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At least 757 records · Page 42

Transcription of hepatitis B surface antigen shifts from cccDNA to integrated HBV DNA during treatment

The cornerstone of functional cure for chronic hepatitis B (CHB) is hepatitis B surface antigen (HBsAg) loss from blood. HBsAg is encoded by covalently closed circular DNA (cccDNA) and HBV DNA integrated into the host genome (iDNA). Nucleos(t)ide analogs (NUCs), the mainstay of CHB treatment, rarely lead to HBsAg loss, which we hypothesized was due to continued iDNA transcription despite decreased cccDNA transcription. To test this, we applied a multiplex droplet digital PCR that identifies the dominant source of HBsAg mRNAs to 3,436 single cells from paired liver biopsies obtained from 10 people with CHB and HIV receiving NUCs. With increased NUC duration, cells producing HBsAg mRNAs shifted their transcription from chiefly cccDNA to chiefly iDNA. This shift was due to both a reduction in the number of cccDNA-containing cells and diminished cccDNA-derived transcription per cell; furthermore, it correlated with reduced detection of proteins deriving from cccDNA but not iDNA. Despite this shift in the primary source of HBsAg, rare cells remained with detectable cccDNA-derived transcription, suggesting a source for maintaining the replication cycle. Functional cure must address both iDNA and residual cccDNA transcription. Further research is required to understand the significance of HBsAg when chiefly derived from iDNA.

59 BASIC BIOLOGICAL SCIENCES↗

Mocking the u-plane integral

Abstract The u -plane integral is the contribution of the Coulomb branch to correlation functions of $${\mathcal {N}}=2$$ N = 2 gauge theory on a compact four-manifold. We consider the u -plane integral for correlators of point and surface observables of topologically twisted theories with gauge group $$\mathrm{SU}(2)$$ SU ( 2 ) , for an arbitrary four-manifold with $$(b_1,b_2^+)=(0,1)$$ ( b 1 , b 2 + ) = ( 0 , 1 ) . The u -plane contribution equals the full correlator in the absence of Seiberg–Witten contributions at strong coupling, and coincides with the mathematically defined Donaldson invariants in such cases. We demonstrate that the u -plane correlators are efficiently determined using mock modular forms for point observables, and Appell–Lerch sums for surface observables. We use these results to discuss the asymptotic behavior of correlators as function of the number of observables. Our findings suggest that the vev of exponentiated point and surface observables is an entire function of the fugacities.

Mathematics↗

Discovery of a Hybrid System for Photocatalytic CO 2 Reduction via Attachment of a Molecular Cobalt-Quaterpyridine Complex to a Crystalline Carbon Nitride

While recent reports have demonstrated the attachment of molecular catalysts to amorphous, graphitic carbon nitrides (g-CN) for light-driven CO 2 reduction, approaches to the utilization of crystalline carbon nitrides have remained undiscovered. Herein, a functional hybrid photocatalyst system has been found using a crystalline carbon nitride semiconductor, poly(triazine imide) lithium chloride (PTI-LiCl), with a surface-attached CoCl 2 (qpy-Ph-COOH) catalyst for CO 2 reduction. The molecular catalyst attaches to PTI-LiCl at concentrations from 0.10 to 4.30 wt % and exhibits ∼96% selectivity for CO production in a CO 2 -saturated, aqueous 0.5 M KHCO 3 solution. Optimal loadings were found to be within 0.42–1.04 wt % with rates between 1,400 and 1,550 μmol CO/g·h at an irradiance of 172 mW/cm 2 (λ = 390 nm) and apparent quantum yields of ∼2%. This optimized loading is postulated to represent a balance between maximal turnover frequency (TOF; 300+ h –1 ) and excess catalyst that can limit excited-electron lifetimes, as probed via transient absorption spectroscopy. An increase in the incident irradiance yields a concomitant increase in the TOFs and CO rates only for the higher catalyst loadings, reaching up to 2,149 μmol CO/g·h with a more efficient use of the catalyst surface capacity. The lower catalyst loadings, by comparison, already function at maximal TOFs. Higher surface loadings are also found to help mitigate deactivation of the molecular catalysts during extended catalytic testing (>24 h) owing to the greater net surface capacity for CO 2 reduction, thus representing an effective strategy to extend lifetime. The hybrid particles can be deposited onto an FTO substrate to yield ∼60% Faradaic efficiency for photoelectrochemical CO production at −1.2 V vs Ag/AgCl bias. In conclusion, these results demonstrate the synergistic combination of a crystalline carbon nitride with a molecular catalyst that achieves among the highest known rates in carbon-nitride systems for the light-driven CO 2 reduction to CO in aqueous solution with >95% selectivity.

