterized by EPR spectroscopy. Prior to illumination, the CdS:MoFe protein complex EPR spectrum was composed of a S = 3/2 rhombic signal (g = 4.33, 3.63, and 2.01) consistent with the FeMo-cofactor in the resting state, E 0 . Illumination for sequential 1-h periods at 233 K under 1 atm of N 2 led to a cumulative attenuation of E 0 by 75%. This coincided with the appearance of S = 3/2 and S = 1/2 signals assigned to two-electron (E 2 ) and four-electron (E 4 ) reduced states of the FeMo-cofactor, together with additional S = 1/2 signals consistent with the formation of E 6 and E 8 states. Simulations of EPR spectra allowed quantification of the different E-state populations, along with mapping of these populations onto the Lowe–Thorneley kinetic scheme. The outcome of this work demonstrates that the photochemical delivery of electrons to the MoFe protein can be used to populate all of the EPR active E-state intermediates of the nitrogenase MoFe protein cycle.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Genetic mapping and prediction of flowering time and plant height in a maize Stiff Stalk MAGIC population

Abstract The Stiff Stalk heterotic pool is a foundation of US maize seed parent germplasm and has been heavily utilized by both public and private maize breeders since its inception in the 1930s. Flowering time and plant height are critical characteristics for both inbred parents and their test crossed hybrid progeny. To study these traits, a 6-parent multiparent advanced generation intercross population was developed including maize inbred lines B73, B84, PHB47 (B37 type), LH145 (B14 type), PHJ40 (novel early Stiff Stalk), and NKH8431 (B73/B14 type). A set of 779 doubled haploid lines were evaluated for flowering time and plant height in 2 field replicates in 2016 and 2017, and a subset of 689 and 561 doubled haploid lines were crossed to 2 testers, respectively, and evaluated as hybrids in 2 locations in 2018 and 2019 using an incomplete block design. Markers were derived from a practical haplotype graph built from the founder whole genome assemblies and genotype-by-sequencing and exome capture-based sequencing of the population. Genetic mapping utilizing an update to R/qtl2 revealed differing profiles of significant loci for both traits between 635 of the DH lines and 2 sets of 570 and 471 derived hybrids. Genomic prediction was used to test the feasibility of predicting hybrid phenotypes based on the per se data. Predictive abilities were highest on direct models trained using the data they would predict (0.55–0.63), and indirect models trained using per se data to predict hybrid traits had slightly lower predictive abilities (0.49–0.55). Overall, this finding is consistent with the overlapping and nonoverlapping significant quantitative trait loci found within the per se and hybrid populations and suggests that selections for phenology traits can be made effectively on doubled haploid lines before hybrid data is available.

Genetics & Heredity↗

Magnetic field induced partially polarized chiral spin liquid in a transition metal dichalcogenide moiré system

As one of the most intriguing states of matter, the chiral spin liquid (CSL) has attracted much scientific interest while its existence and mechanism in crystalline strongly correlated systems remain hotly debated. On the other hand, strong correlation driven emergent phenomena can be realized in twisted transition metal dichalcogenide bilayers with a tremendously tunable large length scale providing a new platform for the emergence of CSLs. Here, we focus on a strongly correlated model relevant to heterobilayer WSe 2 /MoSe 2 and investigate the Mott insulating phase at half filling under an out-of-plane magnetic field. Considering both its orbital and spin Zeeman effects we identify three conventionally ordered phases including a 120° Néel phase, a stripe phase, and an up-up-down phase. For intermediate fields an emergent quantum spin liquid phase is identified with partial spin polarization. We further characterize its topological nature as the v = 1/2 Laughlin CSL through the topological entanglement spectrum and quantized spin pumping under spin flux insertion. In addition, we map out the quantum phase diagram for different twisted angles in an experimentally accessible parameter regime.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Investigating the clinico-anatomical dissociation in the behavioral variant of Alzheimer disease

