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At least 1,297 records · Page 72

The evolution of analytical techniques for multiplex analysis of protein biomarkers

Introduction: The landscape of biomarker development has evolved with advanced analytical technologies, particularly affinity- and mass spectrometry-based techniques. These advancements have deepened our understanding of disease mechanisms, enabling the development of precise diagnostic tools and personalized medicine. Protein biomarkers, which play pivotal roles in biological processes, have become invaluable in diagnosing and monitoring diseases, aided by their presence in various biological samples and the availability of established detection methods. Areas covered: This review covers the role of protein biomarkers in clinical practice, the development and dimensionality of protein biomarkers, advancements in detection technologies, a comparison of these technologies, and future directions in biomarker discovery and disease mechanism elucidation. Expert opinion: Advances in biomarker technologies have the potential to transform diagnostics and personalized treatment but face challenges such as high costs and technical complexity. Enhancing reproducibility and integrating multi-omics approaches may offer better insights. In conclusion, the field should evolve toward high-throughput, automated methods, continuously adapting research, and clinical practices.

59 BASIC BIOLOGICAL SCIENCES↗

Autonomous x-ray scattering

Autonomous experimentation (AE) is an emerging paradigm that seeks to automate the entire workflow of an experiment, including—crucially—the decision-making step. Beyond mere automation and efficiency, AE aims to liberate scientists to tackle more challenging and complex problems. We describe our recent progress in the application of this concept at synchrotron x-ray scattering beamlines. We automate the measurement instrument, data analysis, and decision-making, and couple them into an autonomous loop. We exploit Gaussian process modeling to compute a surrogate model and associated uncertainty for the experimental problem, and define an objective function exploiting these. We provide example applications of AE to x-ray scattering, including imaging of samples, exploration of physical spaces through combinatorial methods, and coupling to in situ processing platforms These uses demonstrate how autonomous x-ray scattering can enhance efficiency, and discover new materials.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Unsupervised atomic data mining via multi-kernel graph autoencoders for machine learning force fields

Constructing a chemically diverse dataset while avoiding sampling bias is critical to training efficient and generalizable force fields. However, in computational chemistry and materials science, many common dataset generation techniques are prone to oversampling regions of the potential energy surface. Furthermore, these regions can be difficult to identify and isolate from each other or may not align well with human intuition, making it challenging to systematically remove bias in the dataset. While traditional clustering and pruning (down-sampling) approaches can be useful for this, they can often lead to information loss or a failure to properly identify distinct regions of the potential energy surface due to difficulties associated with the high dimensionality of atomic descriptors. In this work, we introduce the Multi-kernel Edge Attention-based Graph Autoencoder (MEAGraph) model, an unsupervised approach for analyzing atomic datasets. MEAGraph combines multiple linear kernel transformations with attention-based message passing to capture geometric sensitivity and enable effective dataset pruning without relying on labels or extensive training. Demonstrated applications on niobium, tantalum, and iron datasets show that MEAGraph efficiently groups similar atomic environments, allowing for the use of basic pruning techniques for removing sampling bias. This approach provides an effective method for representation learning and clustering that can be used for data analysis, outlier detection, and dataset optimization.

Materials science↗

Discovery of a luminous starburst galaxy with hundreds of thousands of Wolf–Rayet stars

