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At least 163 records · Page 9

Preexisting memory CD4 + T cells contribute to the primary response in an HIV-1 vaccine trial

Naive and memory CD4 + T cells reactive with human immunodeficiency virus type 1 (HIV-1) are detectable in unexposed, unimmunized individuals. The contribution of preexisting CD4 + T cells to a primary immune response was investigated in 20 HIV-1–seronegative volunteers vaccinated with an HIV-1 envelope (Env) plasmid DNA prime and recombinant modified vaccinia virus Ankara (MVA) boost in the HVTN 106 vaccine trial (clinicaltrials.gov NCT02296541). Prevaccination naive or memory CD4 + T cell responses directed against peptide epitopes in Env were identified in 14 individuals. After priming with DNA, 40% (8/20) of the elicited responses matched epitopes detected in the corresponding preimmunization memory repertoires, and clonotypes were shared before and after vaccination in 2 representative volunteers. In contrast, there were no shared epitope specificities between the preimmunization memory compartment and responses detected after boosting with recombinant MVA expressing a heterologous Env. Preexisting memory CD4 + T cells therefore shape the early immune response to vaccination with a previously unencountered HIV-1 antigen.

60 APPLIED LIFE SCIENCES↗

Updated HIV-1 Consensus Sequences Change but Stay Within Similar Distance From Worldwide Samples

HIV consensus sequences are used in various bioinformatic, evolutionary, and vaccine related research. Since the previous HIV-1 subtype and CRF consensus sequences were constructed in 2002, the number of publicly available HIV-1 sequences have grown exponentially, especially from non-EU and US countries. Here, we reconstruct 90 new HIV-1 subtype and CRF consensus sequences from 3,470 high-quality, representative, full genome sequences in the LANL HIV database. While subtypes and CRFs are unevenly spread across the world, in total 89 countries were represented. For consensus sequences that were based on at least 20 genomes, we found that on average 2.3% (range 0.8–10%) of the consensus genome site states changed from 2002 to 2021, of which about half were nucleotide state differences and the rest insertions and deletions. Interestingly, the 2021 consensus sequences were shorter than in 2002, and compared to 4,674 HIV-1 worldwide genome sequences, the 2021 consensuses were somewhat closer to the worldwide genome sequences, i.e., showing on average fewer nucleotide state differences. Some subtypes/CRFs have had limited geographical spread, and thus sampling of subtypes/CRFs is uneven, at least in part, due to the epidemiological dynamics. Thus, taken as a whole, the 2021 consensus sequences likely are good representations of the typical subtype/CRF genome nucleotide states. The new consensus sequences are available at the LANL HIV database.

60 APPLIED LIFE SCIENCES↗

A Coupled Analysis of Atmospheric Mass Loss and Tidal Evolution in XUV Irradiated Exoplanets: The TRAPPIST-1 Case Study

Exoplanets residing close to their stars can experience evolution of both their physical structures and their orbits due to the influence of their host stars. In this work, we present a coupled analysis of dynamical tidal dissipation and atmospheric mass loss for exoplanets in X-ray and ultraviolet (XUV) irradiated environments. As our primary application, we use this model to study the TRAPPIST-1 system and place constraints on the interior structure and orbital evolution of the planets. We start by reporting on an ultraviolet continuum flux measurement (centered around ∼1900 Å) for the star TRAPPIST-1, based on 300 ks of Neil Gehrels Swift Observatory data, and which enables an estimate of the XUV-driven thermal escape arising from XUV photodissociation for each planet. We find that the X-ray flaring luminosity, measured from our X-ray detections, of TRAPPIST-1 is 5.6 × 10{sup −4} L {sub *}, while the full flux including non-flaring periods is 6.1 × 10{sup −5} L {sub *}, when L {sub *} is TRAPPIST-1's bolometric luminosity. We then construct a model that includes both atmospheric mass loss and tidal evolution and requires the planets to attain their present-day orbital elements during this coupled evolution. We use this model to constrain the ratio Q{sup ′}=3Q/2k{sub 2} for each planet. Finally, we use additional numerical models implemented with the Virtual Planet Simulator VPLanet to study ocean retention for these planets using our derived system parameters.

