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At least 289 records · Page 16

Validation of an integrated modeling framework for investigating 3D plasma responses in tokamak plasmas

As contemporary experimental tokamaks are pushed toward reactor-relevant operation, they provide essential testbeds for demonstrating and exploring ELM control strategies for deployment in future fusion pilot plants. Accurate predictions of full plasma responses are essential to guide and optimize these demonstrations. This paper introduces and validates an integrated modeling framework over a historical range of DIII-D operational space. The integrated modeling framework uses only scalar plasma parameters and optional reference boundary to self-consistently and flexibly scan through tokamak operational space and estimate the corresponding ELM-suppression relevant plasma response over 3D coil phase space. The framework generates tightly converged equilibria that satisfy a target set of plasma parameters (I p , β N , l i ), with kinetic profiles constrained by an EPED(NN)-computed pedestal and empirical core model. The plasma response of these modeled equilibria is calculated with GPEC. Validated against 55 distinct DIII-D equilibria, the framework consistently reproduces experimentally constrained equilibrium pressure, q, and other representative profiles using the time-varying information from only evolving scalar plasma parameters; plasma response validation is performed for the n=3 perturbation. In particular, the plasma response of a DIII-D discharge scanning q 95 in search of ELM suppression windows is quantitatively reproduced. By accurately reproducing experimental equilibria and plasma responses across wide parameter variation, the framework supports potential for synthetic parameter scans in key operational, stability, and plasma response dimensions to investigate RMP ELM-suppression experiments and inform predictive RMP scenario optimization.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Modeling temporal and hormonal regulation of plant transcriptional response to wounding

Plants respond to wounding stress by changing gene expression patterns and inducing the production of hormones including jasmonic acid. This wounding transcriptional response activates specialized metabolism pathways such as the glucosinolate pathways in Arabidopsis thaliana. While the regulatory factors and sequences controlling a subset of wound-response genes are known, it remains unclear how wound response is regulated globally. Here, we how these responses are regulated by incorporating putative cis-regulatory elements, known transcription factor binding sites, in vitro DNA affinity purification sequencing, and DNase I hypersensitive sites to predict genes with different wound-response patterns using machine learning. We observed that regulatory sites and regions of open chromatin differed between genes upregulated at early and late wounding time-points as well as between genes induced by jasmonic acid and those not induced. Expanding on what we currently know, we identified cis-elements that improved model predictions of expression clusters over known binding sites. Using a combination of genome editing, in vitro DNA-binding assays, and transient expression assays using native and mutated cis-regulatory elements, we experimentally validated four of the predicted elements, three of which were not previously known to function in wound-response regulation. Our study provides a global model predictive of wound response and identifies new regulatory sequences important for wounding without requiring prior knowledge of the transcriptional regulators.

59 BASIC BIOLOGICAL SCIENCES↗

Charge Conservation beyond Uniformity: Spatially Inhomogeneous Electromagnetic Response in Periodic Solids

Nonlinear electromagnetic response functions have reemerged as a crucial tool for studying quantum materials, due to recently appreciated connections between optical response functions, quantum geometry, and band topology. Most attention has been paid to responses to spatially uniform electric fields, relevant to low-energy optical experiments in conventional solid state materials. However, magnetic and magnetoelectric phenomena are naturally connected by responses to spatially varying electric fields due to Maxwell’s equations. Furthermore, in the emerging field of moiré materials, characteristic lattice scales are much longer, allowing spatial variation of optical electric fields to potentially have a measurable effect in experiments. In order to address these issues, we develop a formalism for computing linear and nonlinear responses to spatially inhomogeneous electromagnetic fields. Starting with the continuity equation, we derive an expression for the second-quantized current operator that is manifestly conserved and model independent. Crucially, our formalism makes no assumptions on the form of the microscopic Hamiltonian and so is applicable to model Hamiltonians derived from tight-binding or calculations. We then develop a diagrammatic Kubo formalism for computing the wave vector dependence of linear and nonlinear conductivities, using Ward identities to fix the value of the diamagnetic current order by order in the vector potential. We apply our formula to compute the magnitude of the Kerr effect at oblique incidence for a model of a moiré-Chern insulator and demonstrate the experimental relevance of spatially inhomogeneous fields in these systems. We further show how our formalism allows us to compute the (orbital) magnetic multipole moments and magnetic susceptibilities in insulators. Turning to nonlinear response, we use our formalism to compute the second-order transverse response to spatially varying transverse electric fields in our moiré-Chern insulator model, with an eye toward the next generation of experiments in these systems. Published by the American Physical Society 2024