This paper reports the detection of a strong Wolf–Rayet (W-R) emission bump feature at 4400–4700 Å in the optical spectrum of a distant galaxy SDSS J150009.81+452844.4 at a redshift of 0.453. The estimated number of W-R stars is 1.5 × 10 5 without applying any internal extinction correction, and at least 4.5 × 10 5 after correcting for dust extinction. Such a number, though with uncertainties inherent from the extinction correction and others, appears to outnumber those in previous W-R galaxies after correcting for intrinsic dust extinction with the numbers available in the literature. These massive stars must have formed in an instantaneous star-forming episode lasting less than about 5 Myr. We estimate a star formation rate of at least ~80 $\mathrm{M}_{\odot }\, \mathrm{yr^{-1}}$, indicative of a violent starburst. Its mid-infrared spectrum resembles closely those of typical local ultraluminous infrared galaxies (ULIRGs). From optical to ultraviolet, it possesses a luminous blue continuum, indicating that the starburst is not heavily obscured, in contrast to that found in most ULIRGs. There is evidence for strong outflows based on the detection of systematically blue-shifted broad wings in the nebular emission lines (a bulk velocity -190 km s -1 ), as well as in the blue-shifted Mg ii absorption lines. The emission-line gases show a wide velocity range, from -1200 to ~-2000 km s -1 in blueshift to 570 km s -1 in redshift. We interpret this as a galactic fountain, of which part of the outflowing gas may be falling back to the galactic plane. Our method could be used to find a sample of similar objects, which would help understand the star formation history and stellar feedback in starburst galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗

SDSS-IV MaNGA: the chemical co-evolution of gas and stars in spiral galaxies

ABSTRACT We investigate archaeologically how the metallicity in both stellar and gaseous components of spiral galaxies of differing masses evolve with time, using data from the SDSS-IV MaNGA survey. For the stellar component, we can measure this evolution directly by decomposing the galaxy absorption-line spectra into populations of different ages and determining their metallicities. For the gaseous component, we can only measure the present-day metallicity directly from emission lines. However, there is a well-established relationship between gas metallicity, stellar mass, and star formation rate which does not evolve significantly with redshift; since the latter two quantities can be determined directly for any epoch from the decomposition of the absorption-line spectra, we can use this relationship to infer the variation in gas metallicity over cosmic time. Comparison of present-day values derived in this way with those obtained directly from the emission lines confirms the validity of the method. Application of this approach to a sample of 1619 spiral galaxies reveals how the metallicity of these systems has changed over the last 10 billion yr since cosmic noon. For lower-mass galaxies, both stellar and gaseous metallicity increase together, as one might expect in well-mixed fairly isolated systems. In higher-mass systems, the average stellar metallicity has not increased in step with the inferred gas metallicity, and actually decreases with time. Such disjoint behaviour is what one might expect if these more massive systems have accreted significant amounts of largely pristine gas over their lifetimes, and this material has not been well mixed into the galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗

Crystal structures and formation mechanisms of boron-rich tungsten borides

Boron-rich tungsten borides tend to adopt mechanically unfavorable layered structures but experimentally exhibit excellent mechanical properties rivalling traditional superhard solids. Unravelling the contraindicated structure-property relationship, however, has been impeded by their structural ambiguities because of the difficulty in probing boron and atomic deficiency of these borides. Here, we study crystal structures of boron-rich tungsten borides WB 3+x and WB 2+x by neutron diffraction based on high-quality samples prepared by a high-pressure method, leading to definitive structural resolutions for both borides with unique compositions of WB 5.14 and WB 2.34 . Combined with theoretical calculations, their structural stability is revealed to be closely related to atomic deficiency, which is governed by the valence-band filling with an optimal valence-electron concentration of ~10 per cell. The presence of interstitial boron trimers at the vacant W : 2b sites in WB 5.14 alters the crystal symmetry, making the Wyckoff 2d site more favorably occupied by W, rather than the 2c site, as previously misassigned. Here, the staggered planar boron layers and wrinkled boron bonding in WB 2.34 are identified to be crucial for stabilizing its structure. These findings unveil the longstanding structural mysteries of boron-rich tungsten borides and offer powerful insights for rational design of borides by defect chemistry.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Simulation of open quantum systems via low-depth convex unitary evolutions