79 ASTRONOMY AND ASTROPHYSICS↗

The GD-1 Stellar Stream Perturber as a Core-collapsed Self-interacting Dark Matter Halo

The GD-1 stellar stream exhibits spur and gap structures that may result from a close encounter with a dense substructure. When interpreted as a dark matter subhalo, the perturber is denser than predicted in the standard cold dark matter (CDM) model. In self-interacting dark matter (SIDM), however, a halo could evolve into a phase of gravothermal collapse, resulting in a higher central density than its CDM counterpart. We conduct high-resolution controlled N-body simulations to show that a collapsed SIDM halo could account for the GD-1 perturber's high density. We model a progenitor halo with a mass of 3 × 10 8 M ⊙ , motivated by a cosmological simulation of a Milky Way analog, and evolve it in the Milky Way's tidal field. For a cross section per mass of σ/m ≈ 30–100 cm 2 g −1 at ${V}_{{\rm{\max }}}\unicode{x0007E}10\,{\rm{km}}\,{{\rm{s}}}^{-1}$, the enclosed mass of the SIDM halo within the inner 10 pc can be increased by more than 1 order of magnitude compared to its CDM counterpart, leading to a good agreement with the properties of the GD-1 perturber. Our findings indicate that stellar streams provide a novel probe into the self-interacting nature of dark matter.

dark matter↗

Methods related to a structure of high-affinity human PD-1/PD-L2 complex

Variants of human PD-1 comprising one or more of amino acid substitutions in residues corresponding to N74, T76 and A132 of SEQ ID NO:1 are described. Also described are structures, obtained using X-ray crystallography, of the human PD-1/PD-L2 complex and mutant PD-1 variants. The structures of human PD-1 described in the present disclosure are useful in drug discovery, including small-molecule drug discovery. Accordingly, methods of using the structures in drug discovery are also described.

59 BASIC BIOLOGICAL SCIENCES↗

Microstructural and Micro-Chemical Evolutions in the Irradiated UCO Fuel Kernels of AGR-1 and AGR-2 TRISO Fuel Particles

AGR-1 and AGR-2 TRISO fuel particles were fabricated with slightly different fuel kernel chemical compositions, modified fabrication processes, different fuel kernel diameters, and changed 235U enrichments. To correlate those differences with the fuel kernel responses to neutron irradiations in terms of irradiated fuel microstructure, fission products chemical and physical states, and fission gas bubble evolutions, extensive microstructural and analytical characterizations were conducted. The studies used a state of art transmission electron microscopy (TEM) equipped with Energy-dispersive X-ray spectroscopy (EDS) of four silicon solid-state detectors which have super sensitivity and fast speed. The TEM specimens were prepared from selected AGR-1 and AGR-2 irradiated fuel kernels exposed to safety testing after irradiation. The particles were chosen to represent a representative irradiation conditions with a fuel burnup within the range from 10.8 to 18.6% FIMA, and the time-average volume-average temperatures vary from 1070 to 1287°C. The 235U enrichment was 19.74 wt.% for the AGR1 fuel kernels and 14.03 wt.% for the AGR-2 fuel kernels. The TEM results show that there were significant microstructural reconstructions in the irradiated fuel kernels for both the AGR-1 and AGR-2 fuels. There are four major phases including fuel matrix of UO2 and UC, U2RuC2, and UMoC2 in the irradiated AGR2 fuel kernel. Zr and Nb form solid solution in the UC phase. UMoC2 phase often shows a detectable concentration of Tc. Pd was found to mainly locate in the buffer layer or to be associated with fission gas bubble within the UMoC2 phase. The EDS maps qualitatively show that the rare-earth fission products (Nb, et al.) preferentially reside in the UO2 phase. In contrast, in the irradiated AGR1 fuel kernel, no U2RuC2 or UMoC2 precipitates were positively identified. Instead, there is a high number of rod-shape precipitates enriched with Ru, Tc, Rh, and Pd observed in the fuel kernel center and edge zone. The difference of microstructural and micro-chemical evolutions in irradiated fuel kernels between the AGR-1 and AGR-2 TRISO fuel particle may result from a combined factor of irradiation temperature, fuel geometry and chemical composition. However, the irradiation temperature probably play a more deterministic role. Limited electron energy loss spectroscopy (EELS) characterizations on the AGR2 fuel kernel show that there is nearly no carbon in the UO2 phase while a small fraction of oxygen was detected in the UC/UMoC2 phase.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Update on ASME AG-1 and Revision of the DOE Nuclear Air Cleaning Handbook - 20536

