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At least 415 records · Page 23

The Human Phenotype Ontology in 2024: phenotypes around the world

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs.

59 BASIC BIOLOGICAL SCIENCES↗

Ion Channel Laser Based on Direct Laser Acceleration of a Shaped Beam Driver (Final Technical Report)

The main focus of our research was to understand the synergies between an electron bunch and a laser pulse when the two co-propagate through the plasma. We have clearly demonstrated using theoretical and computational modeling that the propagation distance of both the bunch and the laser pulse could be extended. The ability of the combined bunch/pulse system to extend the propagation distance and the size of the plasma bubble enables highly-efficient sources of relativistic electrons. As pointed out by the Plasma Decadal Study, such electron sources can be used for generating extremely bright x-rays for a variety of applications can serve as probes and diagnostics for other plasma experiments: high energy density (HED) sciences, inertial confinement fusion (ICF), and potentially Fusion Materials and Technology (FM&T). Development of advanced diagnostics of plasma-based accelerators is yet another key area identified by recent reports. Even broader security and medical applications of compact accelerator-based radiation sources, such as very high energy electron (VHEE) sources for FLASH radiobiology, have been identified by a recent multi-agency panel. A number of key technical issues were considered and successfully resolved during the course of the grant. Those include: beam loading effect of both the driver and witness bunches on the wake, laser channeling by the bunch, and the direct laser acceleration (DLA) of the driver bunch by the laser pulse. To demonstrate clear synergy, we were able to ascertain that the total energy gain of a witness bunch in the wake of the combined bunch/laser complex is large than the sum of the energy gains in the wake of the laser pulse alone, and the driver bunch alone. We have also demonstrated that not only the energy gain is improved, but the energy spread is not sacrificed. To carry out these simulations, we have to develop a range of in-house computational tools, including a fully-3D code WAND-PIC.

43 PARTICLE ACCELERATORS↗

Development of spatially and temporally resolved electron density measurements for the assessment of radiation hydrodynamics simulations of laboratory X-ray photoionized plasmas

The photoionized plasma gas cell experiment is an established platform we use to make at-parameter (ξ > > 1 ergs cm s –1 ) measurements of plasma properties with application to high-energy astrophysical systems. We model the experiments with 1D radiation hydrodynamics simulations using the HELIOS-CR code to inform our understanding and assist in the interpretation of results. The simulations predict that the bulk of the plasma is in a quasi-uniform and hydrodynamically unperturbed state throughout the duration of the experiment. To evaluate this prediction, we introduced a photonic Doppler velocimetry (PDV) diagnostic to measure spatially and temporally resolved plasma electron density. The initial measurements were successful but had limitations that made model-data comparisons challenging. To address this, we re-designed the gas cell PDV diagnostic and doubled the number of measurement locations to sample across two thirds of the depth of the cell. We also present a comparison of the results from the upgraded PDV diagnostic to the HELIOS-CR simulations for the first time. As a result, the experimental data confirms the prediction of an unperturbed region in the bulk of the plasma but reveals discrepancies in the time evolution and spatial distribution of the simulated electron density.

79 ASTRONOMY AND ASTROPHYSICS↗

An experimental and one-dimensional modeling analysis of turbulent gas ejection in pre-chamber engines

In this work, experimental results from a study on the evolution of gas jets ejected through the orifices of a pre-chamber in a heavy-duty optical engine are presented. The work examines conditions without fuel inside the main-chamber, which helps to describe the dynamics of the ejected gas jets without the interference of subsequent combustion in the main-chamber. Experimental diagnostics consist of high-speed visible intensified imaging and low-speed infrared imaging. Additionally a one-dimensional gas jet model is used to characterize the spatial distribution of the ejected flow, including parameters such as tip penetration, which are then validated based on experimental results. Different stages in the ejection of pre-chamber jets are identified, with chemical activity restricted to a maximum distance of 5 to 10 orifice diameters downstream of the orifice as indicated by the recorded visible radiation. Sensitivity of cycle-to-cycle variations in pre-chamber jet development to the air-to-fuel ratio in the pre-chamber observed in the experiments is in most part attributed to the variations in the timing of combustion initiation in the pre-chamber. The influence of the ejection flow on the penetration of the gas jet on a cycle-to-cycle basis is presented using the one-dimensional model. The one-dimensional model also indicates that the local flow exhibits highest sensitivity to operating conditions during the start of ejection until the timing when maximum flow is attained. Differences that exist during the decreasing mass-flow ejection time-period tend to smear out in part due to the transient slowdown of the ejection process.