Simulating physical systems on quantum devices is one of the most promising applications of quantum technology. Current quantum approaches to simulating open quantum systems are still practically challenging on NISQ-era devices, because they typically require ancilla qubits and extensive controlled sequences. In this work, we propose a hybrid quantum-classical approach for simulating a class of open system dynamics called random-unitary channels. These channels naturally decompose into a series of convex unitary evolutions, which can then be efficiently sampled and run as independent circuits. The method does not require deep ancilla frameworks and thus can be implemented with lower noise costs. We implement simulations of open quantum systems up to dozens of qubits and with large channel ranks. Published by the American Physical Society 2024

Peetz, Joseph (ORCID:0000000274458028)↗

Machine-learning-assisted automation of single-crystal neutron diffraction

Neutron scattering is a powerful but expensive technique to study materials and discover new matter. Advanced detector technology has significantly improved the efficiency of neutron experiments, increasing the complexity of neutron data reduction and analysis. Machine learning (ML) brings new directions for neutron diffraction data reduction and experiment operation. Here, this work presents an ML-assisted data reduction and analysis method for precise recognition of Bragg peaks and the corresponding regions of interest; it can then automatically screen and align a measured crystal using the recognized peaks, and subsequently plan and optimize the data collection with user-provided information and uncertainty quantification values of detected peaks. This method shows robust performance in different complex sample environments and enables automated single-crystal neutron diffraction.

47 OTHER INSTRUMENTATION↗

Nano-laminography with a transmission X-ray microscope

Nano-laminography combines the penetrating power of hard X-rays with a tilted rotational geometry to deliver high-resolution, three-dimensional images of laterally extended, flat specimens that are otherwise incompatible with, or difficult to image using, conventional nano-tomography. In this work, we demonstrate a full-field, X-ray nano-laminography system implemented with the transmission X-ray microscope at beamline 32-ID of the upgraded Advanced Photon Source at Argonne National Laboratory, USA. By rotating the sample around an axis inclined by 20° to the incident beam, the technique minimizes the long optical path lengths that would otherwise generate excessive artifacts when planar samples are imaged edge-on. The efficiency of the technique is demonstrated with 50 nm spatial resolution and minute-scale temporal resolution 3D imaging of a planar integrated circuit sample and targeted imaging of an individual particle within a powder sample, where mounting procedures are typically challenging in regular nano-tomography. The sample mounting strategy, data acquisition, and reconstruction method will also be discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Fault Detection Utilizing Convolution Neural Network on Timeseries Synchrophasor Data From Phasor Measurement Units

An end-to-end supervised learning method is proposed for fault detection in the electric grid using Big Data from multiple Phasor Measurement Units (PMUs). The approach consists of preprocessing steps aimed at reducing data noise and dimensionality, followed by utilization of six classification models considered for detecting faults. Three of the models were variants of Convolutional Neural Network (CNN) architectures that consider a single type of measurement (voltage, current or frequency) at all PMUs or all types together also at all PMUs. CNN based models were compared to traditional methods of Logistic Regression (LR), Multi-layer Perceptron (MLP) and Support Vector Machine (SVM). Evaluation was conducted on two-year data measured by PMUs at 37 locations in a large electric grid. Here, the response variable for classification were extracted from the grid-wide outage event log. Experiments show that CNN-based models outperformed traditional methods on one year out-of-sample outage detection over the entire grid.

42 ENGINEERING↗

Modeling thin layers of analytes on substrates for spectral analysis: use of solid/liquid n and k values to model reflectance spectra