The American Society of Mechanical Engineers AG-1 Code on Nuclear Air and Gas Treatment is updated every two years. This paper provides an overview of issues being discussed within AG-1 committee meetings and revisions that will be included in the next version of the code. Additional information is provided on issues being discussed ranging from media velocity limits, control of airflow using actual versus and standard cubic feet per minute. Navigation and identification of applicable high-efficiency particulate air (HEPA) filter code sections can be confusing for those unfamiliar with AG-1. A general reorganization of filtration code sections clarifies geometry, flow, and performance envelopes for nuclear grade HEPA filters. The initial step consists of establishment of Section FN covering qualification of conventional, ceramic, metal, and high strength fibrous glass media. Future filter sections are currently expected to be characterized by geometry and flow direction (axial vs. radial). The Department of Energy's (DOE) Nuclear Air Cleaning Handbook (NACH) is also undergoing revision. An update on the status of that effort, along with issues and changes being considered. The original charter of the AG-1 Code was specific to commercial nuclear power plants, and to safety-related air cleaning systems. This has evolved over the years to include normal non-safety ventilation systems and process gas systems. Corollary guidance for DOE facilities has been available in several editions of the Nuclear Air Cleaning Handbook, starting with ORNL-NSIC 65. The latest edition of the Handbook, 2003, is undergoing revision and modifications. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Joint Modeling of GD-1 and C-19 as Old Streams

DESI observational data for the GD-1 and C-19 streams are compared to stream simulations in a common evolving multi-halo potential of a Milky Way-like galaxy based on a cosmological simulation. The goal is to find the best match of the stream velocity spread and the density power spectrum stream density to simulations having either CDM or WDM subhalos. The cocoon velocity width integrated over the length of the stream is independent of orbital blurring along the stream and the power spectrum integrates over the width of the stream, sidestepping the geometric details of the streams. Streams develop from star clusters inserted at $\simeq$1 Gyr after the Big Bang and evolved for 13 Gyr to their current orbital positions. Streams in a CDM subhalo population provide the best match to the velocity width, with streams younger than 10 Gyr ruled out as insufficiently hot. The progenitor star cluster masses, which determine the fraction of stars released at late times which comprise the stream core, are found to be $\simeq 8\times 10^4 M_\odot$ for GD-1 and $\simeq 4\times 10^4 M_\odot$ for C-19, although the mass depends on the star cluster half mass radius. Stream heating leads to stream lumpiness which is measurable for the relatively large and clean GD-1 dataset. The stream density power spectrum measured along the length of the DESI GD-1 sample is in good agreement with CDM simulations, with 1.7 to 1.9 times more power than WDM 7 keV and 5.5 keV simulations.

Carlberg, Raymond G. [Toronto U.] (ORCID:000000027↗

HIV-1 transmitted drug resistance surveillance: shifting trends in study design and prevalence estimates

HIV-1 transmitted drug resistance (TDR) prevalence increased during the initial years of the antiretroviral therapy (ART) global scale-up. Few studies have examined recent trends in TDR prevalence using published genetic sequences and described the characteristics of ART-naïve persons from whom these published sequences have been obtained. We identified 125 studies published between 2014 and 2019 for which HIV-1 reverse transcriptase (RT) with or without protease from ≥50 ART-naïve adult persons were submitted to the GenBank sequence database. The population characteristics and TDR prevalence were compared to those in 122 studies published in the preceding five years between 2009 and 2013. TDR prevalence was analysed using median study-level and person-level data. The 2009 to 2013 and 2014 to 2019 studies reported sequence data from 32,866 and 41,724 ART-naïve persons respectively. Studies from the low- and middle-income country (LMIC) regions in sub-Saharan Africa, South/Southeast Asia and Latin America/Caribbean accounted for approximately two-thirds of the studies during each period. Between the two periods, the proportion of studies from sub-Saharan Africa and from South/Southeast Asia countries other than China decreased from 43% to 32% and the proportion of studies performed at sentinel sites for recent HIV-1 infection decreased from 33% to 22%. Between 2014 and 2019, median study-level TDR prevalence was 4.1% in South/Southeast Asia, 6.0% in sub-Saharan Africa, 9.1% in Latin America/Caribbean, 8.5% in Europe and 14.2% in North America. In the person-level analysis, there was an increase in overall, NNRTI and two-class NRTI/NNRTI resistance in sub-Saharan Africa; an increase in NNRTI resistance in Latin America/Caribbean, and an increase in overall, NNRTI and PI resistance in North America. Overall, NNRTI and dual NRTI/NNRTI-associated TDR prevalence was significantly higher in sub-Saharan Africa studies published between 2014 and 2019 compared with those published between 2009 and 2013. The decreasing proportion of studies from the hardest hit LMIC regions and the shift away from sentinel sites for recent infection suggests that global TDR surveillance efforts and publication of findings require renewed emphasis.

