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At least 217 records · Page 12

Actinomycetota isolated from the sponge Hymeniacidon perlevis as a source of novel compounds with pharmacological applications: diversity, bioactivity screening, and metabolomic analysis

Abstract Aims To combat health conditions, such as multi-resistant bacterial infections, cancer, and metabolic diseases, new drugs need to be urgently found and, in this respect, marine Actinomycetota have a high potential to produce secondary metabolites with pharmacological importance. We aimed to study the cultivable Actinomycetota community associated with a marine sponge from the Portuguese coast, Hymeniacidon perlevis, and investigate the potential of the retrieved isolates to produce compounds with antimicrobial, anticancer and anti-obesity properties. Methods and results The analysis of the 16S rRNA gene revealed 79 Actinomycetota isolates affiliated with 12 genera—Brachybacterium, Dietzia, Glutamicibacter, Gordonia, Micrococcus, Micromonospora, Nocardia, Nocardiopsis, Paenoartrhobacter, Rhodococcus, Streptomyces, and Tsukamurella, most of which affiliated with the genus Streptomyces. The screening of antimicrobial activity revealed 13 strains, all belonging to the Streptomyces genus, capable of inhibiting the growth of Candida albicans, Bacillus subtilis, or Staphylococcus aureus. Forty-three extracts exhibited cytotoxic activity against at least one tested cell line (HepG2, HCT-116, and hCMEC-D3). Three extracts that were active against the two cancer cell lines tested, did not reduce the viability of the non-cancer endothelial cell line, hCMEC-D3. One Gordonia strain exhibited anti-obesity activity, revealed by its ability to reduce the neutral lipids in zebrafish larvae. Mass spectrometry-based dereplication analysis of active extracts identified several compounds associated with known Actinomycetota natural products. Nonetheless, five clusters contained metabolites that did not match any annotated natural products, suggesting they may represent new bioactive molecules. Conclusions This work contributed to increase the knowledge on the diversity and bioactive potential of Actinomycetota associated with H. perlevis.

Fonseca, Ana C.↗

ROI-Finder : machine learning to guide region-of-interest scanning for X-ray fluorescence microscopy

The microscopy research at the Bionanoprobe (currently at beamline 9-ID and later 2-ID after APS-U) of Argonne National Laboratory focuses on applying synchrotron X-ray fluorescence (XRF) techniques to obtain trace elemental mappings of cryogenic biological samples to gain insights about their role in critical biological activities. The elemental mappings and the morphological aspects of the biological samples, in this instance, the bacterium Escherichia coli ( E. Coli ), also serve as label-free biological fingerprints to identify E. coli cells that have been treated differently. The key limitations of achieving good identification performance are the extraction of cells from raw XRF measurements via binary conversion, definition of features, noise floor and proportion of cells treated differently in the measurement. Automating cell extraction from raw XRF measurements across different types of chemical treatment and the implementation of machine-learning models to distinguish cells from the background and their differing treatments are described. Principal components are calculated from domain knowledge specific features and clustered to distinguish healthy and poisoned cells from the background without manual annotation. The cells are ranked via fuzzy clustering to recommend regions of interest for automated experimentation. The effects of dwell time and the amount of data required on the usability of the software are also discussed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Single cell RNA sequencing reveals shifts in cell maturity and function of endogenous and infiltrating cell types in response to acute intervertebral disc injury

Intervertebral disc (IVD) degeneration contributes to disabling back pain. Degeneration can be initiated by injury and progressively leads to an irreversible loss of cells and function. IVD function restoration through cell replacement therapies have had limited success due to knowledge gaps in the critical cell populations important for repair. Here, in this study, we used single cell RNA sequencing to identify the transcriptional changes of IVD resident and infiltrating cell populations from Control and Injured coccygeal IVDs extracted from 12-week-old female C57BL/6J mice 7 days post injury. Clustering, gene ontology, and pseudotime trajectory analyses determined transcriptomic divergences with injury, flow cytometry identified they types of infiltrating immune cells, and immunofluorescence was utilized to define mesenchymal stem cell (MSC) localization. We identified 11 distinct clusters that included IVD, immune, vascular cells, and MSCs. Differential gene expression analysis determined that Outer Annulus Fibrosus, Neutrophils, Saa2-High MSCs, Macrophages, and Krt18 + Nucleus Pulposus (NP) cells were the major drivers of transcriptomic differences between Control and Injured cells. Gene ontology revealed that the most upregulated biological pathways were angiogenesis and T cell-related while wound healing and ECM regulation were downregulated. Pseudotime trajectory analyses revealed that IVD injury directed cells towards increased differentiation in all clusters, except for Krt18 + NP cells which remained in a less mature cell state. Saa2-High and Grem1-High MSCs populations shifted towards more differentiated IVD cells profiles with injury and localized distinctly within the IVD. This study revealed novel MSC populations with the potential to be leveraged for future IVD repair studies.