Since solids are only sometimes seen en masse in a pure bulk form, and for liquids other than water almost never, a capability to model reflectance spectra from analytes deposited on various substrates would be highly advantageous. If available, the real, n ( ν ) , and imaginary, k ( ν ) , components of the complex refractive index, n n + i k , can be used to simulate infrared spectra, accounting for reflection, refraction, and absorption phenomena as a function of wavelength. We focus on using the Pacific Northwest National Laboratory (PNNL) derived n / k vectors for solid and liquid analytes deposited as thin layers on different types of substrates including conductors, such as aluminum, and inorganic dielectrics, such as glass. The model is an adaptation of the Monte Carlo ray trace modeling program, TracePro, extended through the use of its macrolanguage. The model is tested using thin films of organic liquids including silicone oil and no. 2 diesel fuel, as well as organic solids such as caffeine and acetaminophen on aluminum and glass. The predicted spectra for the solid films were compared to experimental hemispherical reflectance data measured using a Fourier transform spectrometer with an integrating sphere. The thickness of the calculated layer is a parameter for predicting the (transflectance) spectra and is obtained using the areal density measured from gravimetric methods to generate the thin-layer samples. Comparison of the calculated spectra with experimental hemispherical reflectance data shows excellent agreement, indicating promise for the use of measured n / k data to synthesize reference spectral data. In particular, accounting for the inhomogeneity of the deposits greatly improved the match with experimental data. Finally, the theoretical modeling shows that for thicker layers (ca. 20 to 100 μm) of typical organics possessing moderately strong k values, the longwave infrared features are often saturated and better spectral contrast is obtained from the overtone/combination bands in the shortwave infrared.

42 ENGINEERING↗

Monitoring the Caustic Dissolution of Aluminum Alloy in a Radiochemical Hot Cell Using Raman Spectroscopy

Chemical processing of highly radioactive materials commonly takes place in heavily shielded hot cells. The remote, real-time monitoring of chemical processing streams via optical spectroscopic techniques in hot cells may be particularly useful. Here in this paper, we describe the implementation of Raman spectroscopy and chemometric analysis to monitor the dissolution of aluminum-clad targets containing irradiated aluminum–neptunium oxide cermet pellets in caustic solutions in a hot cell environment. Partial least squares regression analysis was used to generate calibration models to quantify the concentration of dissolved aluminum, nitrate, and hydroxide in solutions within the radiochemical hot cell. This work explored a systematic approach to optimize a matrix of calibration standards using a D-optimal experimental design. The Design of Experiments-based regression model, in comparison to more traditional analytical approaches, was found to be the more practical method for building calibration models, with fewer samples, to obtain informative analytical data from Raman spectra.

36 MATERIALS SCIENCE↗

Rapid simulations of hyperspectral near-field images of three-dimensional heterogeneous surfaces – part II

The modeling of the near-field interaction in the scattering-type scanning near-field optical microscope (s-SNOM) is rapidly advancing, although an accurate yet versatile modeling framework that can be easily adapted to various complex situations is still lacking. In this work, we propose a time-efficient numerical scheme in the quasi-electrostatic limit to capture the tip-sample interaction in the near field. This method considers an extended tip geometry, which is a significant advantage compared to the previously reported method based on the point-dipole approximation. Using this formalism, we investigate, among others, nontrivial questions such as uniaxial and biaxial anisotropy in the near-field interaction, the relationship between various experimental parameters (e.g. tip radius, tapping amplitude, etc.), and the tip-dependent spatial resolution. The demonstrated method further sheds light on the understanding of the contrast mechanism in s-SNOM imaging and spectroscopy, while also representing a valuable platform for future quantitative analysis of the experimental observations.

Chen, Xinzhong (ORCID:0000000261033848)↗

Derivation of the Future Time Equation for Analog, Non-Multiplying Monte Carlo Simulation

The expected computational time required to simulate a particle from a point in phase space through a Monte Carlo history, termed the expected future time, is found by solving the Future Time Equation (FTE). The expected future time may be useful when generating variance reduction parameters for a Monte Carlo simulation with a method such as Consistent Adjoint Driven Importance Sampling (CADIS). This report presents a detailed derivation of the Future Time Probability Density Function (FTPDF) and FTE for neutral particle Monte Carlo transport to aid future researchers. For simplicity, this derivation only considers analog transport in non-multiplying media.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Progress report on analytic and numerical studies of x-ray-induced impulse