Physics↗

Foliar respiration is related to photosynthetic, growth and carbohydrate response to experimental drought and elevated temperature

Short-term plant respiration (R) increases exponentially with rising temperature, but drought could reduce respiration by reducing growth and metabolism. Acclimation may alter these responses. We examined if species with different drought responses would differ in foliar R response to +4.8°C temperature and -45% precipitation in a field experiment with mature piñon and juniper trees, and if any differences between species were related to differences in photosynthesis rates, shoot growth and non-structural carbohydrates (NSCs). Short-term foliar R had a Q 10 of 1.6 for piñon and 2.6 for juniper. Piñon foliar R did not respond to the +4.8°C temperatures, but R increased 1.4x for juniper. Across treatments, piñon foliage had higher growth, lower NSC content, 29% lower photosynthesis rates, and 44% lower R than juniper. Removing 45% precipitation had little impact on R for either species. Species differences in the response of R under elevated temperature were related to substrate availability and stomatal response to leaf water potential. Despite not acclimating to the higher temperature and having higher R than piñon, greater substrate availability in juniper suggests it could supply respiratory demand for much longer than piñon. Species responses will be critical in ecosystem response to a warmer climate.

59 BASIC BIOLOGICAL SCIENCES↗

Cyber-physical Architecture For Automated Responses (cyphar) In Adversarial Ot Environments

The ability to react to a malicious attack starts with high fidelity recognition, and with that, an agile response to the attack. The current operational technology (OT) systems for a critical infrastructure may include an intrusion detection system (IDS), but the ability to adapt to an intrusion is a human initiated response. Orchestrators, which are coming of age in the financial sector and allow for levels of automated response, are not prevalent in the OT space. To evolve to such responses in the OT space, a tradeoff analysis is first needed, The tradeoff analysis, which evaluates the mitigation benefits of responses versus the physical affects that result, inform an automated response decision. The intent of this paper is to provide a formulation of a tradeoff analysis and its use in advancing automated, agile responses.

Rieger, CraigG.↗

Comparison of All Solid Cancer Mortality and Incidence Dose-Response in the Life Span Study of Atomic Bomb Survivors, 1958–2009

Recent analysis of all solid cancer incidence (1958–2009) in the Life Span Study (LSS) revealed evidence of upward curvature in the radiation dose response among males but not females. Upward curvature in sex-averaged excess relative risk (ERR) for all solid cancer mortality (1950–2003) was also observed in the 0–2 Gy dose range. As reasons for non-linearity in the LSS are not completely understood, we conducted dose response analyses for all solid cancer mortality and incidence applying similar methods (1958–2009 follow-up, DS02R1 doses, including subjects notin-city (NIC) at the time of the bombing) and statistical models. Incident cancers were ascertained from Hiroshima and Nagasaki cancer registries, while cause of death was ascertained from death certificates over entire Japan. The study included 105,444 LSS subjects who were alive and not known to have cancer before Jan 1, 1958 (80,205 with dose estimates and 25,239 NIC subjects). Between 1958 and 2009, there were 3.1 million person-years (PY) and 22,538 solid cancers for incidence analysis and 3.8 million PY and 15,419 solid cancer deaths for mortality analysis. We fitted sex-specific ERR models adjusted for smoking to both types of data. Over the entire range of doses, solid cancer mortality dose response exhibited a borderline significant upward curvature among males (P=0.062) and significant upward curvature among females (P=0.010); for solid cancer incidence, as before, we found a significant upward curvature among males (P=0.001) but not among females (P=0.624). The sex difference in magnitude of dose response curvature was statistically significant for cancer incidence (P=0.017) but not for cancer mortality (P=0.781). The results of analyses in the 0–2 Gy range and restricted lower dose ranges generally supported inferences made about the sex-specific dose response shape over the entire range of doses for each outcome. Patterns of sex-specific curvature by calendar period (1958–1987 vs 1988–2009) and age at exposure (0–19 vs 20–83) varied between mortality and incidence data, particularly among females, although for each outcome there was an indication of curvature among 0–19 year old male survivors in both calendar periods and among 0–19 year old female survivors in the recent period. Collectively, our findings indicate that the upward curvature in all solid cancer dose response in the LSS is neither specific to males nor to incidence data; it appears to depend on composition of case series and age at exposure or time. Further follow-up and site-specific analyses of cancer mortality and incidence will be important to confirm the emerging trend in dose response curvature among young survivors and unveil the contributing factors and sites.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Experimental Investigation of Low-Frequency Distributed Acoustic Strain-Rate Responses to Propagating Fractures