Cartilage↗

Biological response of eelgrass epifauna, Taylor's Sea hare ( Phyllaplysia taylori ) and eelgrass isopod ( Idotea resecata ), to elevated ocean alkalinity

Abstract. Marine carbon dioxide removal (mCDR) approaches are under development to mitigate the effects of climate change by sequestering carbon in stable reservoirs, with the potential co-benefit of local reductions in coastal acidification impacts. One such method is ocean alkalinity enhancement (OAE). A specific OAE method is the generation of aqueous alkalinity via electrochemistry to enhance the alkalinity of the receiving water by the extraction of acid from seawater, thereby avoiding the issues of solid dissolution kinetics and the release of impurities into the ocean from alkaline minerals. While electrochemical acid extraction is a promising method for increasing the carbon dioxide sequestration potential of the ocean, the biological effects of increasing seawater alkalinity and pH within an OAE project site are relatively unknown. This study aims to address this knowledge gap by testing the effects of increased pH and alkalinity, delivered in the form of aqueous NaOH, on two eelgrass epifauna in the US Pacific Northwest, Taylor's sea hare (Phyllaplysia taylori) and eelgrass isopod (Idotea resecata), chosen for their ecological importance as salmon prey and for their role in eelgrass ecosystems. Four-day experiments were conducted in closed bottles to allow measurements of the evolution of carbonate species throughout the experiment, with water refreshed twice daily to maintain elevated pH, across pHNBS (NBS standard scale) treatments ranging from 7.8 to 9.3. Sea hares experienced mortality in all pH treatments, ranging from 37 % mortality at pHNBS 7.8 to 100 % mortality at pHNBS 9.3. Isopods experienced lower mortality rates in all treatment groups, ranging from 13 % at pHNBS 7.8 to 21 % at pHNBS 9.3, which did not significantly increase with higher pH treatments. These experiments represent an extreme of constant exposure to elevated pH and alkalinity, which should be considered in the context of both the natural variation and the dilution of alkalinity experienced by marine communities across an OAE project site. Different invertebrate species will likely have different responses to increased pH and alkalinity, depending on their physiological vulnerabilities. Investigation of the potential vulnerabilities of local marine species will help inform the decision-making process regarding mCDR planning and permitting.

marine carbon dioxide removal↗

Optimal carbon storage reservoir management through deep reinforcement learning

Model-based optimization plays a central role in energy system design and management. The complexity and high-dimensionality of many process-level models, especially those used for geosystem energy exploration and utilization, often lead to formidable computational costs when the dimension of decision space is also large. This work adopts elements of recently advanced deep learning techniques to solve a sequential decision-making problem in applied geosystem management. Specifically, a deep reinforcement learning framework was formed for optimal multiperiod planning, in which a deep Q-learning network (DQN) agent was trained to maximize rewards by learning from high-dimensional inputs and from exploitation of its past experiences. To expedite computation, deep multitask learning was used to approximate high-dimensional, multistate transition functions. Both DQN and deep multitask learning are pattern based. As a demonstration, the framework was applied to optimal carbon sequestration reservoir planning using two different types of management strategies: monitoring only and brine extraction. Both strategies are designed to mitigate potential risks due to pressure buildup. Results show that the DQN agent can identify the optimal policies to maximize the reward for given risk and cost constraints. Finally, experiments also show that knowledge the agent gained from interacting with one environment is largely preserved when deploying the same agent in other similar environments.

