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At least 1,747 records · Page 97
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Effect of Passive Administration of Monoclonal Antibodies Recognizing Simian Immunodeficiency Virus (SIV) V2 in CH59-Like Coil/Helical or β -Sheet Conformations on Time of SIV mac251 Acquisition

The monoclonal antibodies (MAbs) NCI05 and NCI09, isolated from a vacci nated macaque that was protected from multiple simian immunodeficiency virus (SIV) chal lenges, both target an overlapping, conformationally dynamic epitope in SIV envelope vari able region 2 (V2). Here, we show that NCI05 recognizes a CH59-like coil/helical epitope, whereas NCI09 recognizes a b-hairpin linear epitope. In vitro, NCI05 and, to a lesser extent, NCI09 mediate the killing of SIV-infected cells in a CD4-dependent manner. Compared to NCI05, NCI09 mediates higher titers of antibody-dependent cellular cytotoxicity (ADCC) to gp120-coated cells, as well as higher levels of trogocytosis, a monocyte function that contributes to immune evasion. We also found that passive administration of NCI05 or NCI09 to macaques did not affect the risk of SIV mac251 acquisition compared to controls, demonstrating that these anti-V2 antibodies alone are not protective. However, NCI05 but not NCI09 mucosal levels strongly correlated with delayed SIV mac251 acquisition, and functional and structural data suggest that NCI05 targets a transient state of the viral spike apex that is partially opened, compared to its prefusion-closed conformation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Bayesian estimation of HIV acquisition dates for prevention trials

Accurate timing estimates of when participants acquire HIV in HIV prevention trials are necessary for determining antibody levels at acquisition. The Antibody-Mediated Prevention (AMP) Studies showed that a passively administered broadly neutralizing antibody can prevent the acquisition of HIV from a neutralization-sensitive virus. We developed a pipeline for estimating the date of detectable HIV acquisition (DDA) in AMP Study participants using diagnostic and viral sequence data. Using a Bayesian strategy that combines three streams of data (REN [rev/vpu/env/Δnef] sequence, GP [gag/Δpol] sequence, and diagnostic) where their 95% credible intervals overlap based on pre-specified criteria and decision rules. We evaluated the performance of our AMP pipeline using PacBio viral sequence data from 41 participants across two prospective acute HIV acquisition cohort studies, FRESH and RV217, with twice-weekly sampling. These cohort studies enrolled young women in South Africa and men and women in Kenya and Thailand, respectively, with a high likelihood of HIV acquisition. In evaluating performance, “true DDA” was the center of bounds between last-negative and first-positive RNA diagnostic tests (median time 4 days, range 2–7 days); bias was the mean difference between estimated and true DDA. Using diagnostic data alone yielded timing estimates with a bias of 2.4 days and root mean square error (RMSE) of 7.9 days. These results were improved using sequence + diagnostic data (bias 1.5 days, RMSE 6.9 days), as well as by restricting sequence-based estimation to samples from ≤5 weeks post-DDA (bias 0.2 days, RMSE 7.8 days).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Global Network Analysis of Neisseria gonorrhoeae Identifies Coordination between Pathways, Processes, and Regulators Expressed during Human Infection

Neisseria gonorrhoeae is a Gram-negative diplococcus that is responsible for the sexually transmitted infection gonorrhea, a high-morbidity disease in the United States and worldwide. Over the past several years, N. gonorrhoeae strains resistant to antibiotics used to treat this infection have begun to emerge across the globe. Thus, new treatment strategies are needed to combat this organism. Here, we utilized N. gonorrhoeae transcriptomic data sets, including those obtained from natural infection of the human genital tract, to infer the first global gene coexpression network of this pathogen. Interrogation of this network revealed genes central to the network that are likely critical for gonococcal growth, metabolism, and virulence, including genes encoding hypothetical proteins expressed during mucosal infection. In addition, network analysis revealed overlap in the response of N. gonorrhoeae to incubation with neutrophils and exposure to hydrogen peroxide stress in vitro. Network analysis also identified new targets of the gonococcal global regulatory protein Fur, while examination of the network neighborhood of genes allowed us to assign additional putative categories to several proteins. Collectively, the characterization of the first gene coexpression network for N. gonorrhoeae described here has revealed new regulatory pathways and new categories for proteins and has shown how processes important to gonococcal infection in both men and women are linked. This information fills a critical gap in our understanding of virulence strategies of this obligate human pathogen and will aid in the development of new treatment strategies for gonorrhea.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Serodominant SARS-CoV-2 Nucleocapsid Peptides Map to Unstructured Protein Regions