Summary Low-frequency distributed acoustic sensing (LF-DAS) responds to strain changes due to far-field fracture propagation. To better understand the LF-DAS response to fracture propagation, we performed laboratory-scale hydraulic fracture experiments with embedded optical strain sensors. The objectives of this research are to generate hydraulic fractures of known geometry, measure the strain response along the embedded fiber-optic cable comparable to LF-DAS measurements, and use the results to inform the interpretation of field-derived LF-DAS data. The experiments were conducted in unconfined transparent cubic blocks with a dimension of 8 in. on each side. The block was made of transparent epoxy to visualize the fracture propagation. Fiber-optic sensing cables were embedded in the block at different distances to the source of injection. We injected dyed water through an injection tubing to generate a transverse, radial fracture along an initial flaw. An optical interrogator recorded the response of offset fiber Bragg grating (FBG) strain sensors normal to the plane of the fracture. The strain data were visualized on a waterfall plot, akin to visualizations of field-derived LF-DAS data. Dimensional analysis was used to scale the laboratory results to field conditions. We compared the evolution of the strain response at the fiber-optic cable, injection pressure, and rate with known fracture geometry. The measured strains were compared with Sneddon’s (1946) linear elastic solution for a penny-shaped crack and found to follow this behavior. The generated radial fractures in transparent media can be modeled with Sneddon’s linear elastic radial fracture model and a Mode I critical stress intensity factor. The LF-DAS characteristic response of a narrowing region of extension surrounded by compression was exhibited as a fracture that approached and intersected the fiber-optic cable. The experimentally derived strain and strain-rate waterfall plots with known fracture geometry, injection rate, and pressure response provide insight in understanding LF-DAS responses in the field. Furthermore, we developed a method to estimate fracture geometry evolution from the fiber-optic strain data and validated the method against the experimental data.

Engineering↗

GaAs Neutron Response Functions and Radiation Damage Metrics

The radiation effects community needs clear, well-documented, neutron energy-dependent responses that can be used in assessing radiation-induced material damage to GaAs semiconductors and for correlating observed radiation-induced changes in the GaAs electronic properties with computed damage metrics. In support of the objective, this document provides: a) a clearly defined set of relevant neutron response functions for use in dosimetry applications; b) clear mathematical expressions for the defined response functions; and c) updated quantitative values for the energy- dependent response functions that reflect the best current nuclear data and modelling. This document recaps the legacy response functions. It then surveys the latest nuclear data and updates the recommended response function to support current GaAs damage studies. A detailed tabulation for six of the energy-dependent response functions is provided in an Appendix.

36 MATERIALS SCIENCE↗

RCT Continuing Training: Radiological Emergency Response

Objectives: 1) List the revised initial response and supplemental actions while responding to a major injury inside of a radiological area; 2) List the initial response and supplemental actions while responding to a minor injury inside of a radiological area; 3) List the initial response and supplemental actions for responding to a Continuous Air Monitoring (CAM) alarm; 4) List the initial response and supplemental actions for responding to a radioactive spill; 5) List the initial response and supplemental actions of responding to an Area Radiation Monitor (ARM) alarm; 6) List the initial response and supplemental actions of an Electronic Personal Dosimeter (EPD) dose and dose rate alarm; 7) List the initial response and supplemental actions of responding to a Stationary Contamination Monitor (SCM) alarm; 8) Identify the methods to perform personnel decontamination.