We previously found temporoparietal-predominant atrophy patterns in the behavioral variant of Alzheimer’s disease (bvAD), with relative sparing of frontal regions. Here, we aimed to understand the clinico-anatomical dissociation in bvAD based on alternative neuroimaging markers. We retrospectively included 150 participants, including 29 bvAD, 28 “typical” amnestic-predominant AD (tAD), 28 behavioral variant of frontotemporal dementia (bvFTD), and 65 cognitively normal participants. Patients with bvAD were compared with other diagnostic groups on glucose metabolism and metabolic connectivity measured by [ 18 F]FDG-PET, and on subcortical gray matter and white matter hyperintensity (WMH) volumes measured by MRI. A receiver-operating-characteristic-analysis was performed to determine the neuroimaging measures with highest diagnostic accuracy. bvAD and tAD showed predominant temporoparietal hypometabolism compared to controls, and did not differ in direct contrasts. However, overlaying statistical maps from contrasts between patients and controls revealed broader frontoinsular hypometabolism in bvAD than tAD, partially overlapping with bvFTD. bvAD showed greater anterior default mode network (DMN) involvement than tAD, mimicking bvFTD, and reduced connectivity of the posterior cingulate cortex with prefrontal regions. Analyses of WMH and subcortical volume showed closer resemblance of bvAD to tAD than to bvFTD, and larger amygdalar volumes in bvAD than tAD respectively. The top-3 discriminators for bvAD vs. bvFTD were FDG posterior-DMN-ratios (bvAD bvFTD, area under the curve [AUC] range 0.85–0.91, all p < 0.001). The top-3 for bvAD vs. tAD were amygdalar volume (bvAD>tAD), MRI anterior-DMN-ratios (bvAD<tAD), FDG anterior-DMN-ratios (bvAD<tAD, AUC range 0.71–0.84, all p < 0.05). Subtle frontoinsular hypometabolism and anterior DMN involvement may underlie the prominent behavioral phenotype in bvAD.

59 BASIC BIOLOGICAL SCIENCES↗

Deep Neural Network Algorithm for CMC Microstructure Characterization and Variability Quantification

Microstructure characterization and variability quantification are crucial for understanding ceramic matrix composites (CMCs) mechanical behavior and deformation mechanisms across length scales. Traditionally, analyses of the micrographs obtained from microscopy are labor-intensive. However, with the vast improvement in computer vision (CV) and deep learning (DL), an automated algorithm can be designed to extract essential microstructure variability from micrographs which can then be used to construct a statistically representative volume element (SRVE). The DL-based algorithm spans the taxonomy of microstructure analyses, including semantic segmentation of microstructure constituents, secondary phases, matrix/fiber interface, and defects, and quantifying the microstructure variability in terms of probability distributions. In this work, C/SiNC and SiC/SiNC CMCs microstructures are semantically segmented through a deep convolutional neural network, followed by variability quantification through the implementation of a fully connected regression layer, hence forming a deep regression network. The deep regression network operates in a feedforward regime, in which the neuron output signal traverses through the network in a unidirectional manner. The weight tensor associated with each layer is updated through a backpropagation stochastic gradient descent approach. The input gray-scale image obtained through in-house scanning electron microscope and confocal microscope micrographs is augmented through affine transformations to increase the training set size, which is then processed through four strided convolutional layers. This compresses the image resolution by half at each layer while increasing the image depth by applying different filters (image encoding). The class activation maps (CAMs) corresponding to the applied filters highlight the key architectural features and assist with the semantic segmentation of the microstructure.