The SARS-CoV-2 nucleocapsid (N) protein is highly immunogenic, and anti-N antibodies are commonly used as markers for prior infection. While several studies have examined or predicted the antigenic regions of N, these have lacked consensus and structural context. Using COVID-19 patient sera to probe an overlapping peptide array, we identified six public and four private epitope regions across N, some of which are unique to this study. We further report the first deposited X-ray structure of the stable dimerization domain at 2.05 Å as similar to all other reported structures. Structural mapping revealed that most epitopes are derived from surface-exposed loops on the stable domains or from the unstructured linker regions. An antibody response to an epitope in the stable RNA binding domain was found more frequently in sera from patients requiring intensive care. Since emerging amino acid variations in N map to immunogenic peptides, N protein variation could impact detection of seroconversion for variants of concern.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics

While numerous health-beneficial interactions between host and microbiota have been identified, there is still a lack of targeted approaches for modulating these interactions. Thus, we here identify precision prebiotics that specifically modulate the abundance of a microbiome member species of interest. In the first step, we show that defining precision prebiotics by compounds that are only taken up by the target species but no other species in a community is usually not possible due to overlapping metabolic niches. Subsequently, we use metabolic modeling to identify precision prebiotics for a two-member Caenorhabditis elegans microbiome community comprising the immune-protective target species Pseudomonas lurida MYb11 and the persistent colonizer Ochrobactrum vermis MYb71. We experimentally confirm four of the predicted precision prebiotics, L-serine, L-threonine, D-mannitol, and γ-aminobutyric acid, to specifically increase the abundance of MYb11. L-serine was further assessed in vivo, leading to an increase in MYb11 abundance also in the worm host. Overall, our findings demonstrate that metabolic modeling is an effective tool for the design of precision prebiotics as an important cornerstone for future microbiome-targeted therapies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Multigrid Optimization for Large-Scale Ptychographic Phase Retrieval

Ptychography is a popular imaging technique that combines diffractive imaging with scanning microscopy. The technique consists of a coherent beam that is scanned across an object in a series of overlapping positions, leading to reliable and improved reconstructions. Ptychographic microscopes allow for large fields to be imaged at high resolution at the cost of additional computational expense. Herein, we propose a multigrid-based optimization framework to reduce the computational burdens of large-scale ptychographic phase retrieval. Our proposed method exploits the inherent hierarchical structures in ptychography through tailored restriction and prolongation operators for the object and data domains. Our numerical results show that our proposed scheme accelerates the convergence of its underlying solver and outperforms the ptychographical iterative engine, a workhorse in the optics community.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Efficient Low-Order Refined Preconditioners for High-Order Matrix-Free Continuous and Discontinuous Galerkin Methods

In this paper, we design preconditioners for the matrix-free solution of high-order continuous and discontinuous Galerkin discretizations of elliptic problems based on finite element method--spectral element method (FEM-SEM) equivalence and additive Schwarz methods. The high-order operators are applied without forming the system matrix, making use of sum factorization for efficient evaluation. The system is preconditioned using a spectrally equivalent low-order (p = 1) finite element operator discretization on a refined mesh. The low-order refined mesh is anisotropic and not shape regular in the polynomial degree of the high-order operator, requiring specialized solvers to treat the anisotropy. We make use of an element-structured, geometric multigrid V-cycle with ordered ILU(0) smoothing. The preconditioner is parallelized through an overlapping additive Schwarz method that is robust in h and p. The method is extended to interior penalty and Bassi and Rebay (BR2) discontinuous Galerkin discretizations, for which it is also robust in the size of the penalty parameter. Finally, numerical results are presented on a variety of examples, verifying the uniformity of the preconditioner.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Spectral Equivalence of Low-Order Discretizations for High-Order H(curl) and H(div) Spaces

