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At least 1,099 records · Page 61

Mass Spectrometry-Based Approaches for Clinical Biomarker Discovery in Traumatic Brain Injury

Purpose of Review: Precision treatments to address the multifaceted pathophysiology of traumatic brain injury (TBI) are desperately needed, which has led to the intense study of fluid-based protein biomarkers in TBI. Mass Spectrometry (MS) is increasingly being applied to biomarker discovery and quantification in neurological disease to explore the proteome, allowing for more flexibility in biomarker discovery than commonly encountered antibody-based assays. In this narrative review, we will provide specific examples of how MS technology has advanced translational research in traumatic brain injury (TBI) focusing on clinical studies, and looking ahead to promising emerging applications of MS to the field of Neurocritical Care. Recent Findings: Proteomic biomarker discovery using MS technology in human subjects has included the full range of injury severity in TBI, though critically ill patients can offer more options to biofluids given the need for invasive monitoring. Blood, urine, cerebrospinal fluid, brain specimens, and cerebral extracellular fluid have all been sources for analysis. Emerging evidence suggests there are distinct proteomic profiles in radiographic TBI subtypes, and that biomarkers may be used to distinguish patients sustaining TBI from healthy controls. Metabolomics may offer a window into the perturbations of ongoing cerebral insults in critically ill patients after severe TBI. Summary: Emerging MS technologies may offer biomarker discovery and validation opportunities not afforded by conventional means due to its ability to handle the complexities associated with the proteome. In conclusion, while MS techniques are relatively early in development in the neurosciences space, the potential applications to TBI and neurocritical care are likely to accelerate in the coming decade.

59 BASIC BIOLOGICAL SCIENCES↗

Recent advancements in the genetic engineering of microalgae

The development of more sustainable food, feed, and bio-products is critical to mitigating the environmental stresses facing our world today. Algae, which includes seaweeds, eukaryotic microalgae, and cyanobacteria, are a promising platform to achieving this, as they have low energy and space requirements, are safe for human and animal consumption, and can be manipulated to produce a diversity of valuable bioproducts. This review focuses on microalgae, both eukaryotic and cyanobacteria. In the past, addressing the major challenges of bringing microalgal production systems to an economically viable scale only had a relatively small genetic toolset to work with, in comparison to other microbial systems such as bacteria and yeast. Expanding the molecular tools available for genetic engineering of microalgae will lead to higher product yields, and accelerate the development of new microalgal bioproducts for commercial applications, thereby supporting the shift towards more environmentally friendly products. In this review, we highlight significant advances from recent years on the design of microalgal expression vectors, discovery of genetic regulatory elements (promoters and transcription factors), optimization of transformation methods, and development of new strain improvement techniques, all aimed at advancing microalgae to become a more efficient biomanufacturing platform. We then discuss how these tools have been applied to improving recombinant protein production, and to enhance metabolic pathway engineering.

09 BIOMASS FUELS↗

Simulating low-energy neutrino interactions with MARLEY

Monte Carlo event generators are a critical tool for the interpretation of data obtained by neutrino experiments. Several modern event generators are available which are well-suited to the GeV energy scale used in studies of accelerator neutrinos. However, theoretical modeling differences make their immediate application to lower energies difficult. In this paper, I present a new event generator, MARLEY, which is designed to better address the simulation needs of the low-energy (tens of MeV and below) neutrino community. The code is written in C++14 with an optional interface to the popular ROOT data analysis framework. The current release of MARLEY (version 1.2.0) emphasizes simulations of the reaction 40 Ar ( ν e , e − ) 40 K ⁎ but is extensible to other channels with suitable user input. This paper provides detailed documentation of MARLEY's implementation and usage, including guidance on how generated events may be analyzed and how MARLEY may be interfaced with external codes such as Geant4. Further information about MARLEY is available on the official website at http://www.marleygen.org. Program title:MARLEY 1.2.0 CPC Library link to program files:https://doi.org/10.17632/4v7zxnc8j3.1 Developer's respository link:http://github.com/MARLEY-MC/marley Code Ocean capsule:https://codeocean.com/capsule/9868179 Licensing provisions: GNU General Public License 3.0 Programming language: C++14 External routines/libraries used: GNU Scientific Library [1,2] (required), ROOT [3,4] (optional) Nature of problem: Simulation of neutrino-nucleus scattering events at energies of tens-of-MeV and below Solution method: Initial two-to-two scattering kinematics are sampled using the allowed approximation differential cross section and tables of precomputed nuclear matrix elements. Subsequent de-excitations of the remnant nucleus are simulated using a Monte Carlo implementation of the Hauser-Feshbach statistical model and tabulated γ-ray decay schemes for discrete nuclear levels. Additional comments including restrictions and unusual features: Input data are provided with the code that are suitable for producing simulations of the charged-current reaction 40 Ar ( ν e , e − ) 40 K ⁎ , coherent elastic neutrino-nucleus scattering on spin-zero target nuclei, and neutrino-electron elastic scattering on any atomic target. Preparation of new reaction input files (whose format is documented in Appendix B) would enable other reaction channels and nuclear targets to be handled by the existing code framework. Although there is no maximum neutrino energy enforced by the code itself, realistic neutrino-nucleus scattering events may be generated up to roughly 50 MeV. Above this energy, the effects of forbidden nuclear transitions, which are neglected in the current treatment of the cross sections (see section 2.1), become increasingly important.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Finding inputs that trigger floating-point exceptions in heterogeneous computing via Bayesian optimization