1-D gas jet model↗

Determining spectral response of the National Ignition Facility particle time of flight diagnostic to x rays

The Particle Time of Flight (PTOF) diagnostic is a chemical vapor deposition diamond detector used for measuring multiple nuclear bang times at the National Ignition Facility. Due to the non-trivial, polycrystalline structure of these detectors, individual characterization and measurement are required to interrogate the sensitivity and behavior of charge carriers. In this paper, a process is developed for determining the x-ray sensitivity of PTOF detectors and relating it to the intrinsic properties of the detector. We demonstrate that the diamond sample measured has a significant non-homogeneity in its properties, with the charge collection well described by a linear model ax + b, where a = 0.63 ± 0.16 V –1 mm –1 and b = 0.00 ± 0.04 V –1 . Finally, we also use this method to confirm an electron to hole mobility ratio of 1.5 ± 1.0 and an effective bandgap of 1.8 eV rather than the theoretical 5.5 eV, leading to a large sensitivity increase.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Refined interpretation of electron temperature response to neutral beam injection at DIII-D

Accurate particle and power deposition profiles of neutral beam injection (NBI) are essential to transport studies, and that information is usually acquired through Monte Carlo simulations with a given collisional model. The deposition process of the energetic beam particles leads to the informative electron temperature (T e ) evolution trajectory, which can be captured by electron cyclotron emission (ECE) system due to its good spatial and temporal resolution. Previously, some work has been done to interpret the T e responses to the pulsed NBI as a linear heating source with Fourier-based techniques, although that approach fell short when the fast ion slowing-down time becomes significant (~100 ms). It has been observed in DIII-D that the modulated NBI pulses (10–50 Hz) reduce local core T e values ~0.1 keV through cold electron dilution in high-T e (>2 keV) plasmas alongside accumulative heating. Here, a novel approach to interpret the T e response to NBI was developed by linearizing and modeling the detailed T e evolution trajectory using coherently averaged ECE data based on the different time scales of the terms in the local power and particle balance equations. The technique does not require absolute calibrations of ECE and is independent of collisional models. The resulting beam deposition profiles show good consistency and reasonable agreement with Monte Carlo calculations based on the atomic data from the Atomic Data and Analysis Structure (ADAS). Local electron density response measured by Thomson scattering (TS) also suggests the same features when the beam pulse is large enough for that diagnostic to resolve. The remaining discrepancies are also discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Power Flow Spectroscopy Diagnostics & Platform Development at the Z Pulsed Power Facility

Large pulsed power accelerators deliver multi-MJ pulses of electrical energy to a variety of high energy density (HED) physics experiments that support stockpile science programs. Understanding the plasma formation mechanisms and resulting electrical power transport (or "power flow") in the vacuum magnetically insulated transmission lines (MITLs) is an important area of ongoing research, and could provide a means to improve the performance of today's pulsed power accelerators while improving confidence in the design options for next-generation pulsed power concepts. Power flow science has been studied for decades, but these studies have not provided a predictive understanding of plasma formation and expansion in MITL systems. Several recent factors in pulsed power system design have generated a renewed (and urgent) interest in developing validated, multi-physics power flow engineering models with increased scrutiny and understanding. Examples of these factors include (i) the use of high inductance experimental configurations that could increase current "loss", (ii) interest in long-pulse applications that require predictable pulse shapes, and (iii) the desire to develop a deeper understanding of how current loss phenomena scale to larger accelerator configurations. This work is directed to support the validation of multi-physics power flow engineering models required to realize pulsed power systems for the NNSA mission.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Portable Soft X-Ray Diagnostics for Transformative Fusion-Energy Concepts (Final Scientific/Technical Report)

A time-gated extreme-ultraviolet spectrometer was fielded on a transformative fusion-energy device, FuZE-Q at Zap Energy, Inc. (ZEI), a sheared-flow-stabilized z-pinch. Plasma emission spectra were collected in the 5–40 nm wavelength (30–250 eV) range. This was the first time a direct-vacuum-coupled, high-voltage, deposition-sensitive diagnostic was fielded on this type of dense-plasma fusion device. To overcome the special challenges of such a coupling, a unique, highly effective implementation was developed, with fast (10-ns risetime) pulsed high-voltage electronics and a multi-stage differential pumping system. This enabled the UNR spectrometer to collect three independently timed spectra per FuZE-Q shot while also protecting sensitive internal components. Analysis of line emission identified oxygen (N-, C-, B-, Be-, Li-, and He-like O), peaking in intensity shortly after maximum current (>500 kA). Spectral databases and collisional-radiative modeling have been used to identify impurities and estimate edge-plasma temperatures.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Quantification of MagLIF morphology using the Mallat scattering transformation