CO2 reduction↗

Functional variability in specific root respiration translates to autotrophic differences in soil respiration in a temperate deciduous forest

CO 2 release from forest soils (R s ) is a prominent flux in the global carbon cycle. Rs is derived from roots (autotrophic respiration, R a ) and microbial (heterotrophic) respiration and is highly dynamic, as it depends on edaphic and environmental conditions as well as root functional traits and microbial community composition. It is unclear how root functional traits affect root and microbial respiration rates; however, their consideration may help parse out the relative contributions of root and microbial respiration to R s . At a temperate forest site, root systems of 3–4 functional root orders and their surrounding surface soil were carefully excavated and placed into custom trays designed to repeatedly measure R s in situ on eight temperate tree species that varied in their root functional strategies and mycorrhizal affinity. R s was measured bi-weekly to monthly for nearly one year using a custom chamber attached to a gas exchange system. R s varied over time, ranging from 0.3 to 12 µmol m -2 s -1 . Comparable root systems of the same species were excised from the soil and specific root respiration rates (R r ) were measured. Rr ranged from 2.5 to 9.0 nmol g -1 s -1 and was negatively correlated with root tissue density and positively related to root tissue nitrogen concentration. Using R r to estimate R a , we estimate that R a accounts for <10%, on average 2–3%, of R s for individual root systems (averaging 1.2 g dry biomass) housed in surrounding soil (average 1.3 kg dry mass) in situ; thus, Ra was roughly 20 times greater than Rh per unit mass. The contribution of R a peaked in the fall and coincided with leaf senescence of the forest canopy. A soil-sterilizing experimental treatment designed to help isolate R a in situ reduced bacterial biomass and shifted fungal community composition, but there was no reduction in Rs of the in-situ root-soil tray systems. The relative R a to R s ratio increased with root functional strategies characterized by greater specific root length and tip abundance, but also to greater root tissue density. The ratio of R a to R s also increased with warmer soil temperatures and decreased slightly with increasing soil moisture. We discuss how incorporating root functional traits as modulators of the autotrophic contribution to R s could be considered when modeling total soil CO 2 efflux from forests.

54 ENVIRONMENTAL SCIENCES↗

Surface stability and H adsorption and diffusion near surfaces of W borides: a first-principles study

Abstract Understanding the behavior of tungsten boride (W x B y ) surfaces in a fusion reactor environment is an important topic since boronization is a common wall conditioning method used in fusion Tokamaks. We report the results of density functional theory calculations that investigate the surface stability of W x B y (tetragonal I4 1 /amd -WB, hexagonal P 6 3 / mmc -WB 2 and tetragonal I4/m- W 2 B) with low-index orientations, as well as hydrogen (H) energetics near W x B y surfaces. For single element terminated W x B y surfaces, B terminated surfaces are more energetically stable than W terminated as a result of significant reconstruction of B. The H surface adsorption energy and activation energy of H diffusion penetration below W x B y surfaces are mainly related to the outer termination. Specifically, the WB(001) surface terminated with two B layers, referred to as WB(001)-T BB , has higher H adsorption affinity and lower H diffusivity on this surface than other terminations, which is controlled by the significant charge transfer from B to H. However, B atoms on the WB 2 (0001)-T BB surface decrease both H adsorption and diffusivity on the surface, but enhance H diffusion below the surface in comparison to W terminated WB 2 (0001) surface. H would be trapped and diffuse within atomic surface gaps on the WB 2 ( 2 1 ˉ 1 ˉ 0 ) surface, while H below the surface layer would jump along the [0001] direction rather than diffuse into bulk. The surface diffusion activation energy of H on the W 2 B(001) surface slightly varies with terminations. Once H crosses the surface layer of W 2 B(001) with either termination, it prefers to diffuse into the bulk, or back towards the surface, rather than move parallel to the surface. Interestingly, WB 2 (0001) and WB 2 ( 2 1 ˉ 1 ˉ 0 ) surfaces will have relatively higher H retention than the other W x B y surfaces evaluated in this work.