Testing code for floating-point exceptions is crucial as exceptions can quickly propagate and produce unreliable numerical answers. The state-of-the-art to test for floating-point exceptions in heterogeneous systems is quite limited and solutions require the application’s source code, which precludes their use in accelerated libraries where the source is not publicly available. We present an approach to find inputs that trigger floating-point exceptions in black-box CPU or GPU functions, i.e., functions where the source code and information about input bounds are unavailable. Our approach is the first to use Bayesian optimization (BO) to identify such inputs and uses novel strategies to overcome the challenges that arise in applying BO to this problem. Here, we implement our approach in the XSCOPE framework and demonstrate it on 58 functions from the CUDA Math Library and 81 functions from the Intel Math Library. XSCOPE is able to identify inputs that trigger exceptions in about 73% of the tested functions.

97 MATHEMATICS AND COMPUTING↗

Ion-Exchange Membrane-Centric Durability Testing and Degradation Characterization for Industry-Relevant CO 2 Reduction

Electrochemical CO 2 reduction is a promising conversion process for producing value-added fuels and chemicals from electricity and CO 2 as a sustainable carbon feedstock to domestically produce fuels and chemicals from industrial waste. Having reached industrially viable performance metrics with small-scale CO 2 electrolysis cells, the field must now increasingly focus on extending the device durability of large stacks to achieve equivalent metrics for 35,000+ hours to decrease maintenance and capital costs. Reported device lifetimes have increased in recent years, with the longest stability studies for CO, ethylene, and formic acid production being published in 2024–2025 with operation times of 4500, 1000, and 5200 h, respectively. Unfortunately, significant extension of the device durability is still required. Here, we provide an overview of ion-exchange membranes (IEMs) and provide insight into the variety of degradation mechanisms that must be overcome to enable the community to meet durability targets. In an effort to accelerate the extension of device lifetimes, we propose a general approach for characterizing CO 2 electrolysis cell degradation before and after durability testing to better elucidate the mechanisms and failure modes of IEMs in zero-gap cells. Furthermore, we encourage the adoption of operando characterizations in tandem with accelerated stress and durability tests, postulating that their combined applications will be increasingly valuable. We hope that this perspective motivates future durability studies to evaluate degradation across the entire electrolysis cell.

09 BIOMASS FUELS↗

Ultranarrow electroluminescence from magnetic excitons in the van der Waals antiferromagnetic semiconductor NiPS 3

Electrically driven light emission from two-dimensional (2D) semiconducting materials has enabled numerous optoelectronic technologies, including light-emitting diodes, solid-state lasers, and single-photon sources for quantum communication. Here we report ultranarrow electroluminescence from the magnetic excitonic state of the van der Waals antiferromagnetic semiconductor NiPS 3 . This electroluminescence is enabled by the fabrication of gate-tunable NiPS 3 devices that remain electrically conductive below the antiferromagnetic ordering temperature of 155 K, ultimately allowing field-effect mobilities of 1.3 cm 2 V –1 s –1 and 4.5 cm 2 V –1 s –1 to be directly measured at room temperature and 7 K, respectively. By applying a high-frequency square wave voltage to the gate electrode of the resulting field-effect transistors, electroluminescence is capacitively induced from the magnetic excitons of NiPS 3 . Due to the coupling of these excitons with the underlying NiPS 3 antiferromagnetic order, the electroluminescence has an ultranarrow linewidth of 1 meV and a high degree of linear polarization (ρ = 0.78). In addition to facilitating fundamental studies of the coupling between spin states and excitons in van der Waals magnetic semiconductors, this work will accelerate the development of emerging 2D opto-spintronic applications.