In this paper, we present spectral equivalence results for high-order tensor product edge- and face-based finite elements for the H(curl) and H(div) function spaces. Specifically, we show for certain choices of shape functions that the mass and stiffness matrices of the high-order elements are spectrally equivalent to those for an assembly of low-order elements on the associated Gauss--Lobatto--Legendre mesh. Based on this equivalence, efficient preconditioners can be designed with favorable computational complexity. Numerical results are presented which confirm the theory and demonstrate the benefits of the equivalence results for overlapping Schwarz preconditioners.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Applying an Oriented Divergence Theorem to Swept Face Remap

Here we present a novel oriented divergence theorem and apply the results to a swept face remap method (conservative data transfer between two meshes) in arbitrary Langrangian–Eulerian hydrodynamics. In our setting, we compute the material flux along swept regions between corresponding faces in the source and target meshes. Since the swept region may add material, subtract material, or do both when it intersects itself, we cannot apply the conventional divergence theorem without accounting for orientation and self-overlaps. In this work, we encode the swept region orientation and geometry with a map from the unit n -dimensional cube, and then apply an oriented analog of divergence theorem to compute the material flux. We present efficient implementation strategies for the presented method. We also provide numerical evidence supporting our results and discuss extensions to more general mesh topologies.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Domain Decomposition for Integer Optimal Control with Total Variation Regularization

Total variation integer optimal control problems admit solutions and necessary optimality conditions via geometric variational analysis. In spite of the existence of said solutions, algorithms which solve the discretized objective suffer from high numerical cost associated with the combinatorial nature of integer programming. Hence, such methods are often limited to small and medium-sized problems. We propose a globally convergent, coordinate descent–inspired algorithm that allows tractable subproblem solutions restricted to a partition of the domain. Our decomposition method solves relatively small trust-region subproblems that modify the control variable on a subdomain only. Given nontrivial subdomain overlap, we prove that a global first-order necessary optimality condition is equivalent to a first-order necessary optimality condition per subdomain. We additionally show that a sufficient decrease is achieved on a single subdomain by way of a trust-region subproblem solver using geometric measure–theoretic arguments, which we integrate with a greedy patch selection to prove convergence of our algorithm. In conclusion, we demonstrate the practicality of our algorithm on a benchmark large-scale, PDE-constrained integer optimal control problem and find that our method is faster than the state of the art.

domain decomposition↗
DOE OSTI2020

Threshold $\pi ^-$ photoproduction on the neutron

Recent data from the PIONS@MAX-lab Collaboration, measuring the total cross section of the incoherent pion photoproduction reaction, γd → π – pp, near threshold, have been used to extract the E 0+ multipole and total cross section of the reaction γn → π – p, also near threshold. These are the first measurements of the reaction γd → π – pp in the threshold region. The value of E 0+ is extracted through a fit to the deuteron data in a photoproduction model accounting for final-state interactions. The model takes an S-wave approximation for the elementary reaction γn → π – p with E 0+ = const in the threshold region. The fit over all the 6 deuteron data points gives the value E 0+ = –31.86 ± 0.8 (in units 10 –3 /mπ). We explore the dependence of our results on the choice of data subsets included in the fit. Here, the obtained values of E 0+ , for different subsets, have overlapping errors and agree with previous determinations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Mapping the electromagnetic fields of heavy-ion collisions with the Breit-Wheeler process

Ultra-relativistic heavy-ion collisions are expected to produce the strongest electromagnetic fields in the known Universe. These highly-Lorentz contracted fields can manifest themselves as linearly polarized quasi-real photons that can interact via the Breit-Wheeler process to produce lepton anti-lepton pairs. Furthermore, the energy and momentum distribution of the produced dileptons carry information about the strength and spatial distribution of the colliding fields. Recently it has been demonstrated that photons from these fields can interact even in heavy-ion collisions with hadronic overlap, providing a purely electromagnetic probe of the produced medium. In this review we discuss the recent theoretical progress and experimental advances for mapping the ultra-strong electromagnetic fields produced in heavy-ion collisions via measurement of the Breit-Wheeler process.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Study of the p-p-K + and p-p-K - dynamics using the femtoscopy technique