The morphology of the stagnated plasma resulting from magnetized liner inertial fusion is measured by imaging the self-emission x rays coming from the multi-keV plasma. Equivalent diagnostic responses can be generated by integrated radiation-magnetohydrodynamic (rad-MHD) simulations from programs such as HYDRA and GORGON. There have been only limited quantitative ways to compare the image morphology, that is the texture, of simulations and experiments. We have developed a metric of image morphology based on the Mallat scattering transformation (MST), a transformation that has proved to be effective at distinguishing textures, sounds, and written characters. This metric is designed, demonstrated, and refined by classifying ensembles (i.e., classes) of synthetic stagnation images and by regressing an ensemble of synthetic stagnation images to the morphology (i.e., model) parameters used to generate the synthetic images. We use this metric to quantitatively compare simulations to experimental images, experimental images to each other, and to estimate the morphological parameters of the experimental images with uncertainty. This coordinate space has proved to be very adept at doing a sophisticated relative background subtraction in the MST space. This was needed to compare the experimental self-emission images to the rad-MHD simulation images.

Glinsky, Michael E. (ORCID:0000000324933326)↗

An adaptive approach to machine learning for compact particle accelerators

Abstract Machine learning (ML) tools are able to learn relationships between the inputs and outputs of large complex systems directly from data. However, for time-varying systems, the predictive capabilities of ML tools degrade if the systems are no longer accurately represented by the data with which the ML models were trained. For complex systems, re-training is only possible if the changes are slow relative to the rate at which large numbers of new input-output training data can be non-invasively recorded. In this work, we present an approach to deep learning for time-varying systems that does not require re-training, but uses instead an adaptive feedback in the architecture of deep convolutional neural networks (CNN). The feedback is based only on available system output measurements and is applied in the encoded low-dimensional dense layers of the encoder-decoder CNNs. First, we develop an inverse model of a complex accelerator system to map output beam measurements to input beam distributions, while both the accelerator components and the unknown input beam distribution vary rapidly with time. We then demonstrate our method on experimental measurements of the input and output beam distributions of the HiRES ultra-fast electron diffraction (UED) beam line at Lawrence Berkeley National Laboratory, and showcase its ability for automatic tracking of the time varying photocathode quantum efficiency map. Our method can be successfully used to aid both physics and ML-based surrogate online models to provide non-invasive beam diagnostics.

97 MATHEMATICS AND COMPUTING↗

Metadata Schemas and Ontologies for Building Energy Applications: A Critical Review and Use Case Analysis

With the increasing digitalization of processes throughout the lifecycle of buildings, data exchanged between stakeholders and between building systems has grown significantly. However, a lack of semantic interoperability between data in different systems is still prevalent, hindering the development of applications that can be reused across buildings and limiting the scalability of innovative solutions. Semantics refers to the description of the meaning of the data in a way that can be consistently understood by applications. Recently, several competing initiatives have been developing metadata schemas and ontologies to express this semantic information for different applications in the building domain. This paper systematically reviews these schemas and conducts an analysis of five of them to evaluate their applicability to three high-value use cases for building operations: energy audits, automated fault detection and diagnostics and optimal control. The survey finds 40 schemas published in the last 10 years but but their actual use in industry is difficult to estimate. Among the five selected ontologies, several gaps are highlighted in relation to the three use cases. Recommendations for the future include better harmonization of these initiatives, more centralized repositories and search engines for these schemas as well as better industry engagement to facilitate their adoption.

Smart Building, Sematic, Metadata, Ontology, Data ↗

The characterization of wear-causing particles and silica sand in particular

Erodants and abradants are two types of wear-causing particles (WCP). Despite their effects on the severity and rate of wear, WCP are inadequately characterized in a surprising number of publications, especially those involving impingement erosion and three-body abrasion. That shortfall makes it difficult to correlate features of WCP with the details of worn surfaces, or to develop wear models that account for those features. It is argued that the documentation of WCP should go beyond simply reporting their composition and mean particle size. In late 1985, ASTM Committee G2 on Wear and Erosion established a task group on the characterization of WCP. At that time, image analysis was slower and less sophisticated than it is today. While that ASTM task group failed to produce a consensus standard, computerized particle characterization methods were developing in fields other than tribology, fields like geoscience, heavy sand mining, materials processing, and pharmaceuticals. A notable exception to this is ferrography, which is a widely-used diagnostic for lubricated tribosystems. In the context of dry wear, it is useful to identify which features of WCP would be beneficial to document, and to identify some techniques and scales of detail appropriate to particular tribosystems. In this paper, examples are presented for the morphological and mechanical characterization of silica sand grains, as prompted by a triboanalysis of the abrasive and erosive wear of biomass pre-processing equipment. The authors propose a minimum level of documentation for WCP, one that can enrich tribosystem analysis both in laboratory tests and field studies.