60 APPLIED LIFE SCIENCES↗

Evaluation of darunavir-derived HIV-1 protease inhibitors incorporating P2' amide-derivatives: Synthesis, biological evaluation and structural studies

Here, we report here the synthesis and biological evaluation of darunavir derived HIV-1 protease inhibitors and their functional effect on enzyme inhibition and antiviral activity in MT-2 cell lines. The P2' 4-amino functionality was modified to make a number of amide derivatives to interact with residues in the S2' subsite of the HIV-1 protease active site. Several compounds exhibited picomolar enzyme inhibitory and low nanomolar antiviral activity. The X-ray crystal structure of the chloroacetate derivative bound to HIV-1 protease was determined. Interestingly, the active chloroacetate group converted to the acetate functionality during X-ray exposure. The structure revealed that the P2' carboxamide functionality makes enhanced hydrogen bonding interactions with the backbone atoms in the S2'-subsite.

59 BASIC BIOLOGICAL SCIENCES↗

Exploration of imatinib and nilotinib-derived templates as the P2-Ligand for HIV-1 protease inhibitors: Design, synthesis, protein X-ray structural studies, and biological evaluation

Structure-based design, synthesis, X-ray structural studies, and biological evaluation of a new series of potent HIV-1 protease inhibitors are described. Here, these inhibitors contain various pyridyl-pyrimidine, aryl thiazole or alkylthiazole derivatives as the P2 ligands in combination with darunavir-like hydroxyethylamine sulfonamide isosteres. These heterocyclic ligands are inherent to kinase inhibitor drugs, such as nilotinib and imatinib. These ligands are designed to make hydrogen bonding interactions with the backbone atoms in the S2 subsite of HIV-1 protease. Various benzoic acid derivatives have been synthesized and incorporation of these ligands provided potent inhibitors that exhibited subnanomolar level protease inhibitory activity and low nanomolar level antiviral activity. Two high resolution X-ray structures of inhibitor-bound HIV-1 protease were determined. These structures provided important ligand-binding site interactions for further optimization of this class of protease inhibitors.

60 APPLIED LIFE SCIENCES↗

HIV-1 protease inhibitors with a P1 phosphonate modification maintain potency against drug-resistant variants by increased interactions with flap residues

Protease inhibitors are the most potent antivirals against HIV-1, but they still lose efficacy against resistant variants. Improving the resistance profile is key to developing more robust inhibitors, which may be promising candidates for simplified next-generation antiretroviral therapies. Here, in this study, we explored analogs of darunavir with a P1 phosphonate modification in combination with increasing size of the P1′ hydrophobic group and various P2′ moieties to improve potency against resistant variants. The phosphonate moiety substantially improved potency against highly mutated and resistant HIV-1 protease variants, but only when combined with more hydrophobic moieties at the P1′ and P2′ positions. Phosphonate analogs with a larger hydrophobic P1′ moiety maintained excellent antiviral potency against a panel of highly resistant HIV-1 variants, with significantly improved resistance profiles. The cocrystal structures indicate that the phosphonate moiety makes extensive hydrophobic interactions with the protease, especially with the flap residues. Many residues involved in these protease-inhibitor interactions are conserved, enabling the inhibitors to maintain potency against highly resistant variants. These results highlight the need to balance inhibitor physicochemical properties by simultaneous modification of chemical groups to further improve resistance profiles.