two-dimensional materials↗

Attosecond inner-shell lasing at ångström wavelengths

Since the invention of the laser, nonlinear effects such as filamentation, Rabi cycling and collective emission have been explored in the optical regime, leading to a wide range of scientific and industrial applications. X-ray free-electron lasers (XFELs) have extended many optical techniques to X-rays for their advantages of ångström-scale spatial resolution and elemental specificity. An example is XFEL-driven inner-shell Kα 1 (2p 3/2 → 1s 1/2 ) X-ray lasing in elements ranging from neon to copper, which has been used for nonlinear spectroscopy and development of new X-ray laser sources. Here, in this study, we show that strong lasing effects similar to those in the optical regime can occur at 1.5–2.1 Å wavelengths during high-intensity (>10 19 W cm −2 ) XFEL-driven Kα 1 lasing of copper and manganese. Depending on the temporal XFEL pump pulse substructure, the resulting X-ray pulses (about 10 6 −10 8 photons) can exhibit strong spatial inhomogeneities and spectral splitting, inhomogeneities and broadening. Three-dimensional Maxwell–Bloch calculations show that the observed spatial inhomogeneities result from X-ray filamentation and that the broad spectral features are driven by sub-femtosecond Rabi cycling. Our simulations indicate that these X-ray pulses can have pulse lengths of less than 100 attoseconds and coherence properties that provide opportunities for quantum X-ray optics applications.

47 OTHER INSTRUMENTATION↗

Weak baselines and reporting biases lead to overoptimism in machine learning for fluid-related partial differential equations

One of the most promising applications of machine learning in computational physics is to accelerate the solution of partial differential equations (PDEs). The key objective of machine-learning-based PDE solvers is to output a sufficiently accurate solution faster than standard numerical methods, which are used as a baseline comparison. Here, we first perform a systematic review of the ML-for-PDE-solving literature. Out of all of the articles that report using ML to solve a fluid-related PDE and claim to outperform a standard numerical method, we determine that 79% (60/76) make a comparison with a weak baseline. Second, we find evidence that reporting biases are widespread, especially outcome reporting and publication biases. We conclude that ML-for-PDE-solving research is overoptimistic: weak baselines lead to overly positive results, while reporting biases lead to under-reporting of negative results. To a large extent, these issues seem to be caused by factors similar to those of past reproducibility crises: researcher degrees of freedom and a bias towards positive results. We call for bottom-up cultural changes to minimize biased reporting as well as top-down structural reforms to reduce perverse incentives for doing so.

97 MATHEMATICS AND COMPUTING↗

Cardinal: A Lower-Length-Scale Multiphysics Simulator for Pebble-Bed Reactors

This paper demonstrates a multiphysics solver for pebble-bed reactors, in particular, for Berkeley’s pebble-bed -fluoride-salt-cooled high-temperature reactor (PB-FHR) (Mark I design). The FHR is a class of advanced nuclear reactors that combines the robust coated particle fuel form from high-temperature gas-cooled reactors, the direct reactor auxiliary cooling system passive decay removal of liquid-metal fast reactors, and the transparent, high-volumetric heat capacitance liquid-fluoride salt working fluids (e.g., FLiBe) from molten salt reactors. This fuel and coolant combination enables FHRs to operate in a high-temperature, low-pressure design space that has beneficial safety and economic implications. The PB-FHR relies on a pebble-bed approach, and pebble-bed reactors are, in a sense, the poster child for multiscale analysis. Relying heavily on the MultiApp capability of the Multiphysics Object-Oriented Simulation Environment (MOOSE), we have developed Cardinal, a new platform for lower-length-scale simulation of pebble-bed cores. The lower-length-scale simulator comprises three physics: neutronics (OpenMC), thermal fluids (Nek5000/NekRS), and fuel performance (BISON). Cardinal tightly couples all three physics and leverages advances in MOOSE, such as the MultiApp system and the concept of MOOSE-wrapped applications. Moreover, Cardinal can utilize graphics processing units for accelerating solutions. In this paper, we discuss the development of Cardinal and the verification and validation and demonstration simulations.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Secondary electron emission for reticulated carbon foam surfaces using direct measurements and spectroscopic analysis