15 GEOTHERMAL ENERGY↗

Measurement of anti- 3 He nuclei absorption in matter and impact on their propagation in the Galaxy

In our Galaxy, light antinuclei composed of antiprotons and antineutrons can be produced through high-energy cosmic-ray collisions with the interstellar medium or could also originate from the annihilation of dark-matter particles that have not yet been discovered. On Earth, the only way to produce and study antinuclei with high precision is to create them at high-energy particle accelerators. Although the properties of elementary antiparticles have been studied in detail, the knowledge of the interaction of light antinuclei with matter is limited. We determine the disappearance probability of 3 $\overline{He}$ when it encounters matter particles and annihilates or disintegrates within the ALICE detector at the Large Hadron Collider. We extract the inelastic interaction cross section, which is then used as an input to the calculations of the transparency of our Galaxy to the propagation of 3 $\overline{He}$ stemming from dark-matter annihilation and cosmic-ray interactions within the interstellar medium. For a specific dark-matter profile, we estimate a transparency of about 50%, whereas it varies with increasing 3 $\overline{He}$ momentum from 25% to 90% for cosmic-ray sources. The results indicate that 3 $\overline{He}$ nuclei can travel long distances in the Galaxy, and can be used to study cosmic-ray interactions and dark-matter annihilation.

79 ASTRONOMY AND ASTROPHYSICS↗

Efficient distributed continual learning for steering experiments in real-time

Deep learning has emerged as a powerful method for extracting valuable information from large volumes of data. However, when new training data arrives continuously (i.e., is not fully available from the beginning), incremental training suffers from catastrophic forgetting (i.e., new patterns are reinforced at the expense of previously acquired knowledge). Training from scratch each time new training data becomes available would result in extremely long training times and massive data accumulation. Rehearsal-based continual learning has shown promise for addressing the catastrophic forgetting challenge, but research to date has not addressed performance and scalability. To fill this gap, we propose an approach based on a distributed rehearsal buffer that efficiently complements data-parallel training on multiple GPUs to achieve high accuracy, short runtime, and scalability. It leverages a set of buffers (local to each GPU) and uses several asynchronous techniques for updating these local buffers in an embarrassingly parallel fashion, all while handling the communication overheads necessary to augment input minibatches using unbiased, global sampling. We further propose a generalization of rehearsal buffers to support both classification and generative learning tasks, as well as more advanced rehearsal strategies (notably Dark Experience Replay, leveraging knowledge distillation). We illustrate this approach with a real-life HPC streaming application from the domain of ptychographic image reconstruction. Furthermore, we run extensive experiments on up to 128 GPUs of the ThetaGPU supercomputer to compare our approach with baselines representative of training-from-scratch (the upper bound in terms of accuracy) and incremental training (the lower bound). Results show that rehearsal-based continual learning achieves a top-5 validation accuracy close to the upper bound, while simultaneously exhibiting a runtime close to the lower bound.

Asynchronous data management↗

Experimental investigation of abnormal transverse flow enhancement of α particles in heavy-ion collisions

The mass dependence of the transverse flow for Z = 1–5 fragments from the collisions of 40 Ar + 27 Al, 40 Ar + 48 Ti, and 40 Ar + 58 Ni at 47 MeV/nucleon is investigated experimentally in this article. The transverse flow values are determined using the in-plane components of the fragment transverse momenta, where three conventional methods, i.e., the kinetic flow tensor method, the transverse momentum analysis method, and the azimuthal correlation method, are applied to reconstruct the reaction plane in an event-by-event basis. It is demonstrated from the comparison of the present experimental mass dependent flow measurements and the model simulations using an improved antisymmetrized molecular dynamics model that the experimentally observed abnormal α transverse flow enhancement is closely related to the reaction plane reconstruction procedure in the flow extraction. We further investigate the physical existence of the abnormal α flow behavior using a two-particle azimuthal correlation method, which allows us to provide the relative flow magnitude information with an identification of fragment charge number without the knowledge of the reaction plane differing from the three conventional methods. It is found that the relative flow magnitudes deduced from the two-particle azimuthal correlation functions with an identification of Z, with the correction for the recoil effect imposed by the momentum conservation, show a monotonically increasing trend as a function of fragment charge number, with no exception of the α flow enhancement. These results, in addition to those from the improved antisymmetrized molecular dynamics model simulations, definitely provide experimental evidences for the inexistence of the abnormal α flow behavior in the heavy-ion collisions at the present incident energy region in nature.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Dissecting components of the Campylobacter jejuni fetMP-fetABCDEF gene cluster under iron limitation