60 APPLIED LIFE SCIENCES↗

Structural characterization of HIV-1 matrix mutants implicated in envelope incorporation

During the late phase of HIV-1 infection, viral Gag polyproteins are targeted to the plasma membrane (PM) for assembly. Gag localization at the PM is a prerequisite for the incorporation of the envelope protein (Env) into budding particles. Gag assembly and Env incorporation are mediated by the N-terminal myristoylated matrix (MA) domain of Gag. Nonconservative mutations in the trimer interface of MA (A45E, T70R, and L75G) were found to impair Env incorporation and infectivity, leading to the hypothesis that MA trimerization is an obligatory step for Env incorporation. Conversely, Env incorporation can be rescued by a compensatory mutation in the MA trimer interface (Q63R). The impact of these MA mutations on the structure and trimerization properties of MA is not known. In this study, we employed NMR spectroscopy, X-ray crystallography, and sedimentation techniques to characterize the structure and trimerization properties of HIV-1 MA A45E, Q63R, T70R, and L75G mutant proteins. NMR data revealed that these point mutations did not alter the overall structure and folding of MA but caused minor structural perturbations in the trimer interface. Analytical ultracentrifugation data indicated that mutations had a minimal effect on the MA monomer–trimer equilibrium. The high-resolution X-ray structure of the unmyristoylated MA Q63R protein revealed hydrogen bonding between the side chains of adjacent Arg-63 and Ser-67 on neighboring MA molecules, providing the first structural evidence for an additional intermolecular interaction in the trimer interface. These findings advance our knowledge of the interplay of MA trimerization and Env incorporation into HIV-1 particles.

60 APPLIED LIFE SCIENCES↗

Molecular design and fabrication of PIM-1/polyphosphazene blend membranes with high performance for CO 2 /N 2 separation

New polymeric blend membranes for CO 2 separation were synthesized based on insights from molecular dynamics simulation. A molecular-level structure-property relationship in polymers of intrinsic microporosity (PIM) based blend membranes, was investigated in detail computationally. Calculated local density profiles and energy of interaction of the blend membranes, composed of PIM-1 and various polyphosphazenes, showed that using the polyphosphazene with a higher concentration of ether side chains can improve the compatibility with PIM-1. Furthermore, based on the findings of computational studies, blend membranes were experimentally fabricated from PIM-1 and polyphosphazenes with various polyether side chain concentrations. Polyether concentration in polyphosphazenes was correlated with the film properties and gas transport performance of the blend membranes. Blend membranes showed very high CO 2 permeability (3100-5300 barrer) and improved CO 2 /N 2 selectivity (24-28), outperforming all other PIM-based blend membranes reported to date. Moreover, the CO 2 permeability performance of the blend membranes was tested 566 hours under real post-combustion flue gas from a coal-fired power plant, including CO 2 , N 2 , H 2 O, O 2 , SO x and NO x .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Search for heavy long-lived charged particles with level-1 trigger scouting data from proton-proton collisions at $\sqrt{s} = 13.6$ TeV

A search for heavy long-lived charged particles at the LHC is presented. Particles interacting with the CMS muon detector across several bunch crossings are searched for using a data sample of proton-proton collisions at $\sqrt{s}$ = 13.6 TeV collected with the CMS detector in 2024, corresponding to an integrated luminosity of 3.7 fb$^{-1}$. This is the first search relying on the novel level-1 trigger scouting data set collected without any trigger selection, allowing correlations between bunch crossings to be analyzed. The results are interpreted as upper limits on the cross sections of several benchmark processes with pair production of heavy long-lived charged particles. Upper limits on the fiducial cross section of a heavy long-lived charged particle with $p_\mathrm{T}$$\gt$ 500 GeV and $\lvertη\rvert$$\lt$ 0.83 are also set in different ranges of $β=v/c$. This analysis is a crucial proof of concept for the level-1 trigger data scouting system and complements existing searches for heavy long-lived charged particles by extending the sensitivity to lower $β$ values.