61 RADIATION PROTECTION AND DOSIMETRY↗

Developing a Vaccine Platform for a Balanced Mucosal Immune Response (CB11446), Project Report: Year 1

Mucosal vaccines can elicit protective immune responses at the infection site of respiratory or aerosolized pathogens. Achieving balanced mucosal and systemic responses is a key challenge in the design of mucosal vaccines, especially in terms of developing a broadly applicable vaccine delivery platform amenable to a wide range of subunit vaccine antigens. The overarching goal of the project entitled “Developing a Vaccine Platform for a Balanced Mucosal Immune Response” is to develop a pathogen-agnostic vaccine platform that elicits robust and balanced mucosal immune responses upon intranasal vaccination, in the context of a nanolipoprotein particle (NLP) platform. In year one, we investigated NLP-based vaccine formulations incorporating select immune adjuvants (Monophosphoryl Lipid A (MPLA), FSL-1, L18-muramyl dipeptide (MDP), and cholesterol-tagged ODN2006 (cCpG)) along with antigens relevant to plague (LcrV), tularemia (IglC), and Ebola virus (GP). We demonstrated the ability to prepare, characterize, and quantify these formulations. We then carried out studies in vivo using a BALB/c mouse model, comparing intranasal and intramuscular administration and systematically evaluated the resulting mucosal and systemic immune responses using ELISpot and ELISAs. All proposed tasks (Table 1) were completed within the twelve-month base period, and the established go/no go metric was successfully achieved. Numerous adjuvant:LcrV:NLP formulations were found to have statistically significant increases in IgA titers in serum and/or lung upon IN administration (compared to IM administration), while also producing robust IgG responses in serum. Some formulations also showed significant IFNγ responses using restimulated splenocytes. The data collected during the base period provide valuable insights for the future design of safe and effective mucosal subunit vaccines while also highlighting areas of research that merit further investigation.

59 BASIC BIOLOGICAL SCIENCES↗

Francisella novicida Two-Component System Response Regulator BfpR Modulates iglC Gene Expression, Antimicrobial Peptide Resistance, and Biofilm Production

Response regulators are a critical part of the two-component system of gene expression regulation in bacteria, transferring a signal from a sensor kinase into DNA binding activity resulting in alteration of gene expression. In this study, we investigated a previously uncharacterized response regulator in Francisella novicida, FTN_1452 that we have named BfpR (Biofilm-regulating Francisella protein Regulator, FTN_1452). In contrast to another Francisella response regulator, QseB/PmrA, BfpR appears to be a negative regulator of biofilm production, and also a positive regulator of antimicrobial peptide resistance in this bacterium. The protein was crystallized and X-ray crystallography studies produced a 1.8 Å structure of the BfpR N-terminal receiver domain revealing interesting insight into its potential interaction with the sensor kinase. Structural analysis of BfpR places it in the OmpR/PhoP family of bacterial response regulators along with WalR and ResD. Proteomic and transcriptomic analyses suggest that BfpR overexpression affects expression of the critical Francisella virulence factor iglC, as well as other proteins in the bacterium. We demonstrate that mutation of bfpR is associated with an antimicrobial peptide resistance phenotype, a phenotype also associated with other response regulators, for the human cathelicidin peptide LL-37 and a sheep antimicrobial peptide SMAP-29. F. novicida with mutated bfpR replicated better than WT in intracellular infection assays in human-derived macrophages suggesting that the down-regulation of iglC expression in bfpR mutant may enable this intracellular replication to occur. Response regulators have been shown to play important roles in the regulation of bacterial biofilm production. We demonstrate that F. novicida biofilm formation was highly increased in the bfpR mutant, corresponding to altered glycogen synthesis. Waxworm infection experiments suggest a role of BfpR as a negative modulator of iglC expression with de-repression by Mg 2+ . In this study, we find that the response regulator BfpR may be a negative regulator of biofilm formation, and a positive regulator of antimicrobial peptide resistance in F. novicida.