Campylobacter jejuni is a leading cause of bacterial gastroenteritis worldwide. Acute infection can be an antecedent to highly debilitating long-term sequelae. The expression of iron acquisition systems is vital for C. jejuni to survive the low iron availability within the human gut. The C. jejuni fetMP-fetABCDEF gene cluster is known to be upregulated during human infection and under iron limitation. While FetM and FetP have been functionally linked to iron transport in prior work, here we assess the contribution of each of the downstream genes (fetABCDEF) to C. jejuni growth during both iron-depleted and iron-replete conditions. Significant growth impairment was observed upon disruption of fetA, fetB, fetC, and fetD, suggesting a role in FetMP-mediated iron acquisition for each encoded protein. FetA expression was not dependent on the presence of FetB, FetC, FetD, FetE, or FetF. The functions of the putative thioredoxins FetE and FetF were redundant under iron-limited growth, requiring a double deletion (ΔfetEF) to exhibit a growth defect. C. jejuni FetE was expressed, and the structure was solved to 1.50 Å, revealing structural similarity to thiol-disulfide oxidases. Functional characterization in biochemical assays showed that FetE reduced insulin at a slower rate than Escherichia coli Trx and that together, FetEF promoted substrate oxidation in cell extracts, suggesting that FetE (and presumably FetF) are oxidoreductases that can mediate oxidation in vivo. This study advances our understanding of the contributions of the fetMP-fetABCDEF gene cluster to virulence at a genetic and functional level, providing foundational knowledge toward mitigating C. jejuni-related morbidity and mortality.

59 BASIC BIOLOGICAL SCIENCES↗

Simulation and Development of the Radial Time Projection Chamber For the Bonus12 Experiment in CLAS12

Knowledge of the structure of nucleons (i.e. protons and neutrons) is a central topic of interest to nuclear/particle physicists. Much more is known about the structure of the proton than the neutron due to the lack of high-density free neutron targets. The Barely Off-shell Nucleon Structure experiment (BONuS12) at Jefferson Lab (JLab) is a second generation experiment upgraded/optimized to advance our knowledge of the neutron's structure using the deep-inelastic scattering of electrons off deuterium. Typically, since deuterium is a nuclear target, corrections for off-shell and nuclear binding effects must be taken into account in order to extract results on the neutron. These corrections are model-dependent and therefore have limited our success in extracting neutron information using deuterium targets. In the BONuS12 experiment, 10.6 GeV electrons are scattered off of a deuterium target. By detecting the low momentum spectator proton at backward angles, the uncertainty due to final state interactions is minimized. The goal of the experiment is to measure the ratio of the neutron to proton structure functions ($F^n_2/F^p_2$) as the Bjroken scaling variable x approaches 1. The newly designed Radial Time Projection Chamber (RTPC) for BONuS12 detects the spectator proton in coincidence with the scattered electron, which is detected in the CEBAF Large Acceptance Spectrometer (CLAS12). This work presents the simulation and development of the new BONuS12 RTPC. The design, construction, and testing of the Drift-gas Monitoring Sysytem (DMS) for the BONuS12 experiment is also described. The results of the DMS operation as well as the first preliminary data from the BONuS12 experimental run are given. Because the BONuS12 data analysis depends on CLAS12 working effectively, an effort to verify the CLAS12 operation with the extraction of the inclusive deep inelastic cross section from the first experiment in CLAS12 (Run Group A) will be presented.