CMS↗

ToF-SIMS spectral analysis of Shewanella oneidensis MR-1 biofilms

Analysis of bacterial biofilms is particularly challenging and important with diverse applications from systems biology to biotechnology. Among the variety of techniques that have been applied, time-of-flight secondary ion mass spectrometry (ToF-SIMS) has many powerful features in studying the surface characteristics of biofilms. ToF-SIMS offers high spatial resolution, mass resolution, and mass accuracy, which permit surface sensitive analysis of biofilm components. Thus, ToF-SIMS provides a powerful solution to addressing the challenge of bacterial biofilm analysis. This dataset covers ToF-SIMS analysis of Shewanella oneidensis MR-1 isolated from freshwater lake sediment in New York state. The MR-1 strain is known to have metal and sulfur reducing properties and it can be used for bioremediation and wastewater treatment. There is a current need to identify small molecules and fragments produced from bacterial biofilms, especially those from extracellular polymeric substance (EPS). Static ToF-SIMS spectra of MR-1 were obtained using an IONTOF TOF.SIMS V instrument equipped with a 25 keV Bi$^+_3$ metal ion gun. Identified molecules and molecular fragments are compared against known biological databases and the reported peaks have at least 65 ppm mass accuracy. These molecules range from lipids, fatty acids, flavonoids, and quinolones to other naturally occurring organic compounds. It is anticipated that the mass spectral identification of key peaks will assist detection of metabolites, EPS molecules like polysaccharides, and biologically relevant small organic molecules using ToF-SIMS in future surface and interface research.

59 BASIC BIOLOGICAL SCIENCES↗

Different evolutionary pathways of HIV-1 between fetus and mother perinatal transmission pairs indicate unique immune selection in fetuses

Study of evolution and selection pressure on HIV-1 in fetuses will lead to a better understanding of the role of immune responses in shaping virus evolution and vertical transmission. Detailed genetic analyses of HIV-1 env gene from 12 in utero transmission pairs show that most infections (67%) occur within 2 months of childbirth. In addition, the env sequences from long-term-infected fetuses are highly divergent and form separate phylogenetic lineages from their cognate maternal viruses. Host-selection sites unique to neonate viruses are identified in regions frequently targeted by neutralizing antibodies and T cell immune responses. Identification of unique selection sites in the env gene of fetal viruses indicates that the immune system in fetuses is capable of exerting selection pressure on viral evolution. Studying selection and evolution of HIV-1 or other viruses in fetuses can be an alternative approach to investigate adaptive immunity in fetuses.

60 APPLIED LIFE SCIENCES↗

XRISM high-resolution X-ray spectroscopy of Cygnus X-1: Highly ionized iron absorption structures

We present the first high-resolution X-ray spectral analysis of Cygnus X-1 using XRISM. The observation wa3s carried out from 2024 April 7 to 10, covering the orbital phase range 0.65–0.17 during its low/hard state. Taking advantage of the exceptional energy resolution of the Resolve instrument, we examined highly ionized iron absorption lines and characterized the ionization states, column densities, and line-of-sight velocities of the absorbing plasma. Spectral analysis revealed an ionization parameter of $\xi \sim 3$, column densities of a few $\times 10^{21}$ cm$^{-2}$, and a blueshifted velocity of $\sim$100 km s$^{-1}$. The observation was divided into two phases: before and after orbital phase $\phi _{\rm {orb}} = 0.9$, corresponding to non-dipping and dipping intervals. While only weak absorption features were present before $\phi _{\rm {orb}} = 0.9$, strong absorption by He-like and H-like Fe appeared during the dipping phase. We measured equivalent widths of 2.3, 0.4, and 1.2 eV for He-like Fe K$\alpha$ and H-like Ly$\alpha _1$ and Ly$\alpha _2$, respectively—demonstrating the capability of XRISM Resolve to securely detect narrow absorption features of only a few eV. These measurements trace the motion of the absorbing material and offer insight into the kinematics and spatial distribution of the wind in the vicinity of the black hole. These findings enhance our understanding of wind-fed accretion in Cygnus X-1 and highlight the importance of continued high-resolution X-ray observations to further constrain the physical properties of winds and accretion flows in high-mass X-ray binaries.

Astronomy and AstroPhysics↗