The interactions of kaons (K) and antikaons ($\bar{K}$ ) with few nucleons (N) were studied so far using kaonic atom data and measurements of kaon production and interaction yields in nuclei. Some details of the three-body $\bar{K}$NN and NN dynamics are still not well understood, mainly due to the overlap with multi-nucleon interactions in nuclei. An alternative method to probe the dynamics of three-body systems with kaons is to study the final state interaction within triplet of particles emitted in pp collisions at the Large Hadron Collider, which are free from effects due to the presence of bound nucleons. This Letter reports the first femtoscopic study of p–p–K + and p–p–K - correlations measured in high-multiplicity pp collisions at $\sqrt{s}$ = 13 TeV by the ALICE Collaboration. The analysis shows that the measured p–p–K + and p–p–K - correlation functions can be interpreted in terms of pairwise interactions in the triplets, indicating that the dynamics of such systems is dominated by the two-body interactions without significant contributions from three-body effects or bound states.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Demonstration of the rodeo algorithm on a quantum computer

The rodeo algorithm is an efficient algorithm for eigenstate preparation and eigenvalue estimation for any observable on a quantum computer. This makes it a promising tool for studying the spectrum and structure of atomic nuclei as well as other fields of quantum many-body physics. The only requirement is that the initial state has sufficient overlap probability with the desired eigenstate. While it is exponentially faster than well-known algorithms such as phase estimation and adiabatic evolution for eigenstate preparation, it has yet to be implemented on an actual quantum device. In this work, we apply the rodeo algorithm to determine the energy levels of a random one-qubit Hamiltonian, resulting in a relative error of 0.08% using mid-circuit measurements on the IBM Q device Casablanca. This surpasses the accuracy of directly-prepared eigenvector expectation values using the same quantum device. We take advantage of the high-accuracy energy determination and use the Hellmann-Feynman theorem to compute eigenvector expectation values for a different random one-qubit observable. For the Hellmann-Feynman calculations, we find a relative error of 0.7%. Here, we conclude by discussing possible future applications of the rodeo algorithm for multi-qubit Hamiltonians.

algorithm↗
DOE OSTI2021

Observation of new excited ${B} ^0_{s}$ states

A structure is observed in the ${B} ^{\pm }{K} ^{\mp }$ mass spectrum in a sample of proton–proton collisions at centre-of-mass energies of 7, 8, and 13 TeV, collected with the LHCb detector and corresponding to a total integrated luminosity of 9$\,\text {fb} ^{-1}$. The structure is interpreted as the result of overlapping excited ${B} ^0_{s}$ states. With high significance, a two-peak hypothesis provides a better description of the data than a single resonance. Under this hypothesis the masses and widths of the two states, assuming they decay directly to ${B} ^{\pm }{K} ^{\mp }$, are determined to be $\begin{aligned} m_1&= 6063.5 \pm 1.2 \text { (stat)} \pm 0.8\text { (syst)}\,\text {Me}\text {V}, \\ \Gamma _1&= 26 \pm 4 \text { (stat)} \pm 4\text { (syst)}\,\text {Me}\text {V}, \\ m_2&= 6114 \pm 3 \text { (stat)} \pm 5\text { (syst)}\,\text {Me}\text {V}, \\ \Gamma _2&= 66 \pm 18 \text { (stat)} \pm 21\text { (syst)}\,\text {Me}\text {V}. \end{aligned}$ Alternative values assuming a decay through ${B} ^{*\pm }{K} ^{\mp }$, with a missing photon from the $B^{*\pm } \rightarrow B^{\pm }\gamma $ decay, which are shifted by approximately 45 $\,\text {Me}$V, are also determined. The possibility of a single state decaying in both channels is also considered. The ratio of the total production cross-section times branching fraction of the new states relative to the previously observed $B_{s2}^{*0}$ state is determined to be $0.87 \pm 0.15 \text { (stat)} \pm 0.19 \text { (syst)}$.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Configuration and performance of the ATLAS b -jet triggers in Run 2