Yang, L. (ORCID:0000000322166071)↗

Molecular and Topographical Organization: Influence on Cicada Wing Wettability and Bactericidal Properties

Numerous natural surfaces have micro/nanostructures that result in extraordinary functionality, such as superhydrophobicity, self-cleaning, antifogging, and antimicrobial properties. One such example is the cicada wing, where differences in nanopillar geometry and composition among species can impact and influence the degree of exhibited properties. To understand the relationships between surface topography and chemical composition with multifunctionality, the wing properties of Neotibicen pruinosus (superhydrophobic) and Magicicada cassinii (hydrophobic) cicadas are investigated at time points after microwave-assisted extraction of surface molecules to characterize the chemical contribution to nanopillar functionality. Electron microscopy of the wings throughout the extraction process illustrates nanoscale topographical changes, while concomitant changes in hydrophobicity, bacterial fouling, and bactericidal properties are also measured. Extract analysis reveals the major components of the nanostructures to be fatty acids and saturated hydrocarbons ranging from C17 to C44. Effects on the antimicrobial character of a wing surface with respect to the extracted chemicals suggest that the molecular composition of the nanopillars plays both a direct and an indirect role in concert with nanopillar geometry. The data presented not only correlates the nanopillar molecular organization to macroscale functional properties, but it also presents design guidelines to consider during the replication of natural nanostructures onto engineered substrates to induce desired properties.

59 BASIC BIOLOGICAL SCIENCES↗

Facet-Dependent Cold Welding of Au Nanorods Revealed by Liquid Cell Transmission Electron Microscopy

Cold welding of metals at the nanoscale has been demonstrated to play a significant role in bottom-up manufacturing and self-healing processes of nanostructures and nanodevices. However, the welding mechanism at the nanoscale is not well understood. In this study, a comprehensive demonstration of the cold welding process of gold nanorods with different modes is presented through in situ liquid cell transmission electron microscopy. The experimental results and molecular dynamics simulations reveal that the nanorods are welded through the facet-dependent atomic surface diffusion and rearrangement along {100} facets. The density functional theory calculations indicate that the preferred coalescence of two {100} surfaces is thermodynamically favorable. Unlike the prevalent “oriented attachment” in the nanoparticle coalescence, the misalignment of nanorod orientations and local stresses can induce grain boundaries and stacking faults in the welded interface.

42 ENGINEERING↗

Be Surface Structures on W(110) and W(211): A DFT Study

Beryllium and Tungsten are promising candidates for use as plasma facing materials (PFMs) in upcoming fusion reactors. Many complex and competing phenomena however complicate the understanding and development of materials that operate in the harsh conditions of the reactor. In particular, redeposition of Be onto the W divertor must be considered due to the expected erosion of the Be first wall under exposure to the plasma. It is known that a build up of Be on W allows for the formation of BeW alloys which can harm the longevity and performance of the fusion divertor. In an effort to understand the interaction of Be with W surfaces, a study of Be structures on W(110) and W(211) as a function of Be coverage has been carried out using Density Functional Theory. We have found that both W surfaces develop monolayers of Be characterized by a densely packed hexagonal structure. Below this monolayer coverage, Be structures are found to have two motifs of coverage, a densely packed hexagonal pattern punctuated by areas of low-density coverage. The structures found here produce work function values and trends in good agreement with experimental measurements.