This study investigates secondary electron emission (SEE) characteristics of reticulated foams using direct measurements and analytical modeling. Total SEE was quantified, revealing suppression of up to 44% in carbon foam structures compared to planar graphite surfaces. An optimal geometric configuration was identified and supported by analytical models. SEE angular dependence experiments showed diverse behaviors: fiber-like behavior and directional dependence for pore and ligaments on the mm scale, with fuzz-like characteristics when the foam features are between 10–100 µm. Electron energy analyzer measurements showed that carbon foams preferentially suppress inelastic backscattered electrons (BSEs) more so than true secondary electrons (SEs). The analysis indicated a larger fraction of low-energy SE generation in foams compared to flat surfaces due to increased emission from curved fiber ligaments and tertiary SEs from high-energy BSEs. These findings have implications for design and optimization of materials with tailored electron emission properties for applications like plasma-facing components, spacecraft materials, and accelerator surfaces.

Auger↗

Measurement of directional muon beams generated at the Berkeley Lab Laser Accelerator

We present the detection of directional muon beams produced using a PW laser facility at the Lawrence Berkeley National Laboratory. The muon source is a multi-GeV electron beam generated in a laser-plasma accelerator interacting with a high- converter target. The GeV photons resulting from the interaction are converted into a high-flux, directional muon beam via pair production. By employing scintillators to capture delayed events, we were able to identify the produced muons and characterize the source. Using theoretical knowledge of the muon production process combined with simulations that are in excellent agreement with the experiments, we demonstrate that laser-plasma accelerators have the capability of generating electron beams with characteristics suitable to produce GeV-scale muons that offer unique advantages with respect to the cosmic background. Laser-plasma-accelerator-based muon sources can therefore enhance muon imaging applications thanks to their compactness, directionality, and high yields, which reduce the exposure time by orders of magnitude compared to cosmic ray muons. Using the eant4-based simulation code we developed to gain insight into the experimental results, we can design future experiments and applications based on LPA-generated muons.

Terzani, Davide↗

Secondary neutron production from thick target deuteron breakup

Thick target deuteron breakup is a variable-energy accelerator-based source of high-energy neutrons, with applications in fundamental and applied nuclear science and engineering. However, the breakup mechanism remains poorly understood, and data on neutron yields from thick target breakup remain relatively scarce. In this work, the double-differential neutron yields from deuteron breakup have been measured on a thick beryllium target at ϵ d = 33 and 40 MeV, using both time-of-flight and activation techniques. We have also introduced a simple hybrid model for the double-differential deuteron breakup cross section, applicable in the ϵ d = 10-100 MeV energy range on light (Z ≤ 6) targets. This model features four empirical parameters that have been fit to reproduce experimental breakup measurements on beryllium targets, using the method of least squares. It was shown that these parameters extrapolate well to higher energies, and to other low-Z target materials. Here, we also include optimization of the parameters that modify the Kalbach systematics for compound and preequilibrium reactions, in order to better reproduce the experimental data for beryllium targets at large angles.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

End-to-End Workflow for Machine-Learning-Based Qubit Readout With QICK and hls4ml

In this article, we present an end-to-end workflow for superconducting qubit readout that embeds codesigned neural networks into the quantum instrumentation control kit (QICK). Capitalizing on the custom firmware and software of the QICK platform, which is built on Xilinx radiofrequency system-on-chip field-programmable gate arrays (FPGAs), we aim to leverage machine learning (ML) to address critical challenges in qubit readout accuracy and scalability. The workflow utilizes the hls4ml package and employs quantization-aware training to translate ML models into hardware-efficient FPGA implementations via user-friendly Python application programming interfaces. We experimentally demonstrate the design, optimization, and integration of an ML algorithm for single transmon qubit readout, achieving 96% single-shot fidelity with a latency of 32.25 ns and less than 16% FPGA lookup table resource utilization. Our results offer the community an accessible workflow to advance ML-driven readout and adaptive control in quantum information processing applications.