In a variety of high-energy-density (HED) systems, x-rays of a given energy are used to generate shockwaves, bulk motion, and impulse in materials. As radiation energy is deposited within the material, the material is heated. The number of photons of a certain wavelength absorbed is determined by the spectral intensity of the radiation and the material’s opacity evaluated at that wavelength. This heating results in a pressure increase dictated by the material’s equation of state. Depending on the intensity of the absorbed radiation, it may also cause the material to change phase into a liquid, gas, or plasma. The increased pressure drives the heated surface layer to blow off, imparting impulse and sending a compressive wave into the bulk of the material. Additionally, the compression wave interacts with the solid boundary of the material, resulting in a tensile wave that may cause the material to spall. The impulse generated by the deposition of x-ray energy within the sample can be modeled using purely analytical methods, e.g. the Bethe, Bade, Averell, and Yost (BBAY) model. However, the blow-off process is rather complicated, and proper modeling efforts must account for material ejected by spallation, vaporization, jetting, and plasma ablation. For this reason, analytical models have an unclosed term describing the final energy of the blown-off material Ef(z). Prior modeling efforts have arbitrarily fixed this at some value or modeled it using a limiting set of thermodynamic assumptions. The work we are currently performing uses validated simulations using sophisticated photon transport, equation of state, and strength models/data to provide a fit for Ef(z) that is useful for predictive calculation of impulse. We will apply our methodology and show results for different materials and x-ray sources. This work is particularly useful for the design of experiments studying x-ray impulse generation. The present report is outlined as follows. Section 1.2 describes a series of HED experiments investigating x-ray-generated impulse in materials. Section 1.3 describes the computational approach we employ in this study, and presents validation results against the aforementioned experiments. Section 1.4 introduces analytical models for impulse generation, as well as our method for utilizing impulse from simulations to close the models. We discuss the concept of impulse-spectrum sensitivity, it’s application to uncertainty quantification, and derive a very useful analytical expression for it in 1.5. We then summarize recent progress in this project and discuss future work in section 1.6.

36 MATERIALS SCIENCE↗

IER 557: Godiva Pulse Repeatability and Characterization (CED-3A Report)

Godiva IV is a fast burst critical assembly constructed of approximately 65 kg of highly enriched uranium (HEU) fuel alloyed with 1.5% molybdenum for strength. Godiva IV is proposed as the radiation source for IER 498: Design a Shielding Benchmark with a Metal Critical Source. IER 498 proposes a two-burst method to determine the performance of shielding samples, comparing the transmission of the source radiation to detectors with and without a shielding sample present. This eliminates the need for an absolute calibration and allows many uncertainties to cancel. However, the source term variability must be low compared to other sources of experimental uncertainty to ensure the overall uncertainty meets acceptable levels to provide useful measurements. The primary goal of this experiment is to quantify the source term variability, or reproducibility, of Godiva bursts, focusing on the 70 °C bursts planned for IER 498 measurements. Discussions during IER 498 noted that a number of bursts (on the order of six to ten) as identical as possible would be performed and that a 5-7% standard deviation in source intensity would be acceptable.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

National Opacity Program - Tri-Lab Assessment of Measurements and Models (Milestone 7720)

Opacity-on-NIF has obtained opacity data under conditions similar to those achieved by the entirely different Opacity-on-Z platform. From low- and high-Z elements at different anchor points, rigorously compare the opacity data between the laboratories and to multiple opacity theory models. Compare and assess the data acquisition and processing methods for obtaining opacities and for measuring/inferring sample conditions. Explain, or develop hypotheses for, any discrepancies. Map progress to the National Opacity Strategy and define future directions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Milestone 7720: National Opacity Program - Tri-Lab Assessment of Measurements and Models

Opacity-on-NIF has obtained opacity data under conditions similar to those achieved by the entirely different Opacity-on-Z platform. From low- and high-Z elements at different anchor points, rigorously compare the opacity data between the laboratories and to multiple opacity theory models. Compare and assess the data acquisition and processing methods for obtaining opacities and for measuring/inferring sample conditions. Explain, or develop hypotheses for, any discrepancies. Map progress to the National Opacity Strategy and define future directions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