36 MATERIALS SCIENCE↗

Selective Adsorption of Thiol-Containing Molecules on Copper Sulfide Surfaces via Molecule–Surface Disulfide Bridges

Recent results in the fields of nanoenhanced agriculture and expanding interest in prebiotic chemistry have placed increased emphasis on understanding the chemically selective interaction of small molecules with the surfaces of metal sulfides. Here, we present an integrated experimental and computational study of the interaction of thiol-containing molecules with copper sulfide (covellite) surfaces in aqueous media. In situ Fourier-transform infrared (FTIR) measurements and ex situ X-ray photoelectron spectroscopy (XPS) measurements show that molecules bearing free thiol groups, including glutathione and cysteine, bind strongly to CuS (covellite) nanoparticles and to CuS (001) single crystals, while control studies show that similar molecules lacking the free thiol group exhibit much less binding. Additional experiments show that these thiol-containing molecules interact transiently with CuO nanoparticle surfaces but are readily removed by rinsing. The FTIR and XPS experiments demonstrate that adsorption of molecular thiols to CuS surfaces occurs in a chemically selective manner. Further experimental studies and density functional calculations show that the preferred mode of binding is through the surface S atoms, forming a Solid–S–S–Molecule disulfide linkage. While the role of disulfide linkages in controlling structure and function of proteins and other biomolecules is widely known, the formation of surface disulfide linkages as a motif for covalent molecular binding at surfaces has not been established previously.

36 MATERIALS SCIENCE↗

Molecular Dynamics Simulation of the Structures, Dynamics, and Aggregation of Dissolved Organic Matter

Dissolved organic matter (DOM) plays a significant role in the transport and transformation of pollutants in the aquatic environment. However, the experimental characterization of DOM has been limited mainly to bulk properties, and the molecular-level interactions among various components of DOM remain to be fully characterized. In this study, we use molecular dynamics (MD) simulations to probe the structural properties of model DOM systems at atomic detail. The 200 ns simulations, validated by available experimental data, reveal processes and mechanisms by which chemical species (cations, peptides, lipids, lignin, carbohydrates, and some low-molecular-weight aliphatic and aromatic compounds) aggregate to form complex DOM. The DOM aggregates are dynamic, consisting of a hydrophobic core and amphiphilic exterior. The lipid tails and other hydrophobic fragments form the core, with hydrophilic and amphiphilic groups exposed to water, making DOM accessible to both polar and nonpolar species. Thus, the lipid component acts as a nucleator, whereas cations (especially Ca 2+ ) connect the molecular fragments on the surface by coordinating with the O-containing functional groups of DOM. The structural details revealed here provide new insights including surface accessible atoms, overall assemblage, and interactions among the molecules of DOM for understanding the kinetics and mechanisms through which DOM interacts with metal and other contaminants.

54 ENVIRONMENTAL SCIENCES↗

The C‐Terminal Domain of α‐Synuclein Confers Steric Stabilization on Synaptic Vesicle‐Like Surfaces

Abstract While α‐synuclein, an intrinsically disordered protein linked to Parkinson's disease, has been shown to associate with membrane organelles, its overall cellular function remains nebulous. α‐Synuclein binds to membranes through its amino‐terminal domain (first ≈100 residues), but there is no consensus on the biophysical function of the carboxyl‐terminal domain (last ≈40 residues) due, in part, to its lack of strong interaction partners and persisting intrinsic disorder even when membrane bound. Here, by directly applying force on α‐synuclein bound to spherical nanoparticle‐supported lipid bilayers (SSLBs) and tracking higher‐order structural changes through small‐angle X‐ray scattering, strong evidence is presented that α‐synuclein sterically stabilizes membrane surfaces through its carboxyl‐terminal domain. Full‐length α‐synuclein dramatically increases the critical osmotic pressure at which SSLBs cluster ( P C ≈ 1.3 × 10 5 Pa) compared to α‐synuclein without the carboxyl‐terminal domain ( P C ≈ 1.9 × 10 4 Pa) at physiological salt and temperature conditions. This clustering of α‐synuclein‐bound SSLBs is shown to be reversible and sensitive to monovalent/divalent salt, both features of grafted polyelectrolyte‐mediated steric stabilization. In elucidating the biophysical function of α‐synuclein in the framework of polymer science, it is demonstrated that the carboxyl‐terminal domain can potentially utilize its persisting intrinsic disorder to functionalize membrane surfaces.