36 MATERIALS SCIENCE↗

Crystallography of low Z material at ultrahigh pressure: Case study on solid hydrogen

Diamond anvil cell techniques have been improved to allow access to the multimegabar ultrahigh-pressure region for exploring novel phenomena in condensed matter. However, the only way to determine crystal structures of materials above 100 GPa, namely, X-ray diffraction (XRD), especially for low Z materials, remains nontrivial in the ultrahigh-pressure region, even with the availability of brilliant synchrotron X-ray sources. In this work,we perform a systematic study, choosing hydrogen (the lowest X-ray scatterer) as the subject, to understand how to better perform XRD measurements of low Z materials at multimegabar pressures. The techniques that we have developed have been proved to be effective in measuring the crystal structure of solid hydrogen up to 254 GPa at room temperature [C. Ji et al.,Nature 573, 558–562 (2019)]. We present our discoveries and experiences with regard to several aspects of this work, namely, diamond anvil selection, sample configuration for ultrahigh-pressure XRD studies,XRD diagnostics for low Z materials, and related issues in data interpretation and pressure calibration.We believe that these methods can be readily extended to other low Z materials and can pave the way for studying the crystal structure of hydrogen at higher pressures, eventually testing structural models of metallic hydrogen.

36 MATERIALS SCIENCE↗

Effects of drifts on scrape-off layer transport in W7-X

Abstract Drifts affect particle, momentum, and energy transport in the scrape-off layer (SOL) of tokamaks and stellarators, altering plasma flows and creating asymmetries between divertors. To understand how drifts affect SOL transport in the W7-X island divertor, an experiment was performed to compare plasmas with matched core parameters but opposite magnetic field directions, and therefore opposite drift transport directions. Parallel flow measurements made with coherence imaging spectroscopy are interpreted with the aid of a diagnostic forward model and a 1D simple SOL model that includes the E × B drift. In low-density plasmas ( n ‾ e < 2 × 10 19 m −3 ), the poloidal E × B drift induces a large poloidal density asymmetry within the island SOL, as measured by divertor Langmuir probes. This in turn causes the parallel flow stagnation point to shift from the position halfway between targets to the X-point in the drift direction, leading to near-unidirectional flow throughout the SOL. As density increases, the effects of the poloidal E × B drift decrease substantially, resulting in a smaller density asymmetry and the development of a counter-streaming flow pattern. For the entire density range probed in this experiment ( n ‾ e = 1.5 − 6 × 10 19 m −3 ), the experimental observations are more consistent with the effects of the poloidal E × B drift than the radial E × B drift.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Multi‐Model Ensembles in Ecosystem Modeling: Challenges and Best Practices for Decision‐Making

Ecosystem models are increasingly central to the decision-making for environmental policy, conservation planning, and climate-related investments. Yet, the growing reliance on Multi-Model Ensembles (MMEs) of ecosystem models by practitioners and policymakers, sometimes under tight timelines and imperfect information, has frequently outpaced the scientific rigor required to ensure ensemble reliability. Here, MMEs refer to approaches that combine targeted predictions from multiple models with the expectation of improving robustness and quantifying predictive uncertainty. Poorly designed MMEs may create a false sense of confidence and lead to suboptimal policy and market decisions. This perspective argues that robust decision-making-relevant MMEs must be grounded on two pillars: (1) rigorous Model Intercomparison Projects (MIPs), which identify inter-model agreement and disagreement, characterize model uncertainties, and evaluate robustness with observationally based benchmarks—MIPs' diagnostic evaluation is so critical that it must be needed to drive MME's decision in model selection and weighting, especially when only a limited number of models available; and (2) co-design by both stakeholders and scientists to ensure that scenarios, metrics and uncertainty requirements provide decision-relevant information. Building upon the past success and lessons from the existing MIPs-MMEs efforts (e.g., climate/Earth system/crop), we derived the theoretical basis for MMEs, addressed their specific challenges in ecosystem modeling, and highlighted proper consideration of model numbers and diversity, risk of model inter-dependence, effective calibration of model parameters, possible overdue of some ecosystem model development, critical roles of open benchmark data across a wide range of conditions, and suggested use of Artificial Intelligence to support MIPs-MMEs. We highlighted the under-recognized opportunity for MIPs and MMEs to drive scientific progress and innovation through identifying better performing models, systematic benchmarking, feedback loops, and targeted model improvement. By following actionable best practice guidelines, MMEs can evolve from ad hoc aggregation of models into a trusted backbone of environmental policy and decision-making.