Several improvements to the ATLAS triggers used to identify jets containing b-hadrons (b-jets) were implemented for data-taking during Run 2 of the Large Hadron Collider from 2016 to 2018. These changes include reconfiguring the b-jet trigger software to improve primary-vertex finding and allow more stable running in conditions with high pile-up, and the implementation of the functionality needed to run sophisticated taggers used by the offline reconstruction in an online environment. These improvements yielded an order of magnitude better light-flavour jet rejection for the same b-jet identification efficiency compared to the performance in Run 1 (2011–2012). The efficiency to identify b-jets in the trigger, and the conditional efficiency for b-jets that satisfy offline b-tagging requirements to pass the trigger are also measured. Correction factors are derived to calibrate the b-tagging efficiency in simulation to match that observed in data. The associated systematic uncertainties are substantially smaller than in previous measurements. In addition, b-jet triggers were operated for the first time during heavy-ion data-taking, using dedicated triggers that were developed to identify semileptonic b-hadron decays by selecting events with geometrically overlapping muons and jets.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Search for heavy Majorana or Dirac neutrinos and right-handed $W$ gauge bosons in final states with charged leptons and jets in $pp$ collisions at $\sqrt{s}=13$ TeV with the ATLAS detector

A search for heavy right-handed Majorana or Dirac neutrinos N R and heavy right-handed gauge bosons W R is performed in events with energetic electrons or muons, with the same or opposite electric charge, and energetic jets. The search is carried out separately for topologies of clearly separated final-state products (“resolved” channel) and topologies with boosted final states with hadronic and/or leptonic products partially overlapping and reconstructed as a large-radius jet (“boosted” channel). The events are selected from pp collision data at the LHC with an integrated luminosity of 139 fb -1 collected by the ATLAS detector at $\sqrt{s}=13$ TeV. No significant deviations from the Standard Model predictions are observed. The results are interpreted within the theoretical framework of a left-right symmetric model, and lower limits are set on masses in the heavy right handed W R boson and N R plane. The excluded region extends to about m(W R ) = 6.4 TeV for both Majorana and Dirac N R neutrinos at m(N R ) < 1 TeV. N R with masses of less than 3.5 (3.6) TeV are excluded in the electron (muon) channel at m(W R ) = 4.8 TeV for the Majorana neutrinos, and lim its of m(N R ) up to 3.6 TeV for m(W R ) = 5.2 (5.0) TeV in the electron (muon) channel are set for the Dirac neutrinos. These constitute the most stringent exclusion limits to date for the model considered.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Measurement of the inclusive isolated-photon production cross section in pp collisions at $\mathbf {\sqrt{\textit{s}}=13}$ TeV

The production cross section of inclusive isolated photons has been measured by the ALICE experiment at the CERN LHC in pp collisions at centre-of-momentum energy of $\mathbf {\sqrt{\textit{s}}=13}$ TeV collected during the LHC Run 2 data-taking period. The measurement is performed by combining the measurements of the electromagnetic calorimeter EMCal and the central tracking detectors ITS and TPC, covering a pseudorapidity range of and a transverse momentum range of |η γ | < 0.67 and a transverse momentum range 7 < p$^{γ}_{T}$ < 200 GeV/c. The result extends to lower p$^{γ}_{T}$ and x$^{γ}_{T}$ = 2p$^{γ}_{T}$/$\sqrt{s}$ ranges, the lowest x$^{γ}_{T}$ of any isolated photon measurements to date, extending significantly those measured by the ATLAS and CMS experiments towards lower p$^{γ}_{T}$ at the same collision energy with a small overlap between the measurements. The measurement is compared with next-to-leading order perturbative QCD calculations and the results from the ATLAS and CMS experiments as well as with measurements at other collision energies. The measurement and theory prediction are in agreement with each other within the experimental and theoretical uncertainties.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