Chung, Peter J.↗

Thermodynamic and Kinetic Roles of H2 in Structure Evolution of Urchin-like Co: A density functional theory study

Small gas molecules working as good capping agents play important roles in controlling the morphologies and surface structures of the metal nanocrystals. In present work, the thermodynamic and kinetic roles of H2 molecule played on the morphology of Co nanocrystal were systematically studied based on density functional theory (DFT). The Gibbs surface free energies (?) of Co(100), Co(110) and Co(111) under different hydrogen surface coverages were investigated by ab initio thermodynamics, based on which i) the phase diagrams of stable H coverage on each plane were obtained; ii) the morphology evolutions of the Co nanocrystals with various surface hydrogen coverages were further predicted by Wulff construction. It was revealed that addition of H2 could change the facet stability generating diverse morphological Co nucleus. The kinetic role of H2 was further explored by DFT during adatom Co surface diffusions under different H coverages (?H), which suggested that except for Co(100) at ?H of 0.56 ML, the surface H would hinder Co surface diffusions. The projected density of state (PDOS) gave a deeper insight that the electronic structures of the Co adatom could be alerted by addition of the surface H, which thereby affected its surface diffusion ability. X. Wang, N. Liu, Q. Zhang, X. Liang, and B. Chen were financially supported by the National Natural Science Foundation of China (No. 21476012, 21571012, and 91534201). D. Mei was supported by the US Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the facility user proposal grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). EMSL is a national scientific user facility located at Pacific Northwest National Laboratory (PNNL) and sponsored by DOE’s Office of Biological and Environmental Research.

Nanocrystal Co, Surface free energy, Surface diffu↗

Molecular Fe-N 4 Moieties Coupled with Atomic Co-N 4 Sites Toward Improved Oxygen Reduction Performance

Research on high-efficiency and cost-efficient catalysts for oxygen reduction reaction (ORR) is still a vital but challenging issue for commercializing metal–air batteries. Herein, a single-molecule/atom hybrid catalyst is developed to boost the ORR, in which iron phthalocyanine molecules containing molecular Fe-N 4 moieties couple with atomic Co-N 4 sites on the surface of polyhedral carbon. Density functional theory calculations reveal that face-to-face laminated construction of Fe-N 4 and Co-N 4 in the hybrid catalyst can effectively modulate the electronic structure of active iron atoms and reduce the energy barrier of the rate-determining step for ORR. As a result, this hybrid catalyst demonstrates excellent ORR performance, featuring a half-wave potential of 0.904 V, a peak power density of 238.3 mW cm -2 for zinc–air battery, and outstanding electrocatalytic stability. Here, this work offers a distinctive and robust molecular/atomic engineering approach to creating efficient electrocatalysts, advancing the fields of metal–air batteries.

36 MATERIALS SCIENCE↗

In Situ Formation of Ripplocations in Hybrid Organic–Inorganic MXenes

Abstract Inorganic–organic hybrid MXenes (h‐MXenes) are a family of 2D transition metal carbides and nitrides functionalized with alkylimido and alkylamido surface groups. Using cryogenic and room temperature scanning transmission electron microscopy (STEM) and electron energy‐loss spectroscopy (EELS), it is shown that ripplocations, a form of a fundamental defect in 2D and layered structures, are abundant in this family of materials. Furthermore, detailed studies of electron probe sample interactions, focusing on structural deformations caused by the electron beam are presented. The findings indicate that at cryogenic temperatures (≈100 K) and below a specific dose threshold, the structure of h‐MXenes remains largely intact. However, exceeding this threshold leads to electron beam‐induced deformation through ripplocations. Interestingly, the deformation behavior, required dose, and resultant structure are highly dependent on temperature. At 100 K, it is demonstrated that the electron beam can induce ripplocations in situ with a high degree of precision.