42 ENGINEERING↗

Knocking out barriers to engineered cell activity

Engineered T cell therapies are revolutionizing cancer treatment by achieving long-lasting remission in blood-related cancers, such as leukemia and lymphoma. These therapies involve removal of patient T cells, “reprogramming” them to attack cancer cells, and then transferring them back into the patient. Targeted gene inactivation (knockout) using CRISPR-Cas9 can enhance T cell activity (1, 2) and has the potential to expand cell therapy applications. Until now, it has been unknown whether CRISPR-Cas9–edited T cells would be tolerated and thrive once reinfused into a human. On page 1001 of this issue, Stadtmauer et al. (3) present data from a phase 1 clinical trial (designed to test safety and feasibility) on the first cancer patients treated with CRISPR-Cas9–modified T cells. The findings represent an important advance in the therapeutic application of gene editing and highlight the potential to accelerate development of cell-based therapies.

60 APPLIED LIFE SCIENCES↗

Process Optimization and Modeling for Minerals Sustainability (PrOMMiS) v1.0.0

The U.S. Department of Energy's ("DOE") Process Optimization and Modeling for Minerals Sustainability project ("PrOMMiS Project") was initiated in 2023 to transform the national Critical Minerals and Rare Earth Elements (CM & REE) landscape, thereby supporting DOE's three enduring strategic objectives: security, economic competitiveness, and environmental responsibility. To address this initiative, the PrOMMiS Project will develop, demonstrate, and deploy an open-source, advanced system modeling, optimization, and analysis application ("PrOMMiS Software Application") that will support industry decision-makers by accelerating the scale-up of novel CM & REE technologies by de-risking the development and deployment of commercial scale processes and maximizing learning throughout the development cycle.

Beattie, KeithS [Lawrence Berkeley National Labora↗

Flutter

The following repositories are a set of libraries that are needed for applications that are being developed for users of the Accelerator control system. The programming language used is Dart and for the user interface use the Flutter framework. URL for code repositories: - https://github.com/fermi-ad/flutter-controls-core - https://github.com/fermi-ad/flutter-controls-plotting - https://github.com/fermi-ad/flutter-controls-auth - https://github.com/fermi-ad/flutter-gql-acsys - https://github.com/fermi-ad/flutter-gql-faas - https://github.com/fermi-ad/dart-gql-acsys - https://github.com/fermi-ad/dart-explicit-imports - https://github.com/fermi-ad/dart-gql-faas - https://github.com/fermi-ad/design-system

Neswold, Rich [Fermi National Accelerator Laborato↗

Pulse duration dependent effects of ultrafast laser induced damage on a 1030 nm multi-layer dielectric mirror for high repetition rate, high average power laser systems

High repetition rate, high peak, and average power laser systems are crucial for next-generation particle accelerators, inertial confinement fusion, and secondary particle sources. These applications demand durable laser optics, particularly interference coatings on optics lasting millions of shots at high fluence. This study focuses on designing, testing, and simulating multi-layer dielectric (MLD) mirrors for pulse durations of 260 fs, 77 fs, and 25 fs at 1030 nm wavelength and 45-degree incidence angle with p -polarization. S-on-1 laser-induced damage thresholds (LIDT) for varying pulse numbers were determined, with single-shot LIDT values of 0.98 Jcm -2 , 1.63 Jcm -2 , and 2.3 Jcm -2 for 25 fs, 77 fs, and 260 fs respectively. A strong correlation between blister shape and local fluence was observed, implying that the layer expansion in a blister depends on local fluence. We have also examined mechanisms responsible for laser-induced stress generation and energy release rates in blister formation. Damage mechanisms are further explored by finite-difference time-domain (FDTD) simulations, incorporating Keldysh strong field ionization, whose predictions were in excellent agreement with the onset of damage determined experimentally. These findings offer insights for enhancing MLD coating technology, promising more efficient and resilient laser systems for diverse scientific and industrial applications.

Noor, Mohamed Yaseen (ORCID:000000021036644X)↗

Multiphysics Simulation of the Thermal Response of a Nanofibrous Target in a High-Intensity Beam

Nanofibrous structures are of high interest to the fields of engineering and materials science, and investigation of their properties as well as discovery of novel applications for them both constitute lively areas of research. A very promising application of nanofiber mats lies in the field of accelerator technology: beam targets made from nanofiber mats offer a solution to the problem of advancing the "intensity frontier"–-the limit on the beam intensities that can be realized in fixed target experiments and neutrino production facilities. However, testing has shown that the survivability of these nanofiber targets depends strongly on their manufacturing parameters, such as the packing density of fibers. In this work, we will use multiphysics simulations to perform a thermal study on how nanofiber targets react to high intensity beams, so that the dependency of the targets’ lifetime on their construction parameters can be better understood.

43 PARTICLE ACCELERATORS↗