Dzbenski, Nathan↗

Determination of the Maturation Status of Dendritic Cells by Applying Pattern Recognition to High-Resolution Images

The maturation or activation status of dendritic cells (DCs) directly correlates with their behavior and immunofunction. A common means to determine the maturity of dendritic cells is from high-resolution images acquired via scanning electron microscopy (SEM) or atomic force microscopy (AFM). While direct and visual, the determination has been made by directly looking at the images by researchers. Here we report a machine learning approach using pattern recognition in conjunction with cellular biophysical knowledge of dendritic cells to determine the maturation status of dendritic cells automatically. The determination from AFM images reaches 100% accuracy. The results from SEM images reaches 94.9%. The results demonstrate the accuracy of using machine learning for accelerating data analysis, extracting information, and drawing conclusions from high-resolution cellular images, paving the way for future applications requiring high-throughput and automation, such as cellular sorting and selection based on morphology, quantification of cellular structure, and DC-based immunotherapy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Neural network based analysis of multimodal bond distributions using extended x-ray absorption fine structure spectra

Knowledge of the local coordination environment around atomic species in functional materials is critical for understanding their mechanisms of operation. Heterogeneous mixtures of metal complexes are ubiquitous in catalysts, ionic liquids, molten salts, biological enzymes, and geochemical systems, among many others. Extracting information from ensemble-average measurements about the structural and compositional descriptors of each type of coordination complex comprising the mixture is not generally possible, especially when they possess multimodal bond-length distributions. Here, we developed a method that enables the mapping of an x-ray absorption spectrum on the radial distribution function describing the average environment of the metal ions. The supervised neural network based method utilizes an objective training set, for which the choice of the local structural motifs is completely agnostic to the theoretically expected structure and dynamics of the modeled system. The method was validated using first-principles modeling of structural dynamics of nickel complexation in molten salts, and it applies to a large class of heterogeneous systems, including those studied under in situ and operando conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effects of small marine energy deployments on oceanographic systems

The placement and operation of marine energy deployments in the ocean have the potential to change flow patterns, decrease wave heights, and/or remove energy from the oceanographic system. Changes in oceanographic systems resulting from harvesting marine energy, particularly tidal and wave energy, may be of concern. These changes include alterations in nearfield and farfield physical processes, as well as potential secondary environmental effects such as changes in sediment transport patterns, biological processes, or coastal erosion. Knowledge of changes in oceanographic systems associated with marine energy is primarily available from numerical modeling studies, informed by some laboratory tests and very few field measurements. A literature review was conducted using the Tethys knowledge base and other online sources, building on conclusions from the Ocean Energy Systems-Environmental State of the Science report. Potential changes in oceanographic systems that may be caused by marine energy differ between tidal and wave devices because of different extraction mechanisms and siting locations. Numerical models show that tidal extraction on the order of hundreds of megawatts or with significant channel blockage is required to create changes in oceanographic processes that exceed natural variability. Effects from wave energy extraction in arrays are localized and dependent on array spacing and proximity to the shore. Here the available evidence supports the conclusion that the risk of significant environmental effects from such changes could be retired (i.e., less investigation required for every project) for small deployments—those representative of the state of the industry in 2021. Determining changes in oceanographic systems to be low risk for small deployments can thereby streamline environmental consenting by reducing monitoring needs at this early stage in the industry.

54 ENVIRONMENTAL SCIENCES↗

Understanding fission gas bubble distribution, lanthanide transportation, and thermal conductivity degradation in neutron-irradiated α-U using machine learning

U—10Zr based metallic nuclear fuel is the leading candidate for next-generation sodium-cooled fast reactors in the United States. US research reactors have used and tested this fuel type since the 1960s and accumulated considerable experience and knowledge about the fuel performance. Most of the knowledge, however, remains empirical. The lack of mechanistic understanding of fuel performance puts a large burden on proof through experimental verification for the qualification of U—10Zr fuel for commercial use. Further, this paper proposes an image data-driven machine learning approach, coupled with domain knowledge provided by advanced post irradiation examination, to provide unprecedented quantified insights into the morphology, size, density and the connectivity of fission gas bubbles and their effects on the fission product transportation and thermal conductivity. Specifically, we developed a method to automatically detect, extract statistics, and classify ~19,000 fission gas bubbles into different categories, and quantitatively link the data to lanthanide transportation through connected bubbles and degradation of thermal conductivity along the radial temperature gradient in a neutron irradiated U—10Zr annular fuel. Results indicate the approach can be modified to study other irradiation effects, such as secondary phase redistribution and gaseous fuel swelling in other irradiated nuclear fuels.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Real-Time Health Monitoring for Gas Turbine Components Using Online Learning and High-Dimensional Data