59 BASIC BIOLOGICAL SCIENCES↗

Chromatin Changes in Phytochrome Interacting Factor-Regulated Genes Parallel Their Rapid Transcriptional Response to Light

As sessile organisms, plants must adapt to a changing environment, sensing variations in resource availability and modifying their development in response. Light is one of the most important resources for plants, and its perception by sensory photoreceptors (e.g., phytochromes) and subsequent transduction into long-term transcriptional reprogramming have been well characterized. Chromatin changes have been shown to be involved in photomorphogenesis. However, the initial short-term transcriptional changes produced by light and what factors enable these rapid changes are not well studied. Here, we define rapidly light-responsive, Phytochrome Interacting Factor (PIF) direct-target genes (LRP-DTGs). We found that a majority of these genes also show rapid changes in Histone 3 Lysine-9 acetylation (H3K9ac) in response to the light signal. Detailed time-course analysis of transcript and chromatin changes showed that, for light-repressed genes, H3K9 deacetylation parallels light-triggered transcriptional repression, while for light-induced genes, H3K9 acetylation appeared to somewhat precede light-activated transcript accumulation. However, direct, real-time imaging of transcript elongation in the nucleus revealed that, in fact, transcriptional induction actually parallels H3K9 acetylation. Collectively, the data raise the possibility that light-induced transcriptional and chromatin-remodeling processes are mechanistically intertwined. Histone modifying proteins involved in long term light responses do not seem to have a role in this fast response, indicating that different factors might act at different stages of the light response. This work not only advances our understanding of plant responses to light, but also unveils a system in which rapid chromatin changes in reaction to an external signal can be studied under natural conditions.

59 BASIC BIOLOGICAL SCIENCES↗

A Pentavalent HIV-1 Subtype C Vaccine Containing Computationally Selected gp120 Strains Improves the Breadth of V1V2 Region Responses

Background: HIV-1 envelope (Env) variable loops 1 and 2 (V1V2) directed non-neutralizing antibodies were a correlate of decreased transmission risk in the RV144 vaccine trial. Thus, the elicitation and breadth of antibody responses against the V1V2 of HIV-1 Env are important considerations for HIV-1 vaccine candidates. The V1V2 region’s highly variable nature and the extensive diversity of subtype C HIV-1 Envelopes (Envs) make the V1V2 response breadth a high priority for HIV-1 vaccine regimens aiming for V1V2-mediated protection in Southern Africa. Here, we determined whether the breadth of the anti-V1V2 vaccine response can be broadened by including HIV-1 Env strains computationally designed to enhance the coverage of subtype C V1V2 sequence diversity. Methods: Three subtype C Env strains were selected to maximize antibody binding coverage while complementing subtype C vaccine gp120s that were given in human clinical trials in South Africa, as well as to improve epitope accessibility. Humoral immunogenicity of a novel trivalent gp120 vaccine immunogen, a bivalent gp120 boost already in clinical trials (1086C and TV1), and a pentavalent (all five gp120s combined) were evaluated in a preclinical immunization study in guinea pigs. The pentavalent combination was further evaluated with alum versus glucopyranosyl lipid adjuvants formulated in squalene-in-water emulsion (GLA-SE) adjuvants in non-human primates. The breadth of the anti-V1V2 response was assessed using an array of cross-subtype variable loops 1&2 (V1V2) scaffold proteins and linear V2 peptides. Results: The breadth of the IgG response against V1V2 antigens of the trivalent and pentavalent groups was comparable, and both were greater than the breadth of the bivalent group. Linear epitope mapping showed that two linear epitopes in V2 were targeted by the vaccinated animals: the V2 hotspot focused at 169K that potentially correlated with decreased HIV-1 risk in RV144 and the V2.2 site (179LDV/I181) that is part of the integrin α4β7 binding site. The bivalent vaccine elicited a significantly higher magnitude of binding to the V2 hotspot compared to the trivalent vaccine whereas the trivalent vaccine elicited significantly higher binding to the V2.2 epitope compared to the bivalent vaccine, while the pentavalent recognized both regions. Conclusions: These results demonstrate that the three new computationally selected subtype C Envs successfully complemented 1086C and TV1 for broader V1V2 antibody responses, and, in concert with adjuvants that stimulate V1V2 responses, can be considered as part of a rationale immunogen design to improve V1V2 IgG coverage in future vaccine trials in South Africa.