ecosystem modeling↗

Combining diagnostics, modeling, and control systems for automated alignment of the TES beamline

X-ray beamlines are essential components of all synchrotron light sources. Practical operations involve frequent variation in beamline component positions and orientation, particularly when photon beam parameters shift due to experimental needs, or due to variations in the incoming photon beam. The alignment process can be time consuming and takes away from valuable beam time for experimental data collection. We describe progress in the automation of certain alignment tasks on the tender-energy X-ray spectroscopy (TES) beamline at the National Synchrotron Light Source II (NSLS-II). The beamline is controlled using the BlueSky software in which high level experimental plans guide the beamline components during an experiment. Numerous software packages exist for beamline modeling, and they may be tied to the beamline control system using a package we are continuing to develop called Sirepo-Bluesky. The photon beam distribution may be measured with fluorescent screens, and a relation between beam and machine state can be found by varying the mirror and aperture settings over a multi-dimensional range. We describe the results of such parameter varying measurements and how we are combining Sirepo-Bluesky with machine learning methods and reduced models to automate mirror alignment on the TES beamline.

36 MATERIALS SCIENCE↗

Free-spray characteristics and spray-wall interactions of methanol on a gasoline direct injector under flash-boiling and non-flash-boiling conditions

Methanol is considered a promising alternative fuel for internal combustion engines (ICEs) due to its high-octane number, fast laminar flame speed, and elevated latent heat of vaporization, all of which support higher compression ratios and improved thermal efficiency. However, its substantial latent heat of vaporization also poses cold-start challenges, such as misfire and fuel film deposition. This study aims to investigate methanol spray morphology and spray-wall interaction using the Spray M injector from the Engine Combustion Network within a constant-pressure flow vessel. A recently developed unified numerical framework capable of modeling both flash and non-flash boiling sprays is validated against experimental liquid volume fraction data acquired via 3-D computed tomography. Here, the results reveal that flash boiling significantly alters the spray morphology, leading to smaller droplets and spray collapse due to enhanced air-entrainment-induced turbulence. Quantitative agreement between experiments and simulations confirms this behavior. Coupled 0-D equilibrium and 3-D computational fluid dynamics analyses show that flash boiling accelerates evaporation and reduces fuel residence time, while non-flash conditions maintain a persistent liquid core more susceptible to wall wetting. Wall temperature diagnostics reveal that spray collapse alters heat transfer patterns by shifting cooling effects. Mixture fraction analysis indicates that evaporation is primarily governed by shear-layer turbulence, though deviations from adiabatic equilibrium mixing emerge under low-turbulence conditions. Finally, increasing fuel, ambient, and wall temperatures reduces wall wetting and film thickness, mitigating cold-start risks. These findings enhance the understanding of methanol sprays’ behavior and support its adoption as a viable, alternative fuel for ICEs.

Engine Combustion Network↗

Measurements of the $^{5}D^{°}_{4}$–$^{5}P_{3}$ transition of singly ionized atomic iodine using intermodulated laser induced fluorescence

Iodine has been an element of recent interest for commercial use as fuel in electrostatic propulsion systems. A lingering problem when investigating ionized iodine using non-perturbative, laser-based techniques is determining the spectral width, i.e., the species temperature, of iodine. To this end, the hyperfine structure must be well understood to develop a spatially resolved diagnostic technique capable of ion flow and temperature measurements. Previous work investigated the lineshape of the transition between the $^{5}D^{°}_{4}$ and $^{5}P_{3}$ states of singly-ionized atomic iodine (I II) with laser induced fluorescence (LIF), but the hyperfine structure of the transition was unresolved in those measurements. In this work, an intermodulated LIF technique is used to measure an enhanced lineshape of the same I II transition. Here, a linear least squares fitting algorithm is used to fit the transition lineshape, where hyperfine transition locations and theorized relative amplitudes are constrained by theory. A lineshape model that incorporates hyperfine transition amplitude enhancement introduced from an intermodulated laser technique is implemented into the fitting function, as well as a nonlinear laser saturation effect. We report converged hyperfine coupling coefficients for these I II states.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