Capital-intensive turbomachinery, such as gas turbines and combined cycle plants, are constantly being monitored for performance anomalies, faults, and physical degradation. Although these power-generating assets are equipped with hundreds of sensors, existing monitoring tools can only handle moderate-sized data. As a result, only a handful of aggregate metrics are used to monitor machine health. At the same time, developing advanced tools suitable for large datasets have been restricted by the lack of appropriate data. The objective of this proposal was to demonstrate a Big Data analytics framework for fault detection and diagnosis in gas turbine applications. We develop a predictive analytics framework methodology guided by these experimental data, industrial data from our collaborators, and physics-based models with engineering domain knowledge. Our analytics framework consists of four key components (1) a data curation process that addresses data storage, data quality assessments, and integrity checks, (2) a feature engineering component that utilizes statistical methods and transformation algorithms guided by physics-based models to extract high-fidelity fault features that can be leveraged for fault detection and classifying fault severities, (3) a Machine Learning-based fault detection and diagnostics algorithms for detecting operational and hardware faults in the combustion and the turbines section. We utilize two industry-class gas turbine component test rigs to generate first of its kind data for critical gas turbine faults with varying severity levels. Advanced gas turbine test facilities will be interrogated using state-of-the-art instrumentation techniques to build fault signatures and data trends for key combustor and turbine faults. Data generated from a combustor test rig (Georgia Tech) and a turbine test rig (Penn State) during both normal operation and with seeded faults serve as the basis for the Big Data sets. The test conditions in the two test facilities include common, critical events that occur in the operation. Utilizing the combustor test rig, we examine two common combustor faults: lean blowout and centerbody degradation. For the turbine section we develop analytic models for monitoring cooling faults in the gas turbine

03 NATURAL GAS↗

Real-Time Health Monitoring for Gas Turbine Components Using Online Learning and High-Dimensional Data (Final Report)

Capital-intensive turbomachinery, such as gas turbines and combined cycle plants, are constantly being monitored for performance anomalies, faults, and physical degradation. Although these power-generating assets are equipped with hundreds of sensors, existing monitoring tools can only handle moderate-sized data. As a result, only a handful of aggregate metrics are used to monitor machine health. At the same time, developing advanced tools suitable for large datasets have been restricted by the lack of appropriate data. The objective of this proposal was to demonstrate a Big Data analytics framework for fault detection and diagnosis in gas turbine applications. We develop a predictive analytics framework methodology guided by these experimental data, industrial data from our collaborators, and physics-based models with engineering domain knowledge. Our analytics framework consists of four key components: (1) a data curation process that addresses data storage, data quality assessments, and integrity checks, (2) a feature engineering component that utilizes statistical methods and transformation algorithms guided by physics-based models to extract high-fidelity fault features that can be leveraged for fault detection and classifying fault severities, (3) a Machine Learning-based fault detection and diagnostics algorithms for detecting operational and hardware faults in the combustion and the turbines section. We utilize two industry-class gas turbine component test rigs to generate first of its kind data for critical gas turbine faults with varying severity levels. Advanced gas turbine test facilities will be interrogated using state-of-the-art instrumentation techniques to build fault signatures and data trends for key combustor and turbine faults. Data generated from a combustor test rig (Georgia Tech) and a turbine test rig (Penn State) during both normal operation and with seeded faults serve as the basis for the Big Data sets. The test conditions in the two test facilities include common, critical events that occur in the operation. Utilizing the combustor test rig, we examine two common combustor faults: lean blowout and centerbody degradation. For the turbine section we develop analytic models for monitoring cooling faults in the gas turbine.

20 FOSSIL-FUELED POWER PLANTS↗

Dual-wavelength channel GHz repetition rate mode-locked VECSEL cavities sourced from a common gain medium

Mode-locked vertical external cavity semiconductor lasers are a unique class of nonlinear dynamical systems driven far from equilibrium. We present a novel, to the best of our knowledge, experimental result, supported by rigorous microscopic simulations, of two coexisting mode-locked V-cavity configurations sourced by a common gain medium and operating as independent channels at angle controlled separated wavelengths. Microscopic simulations support pulses coincident on the common gain chip extracting photons from a nearby pair of coexisting kinetic holes burned in the carrier distributions.

47 OTHER INSTRUMENTATION↗