Immunology↗

Response time to colored stimuli in the full visual field

Peripheral visual response time was measured in seven dark adapted subjects to the onset of small (45' arc diam), brief (50 msec), colored (blue, yellow, green, red) and white stimuli imaged at 72 locations within their binocular field of view. The blue, yellow, and green stimuli were matched for brightness at about 2.6 sub log 10 units above their absolute light threshold, and they appeared at an unexpected time and location. These data were obtained to provide response time and no-response data for use in various design disciplines involving instrument panel layout. The results indicated that the retina possesses relatively concentric regions within each of which mean response time can be expected to be of approximately the same duration. These regions are centered near the fovea and extend farther horizontally than vertically. Mean foveal response time was fastest for yellow and slowest for blue. Three and one-half percent of the total 56,410 trials presented resulted in no-responses. Regardless of stimulus color, the lowest percentage of no-responses occurred within 30 deg arc from the fovea and the highest within 40 deg to 80 deg arc below the fovea.

Haines, R. F.↗

Brainstem auditory evoked responses in man. 1: Effect of stimulus rise-fall time and duration

Short latency (under 10 msec) responses elicited by bursts of white noise were recorded from the scalps of human subjects. Response alterations produced by changes in the noise burst duration (on-time), inter-burst interval (off-time), and onset and offset shapes were analyzed. The latency of the most prominent response component, wave V, was markedly delayed with increases in stimulus rise time but was unaffected by changes in fall time. Increases in stimulus duration, and therefore in loudness, resulted in a systematic increase in latency. This was probably due to response recovery processes, since the effect was eliminated with increases in stimulus off-time. The amplitude of wave V was insensitive to changes in signal rise and fall times, while increasing signal on-time produced smaller amplitude responses only for sufficiently short off-times. It was concluded that wave V of the human auditory brainstem evoked response is solely an onset response.

Hecox, K.↗

Theoretical and lidar studies of the density response of the mesospheric sodium layer to gravity wave perturbations

The density response of atmospheric layers to gravity waves is developed in two forms, an exact solution and a perturbation series solution. The degree of nonlinearity in the layer density response is described by the series solution whereas the exact solution gives insight into the nature of the responses. Density perturbation in an atmospheric layer are shown to be substantially greater than the atmospheric density perturbation associated with the propagation of a gravity wave. Because of the density gradients present in atmospheric layers, interesting effects were observed such as a phase reversal in the linear layer response which occurs near the layer peak. Once the layer response is understood, the sodium layer can be used as a tracer of atmospheric wave motions. A two dimensional digital signal processing technique was developed. Both spatial and temporal filtering are utilized to enhance the resolution by decreasing shot noise by more han 10 dB. Many of the features associated with a layer density response to gravity waves were observed in high resolution density profiles of the mesospheric sodium layer. These include nonlinearities as well as the phase reversal in the linear layer response.

Shelton, J. D.↗

The dynamic response of composite beams to axial impact

Large deformation response of simple composite structural elements to intense dynamic loadings is studied by focusing on the response of beams. Overall goals are to: design a simple test fixture to introduce crash related bending loads in beams; determine any difference between large deformation static and large deformation dynamic response; determine the influence of laminate stacking arrangements on the dynamic response, failure mode, and energy absorbed; and predict the dynamic response. Twelve different laminate orientations were investigated. Modeling of the response was done with an existing finite element program. The program computed nonlinear transient response analysis of a structure objected to a time varying load.

Derian, E. J.↗

Responses of a hot film and a pressure probe to acoustic excitation in mean flow

The responses of a hot film sensor and a pressure probe to acoustic excitation in steady flow up to a Mach number of 0.5 were measured and compared with the responses of a microphone, flush mounted in the wall of the flow duct. When compared in terms of fluctuating pressure, the response of the pressure probe was less than that of the wall microphone by about 2.1 dB or less at the 0.5 Mach number, while the response of the ho film probe was as much as 6.0 dB above that of the wall sensor, at the Mach numbers 0.3 and 0.5. In terms of fluctuating Reynolds number, the response of the hot film probe was greater than that of the wall-mounted sensor by at most 5.0 dB at the same Mach numbers. Removing the response contribution from fluctuating temperature in the hot film mathematical model improved the agreement between the two transducer responses for both comparisons.

Jones, M. G.↗