Hamza, Mohamed H.↗

TNSL Overview

Thermal neutron scattering law (TNSL) data describe low-energy neutrons scattering off of bound materials, and can have a significant impact on modeling any system with slow neutrons, including nuclear reactors. Previous work to introduce TNSL data to neutron transport codes at LLNL focused on COG and TART [1], with the limitation that these codes require highly specialized data processing and formatting. We have recently increased efforts to process TNSL data with the central LLNL nuclear data processing code FUDGE, to be stored in the generalized nuclear database structure (GNDS) for use in any general transport code with the ability to read GNDS data. The first step in this effort is to verify that the TNSL processing with FUDGE yields results comparable to results obtained using the LANL nuclear data processing code NJOY. The next step is to verify the transport of thermal neutrons in Mercury (a Monte Carlo code) and Ardra (a deterministic code) against one another, as well as against the LANL Monte Carlo neutron transport code MCNP. This verification step has not been completed, due to a number of discrepancies between results obtained using differently processed data. There is ongoing effort to understand differences between FUDGE and NJOY. Finally, we map out our current capability to validate TNSL data against benchmark systems.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Assessing and mapping extreme wave height along the Gulf of Mexico coast

The effect of extreme waves on the coastal community includes inundation, loss of habitats, increasing shoreline erosion, and increasing risks to coastal infrastructures (e.g., ports, breakwaters, oil and gas platforms), important for supporting coastal resilience. The coastal communities along the US Gulf of Mexico are very low-lying, which makes the region particularly vulnerable to impacts of extreme waves generated by storm events. We propose assessing and mapping the risks from extreme waves for the Gulf of Mexico coast to support coastal resiliency planning. The risks will be assessed by computing n-year recurring wave height (e.g., 1, 5, 50, 100-year) using 32-year wave hindcast data and various extreme value analysis techniques including Peak- Over-Threshold and Annual Maxima method. The characteristics of the extreme waves, e.g., relations between the mean and extreme wave climates, directions associated with extreme waves, will be investigated. Hazard maps associated with extreme wave heights at different return periods will be generated to help planners identify potential risks and envision places that are less susceptible to future storm damage.

54 ENVIRONMENTAL SCIENCES↗

Phenology satellite experiment

The author has identified the following significant results. The detection of a phenological event (the Brown Wave-vegetation sensescence) for specific forest and crop types using ERTS-1 imagery is described. Data handling techniques including computer analysis and photointerpretation procedures are explained. Computer analysis of multspectral scanner digital tapes in all bands was used to give the relative changes of spectral reflectance with time of forests and specified crops. These data were obtained for a number of the twenty-four sites located within four north-south corridors across the United States. Analysis of ground observation photography and ERTS-1 imagery for sites in the Appalachian Corridor and Mississippi Valley Corridor indicates that the recession of vegetation development can be detected very well. Tentative conclusions are that specific phenological events such as crop maturity or leaf fall can be mapped for specific sites and possible for different regions. Preliminary analysis based on a number of samples in mixed deciduous hardwood stands indicates that as senescence proceeds both the rate of change and differences in color among species can be detected. The results to data show the feasibility of the development and refinement of phenoclimatic models.

Dethier, B. E.↗

To evaluate ERTS-1 data for usefulness as a geological sensor in the diverse geological terraines of New York State

The author has identified the following significant results. Linear anomalies dominate the new geological information derived from ERTS-1 imagery, total lengths now exceeding 6000 kms. Experimentation with a variety of viewing techniques suggests that conventional photogeologic analyses of band 7 results in the location of more than 97 percent of all linears found. Bedrock lithologic types are distinguishable only where they are topographically expressed or govern land use signatures. The maxima on rose diagrams for ERTS-1 anomalies correspond well with those for mapped faults and topographic lineaments, despite a difference in relative magnitudes of maxima thought due to solar illumination direction. A multiscale analysis of linears showed that single topographic linears at 1:2,500,000 became dashed jugate linears at 1:500,000, and shorter linears lacking any conspicuous zonal alignment at 1:250,000. Most circular features found were explained away by U-2 airphoto analysis but several remain as anomalies. Visible glacial features include individual drumlins, best seen in winter imagery, drumlinoids, eskers, ice-marginal drainage channels, glacial lake shorelines and sand plains, and end moraines.

Isachsen, Y. W.↗