Chemistry↗

Facile Fabrication of Self‐Assembly Functionalized Polythiophene Hole Transporting Layer for High Performance Perovskite Solar Cells

Abstract Crystallinity and crystal orientation have a predominant impact on a materials’ semiconducting properties, thus it is essential to manipulate the microstructure arrangements for desired semiconducting device performance. Here, ultra‐uniform hole‐transporting material (HTM) by self‐assembling COOH‐functionalized P3HT (P3HT‐COOH) is fabricated, on which near single crystal quality perovskite thin film can be grown. In particular, the self‐assembly approach facilitates the P3HT‐COOH molecules to form an ordered and homogeneous monolayer on top of the indium tin oxide (ITO) electrode facilitate the perovskite crystalline film growth with high quality and preferred orientations. After detailed spectroscopy and device characterizations, it is found that the carboxylic acid anchoring groups can down‐shift the work function and passivate the ITO surface, retarding the interface carrier recombination. As a result, the device made with the self‐assembled HTM show high open‐circuit voltage over 1.10 V and extend the lifetime over 4,300 h when storing at 30% relative humidity. Moreover, the cell works efficiently under much reduced light power, making it useful as power source under dim‐light conditions. The demonstration suggests a new facile way of fabricating monolayer HTM for high efficiency perovskite devices, as well as the interconnecting layer needed for tandem cell.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Silica–Derived Nanostructured Electrode Materials for ORR, OER, HER, CO 2 RR Electrocatalysis, and Energy Storage Applications: A Review**

Silica-derived nanostructured catalysts (SDNCs) are a class of materials synthesized using nanocasting and templating techniques, which involve the sacrificial removal of a silica template to generate highly porous nanostructured materials. The surface of these nanostructures is functionalized with a variety of electrocatalytically active metal and non-metal atoms. SDNCs have attracted considerable attention due to their unique physicochemical properties, tunable electronic configuration, and microstructure. These properties make them highly efficient catalysts and promising electrode materials for next generation electrocatalysis, energy conversion, and energy storage technologies. The continued development of SDNCs is likely to lead to new and improved electrocatalysts and electrode materials. This review article provides a comprehensive overview of the recent advances in the development of SDNCs for electrocatalysis and energy storage applications. It analyzes 337,061 research articles published in the Web of Science (WoS) database up to December 2022 using the keywords “silica”, “electrocatalysts”, “ORR”, “OER”, “HER”, “HOR”, “CO 2 RR”, “batteries”, and “supercapacitors”. The review discusses the application of SDNCs for oxygen reduction reaction (ORR), oxygen evolution reaction (OER), hydrogen evolution reaction (HER), carbon dioxide reduction reaction (CO 2 RR), supercapacitors, lithium-ion batteries, and thermal energy storage applications. It concludes by discussing the advantages and limitations of SDNCs for energy applications.

25 ENERGY STORAGE↗

Measurement of High Density Electrons Above a Helium Film on an Amorphous Metal Substrate

Here we have measured two-dimensional electron systems bound to a thin helium film supported by a metallic substrate. We report on our measurement of electron density obtained via a Kelvin probe technique. The underlying metallic substrate is an amorphous metallic alloy (TaWSi), which can support large uniform densities due to its low surface roughness and homogeneous work function. We find that this substrate is able to support high enough densities that the electrons are expected to be Fermi-degenerate.

42 ENGINEERING↗

Anisotropic thermal diffusivity and conductivity in SiC/SiC tubes studied by infrared imaging and X-ray computed tomography

Traditional flash diffusivity evaluation of thermal diffusivity/conductivity of composite tubes require machining of specimens. For a thin-wall tube, this method can only be used to obtain through-thickness transport property. A novel method to evaluate anisotropic thermal diffusivity in a composite tube has been developed. Braided SiC/SiC composite tubes were subjected to a xenon flash heating pulse. A high-speed, high-sensitivity infrared camera was used to measure surface temperature changes as a function of time and nondestructively detect subsurface defects/damages, such as macroscopic pores. Standard reference material (Pyroceram 9606) and curved SiC/SiC composite tube specimens were used to validate thermal diffusivity obtained from infrared imaging. Unlike the traditional method, there is no need prepare special specimens, and thermal diffusivity values in three orientations are obtained after a single flash. A finite element analysis model based on x-ray computed tomography scans was developed to simulate the heat transfer. In conclusion, this technique is significant in assessing thermal conductivity and inspecting the health of ceramic tubes during and after service.

36 MATERIALS SCIENCE↗