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At least 361 records · Page 20

Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences

Certain genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are of substantial concern because they may be more transmissible or detrimentally alter the pandemic course and disease features in individual patients. SARS-CoV-2 genome sequences from 12,476 patients in the Houston Methodist health care system diagnosed from January 1 through May 31, 2021 are reported here. Prevalence of the B.1.1.7 (Alpha) variant increased rapidly and caused 63% to 90% of new cases in the latter half of May. Eleven B.1.1.7 genomes had an E484K replacement in spike protein, a change also identified in other SARS-CoV-2 lineages. Compared with non–B.1.1.7-infected patients, individuals with B.1.1.7 had a significantly lower cycle threshold (a proxy for higher virus load) and significantly higher hospitalization rate. Other variants [eg, B.1.429 and B.1.427 (Epsilon), P.1 (Gamma), P.2 (Zeta), and R.1] also increased rapidly, although the magnitude was less than that in B.1.1.7. Twenty-two patients infected with B.1.617.1 (Kappa) or B.1.617.2 (Delta) variants had a high rate of hospitalization. Breakthrough cases (n = 207) in fully vaccinated patients were caused by a heterogeneous array of virus genotypes, including many not currently designated variants of interest or concern. Finally, in the aggregate, this study delineates the trajectory of SARS-CoV-2 variants circulating in a major metropolitan area, documents B.1.1.7 as the major cause of new cases in Houston, TX, and heralds the arrival of B.1.617 variants in the metroplex.

60 APPLIED LIFE SCIENCES↗

Effective field theory for two-body systems with shallow S -wave resonances

Resonances are of particular importance to the scattering of composite particles in quantum mechanics. We build an effective field theory for two-body scattering which includes a low-energy S-wave resonance. Our starting point is the most general Lagrangian with short-range interactions. We demonstrate that these interactions can be organized into various orders so as to generate a systematic expansion for an S matrix with two low-energy poles. The pole positions are restricted by renormalization at leading order, where the common feature is a non-positive effective range. We carry out the expansion explicitly to next-to-leading order and illustrate how it systematically accounts for the results of a toy model — a spherical well with a delta shell at its border.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Tuning the fluid wetting dynamics on gold microstructures using photoactive compounds

This work demonstrates how photoactive compounds can be used to tune the surface chemistry, surface free energy, and the wetting velocity of fluids on Spiropyran functionalized surfaces with different surface microstructures. Evidence of this photowetting effect is based on data showing: (1) the cyclic changes in the static, advancing, and receding contact angles $\theta$ CA for multiple UV$\rightleftarrows$vis photoswitching cycles with both smooth and microstructured surfaces and (2) the changes in the fluid wicking velocity (via UV$\rightleftarrows$vis photoswitching) on different Spiropyran functionalized hemiwicking surfaces. X-ray photoelectron spectroscopy is used to determine the efficiency of photoswitching caused by the quality of the Spiropyran functionalization. Reversible photoisomerization of Spiropyran generates a gradient in surface free energy, resulting in a similar change in contact angle ($\theta$ CA ) in the photoswitchable surfaces. In conclusion, by incorporating these changes into the Owens-Wendt and Van Oss surface energy models, the energy of smooth Au surfaces can also be predicted for both UV and visible light irradiations, where reversible contact angle variations of $\Delta$$\theta$ CA ≈ 5–10° are achieved with both water and water-ethanol mixtures due to the conversion of SP to merocyanine, which corresponds to a total free energy change of ~13% on the photoswitchable surface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Source attribution of near-surface ozone pollution in Jiangsu Province of China over 2013–2019

Near-surface ozone (O3) is one of the most severe air pollutants in China, particularly over densely populated Jiangsu Province in the Yangtze River Delta. In this study, an O3 source tagging technique is utilized in a chemistry-climate model to quantify the source contributions of various emission sectors and regions for nitrogen oxides (NOx) and volatile organic compounds (VOCs) to O3 concentrations in Jiangsu Province during 2013–2019. The results show that the near-surface O3 in Jiangsu Province is mainly contributed by surrounding and remote anthropogenic NOx emissions through long-range transport. Local anthropogenic NOx emissions account for only 13 % and 18 % of the annual and summertime mean near-surface O3 in Jiangsu Province, respectively. Anthropogenic NOx emissions from the surface transportation, industry, and energy sectors account for 21 %, 22 % and 20 % of the annual mean near-surface O3 concentration in Jiangsu Province, respectively. Biogenic and anthropogenic VOCs emissions each explains one-third of the annual mean near-surface O3 concentration in Jiangsu, while methane and stratospheric chemical production contribute 21 % and 6 %, respectively. The sources from stratospheric production, aircraft, lightning, and foreign emissions are the primary contributors to O3 in the mid- and high troposphere. During high pollution days in Jiangsu Province, the near-surface O3 concentrations increase with the maximum exceeding 20 ppb, which is attributed to both the enhanced photochemical production and regional transport in favorable meteorological conditions.

ozone pollution↗

Anisotropic elastoplastic response of double-porosity media

Here we present a continuum framework to simulate fluid flow through anisotropic elastoplastic media with double porosity. Two effective stress measures σ' and δ" emerge from the thermodynamic formulation, which are energy-conjugate to the elastic and plastic components of strain, respectively. Both effective stress measures can be expressed as a combination of the total Cauchy stress σ and the average pore pressure $\bar{p}$ in the two pore scales. In the effective stress for elasticity, $\bar{p}$ is scaled with a rank-2 Biot tensor, whereas the effective stress for plasticity follows the Terzaghi form in which $\bar{p}$ is scaled by the Kronecker delta. The Biot tensor and storage coefficients are derived as functions of elasticity parameters and porosities. A mixed finite element formulation is introduced to discretize the domain and solve initial boundary-value problems. A stabilization scheme is employed on equal-order interpolation for both displacement and pressure fields throughout the entire range of drainage responses. Numerical simulations reproduce the hydromechanical response of Opalinus shale in one-dimensional consolidation tests throughout the range of primary and secondary consolidation under different external loads. Numerical simulations of the consolidation of a rectangular domain subjected to a strip load demonstrate the efficacy of the proposed stabilization scheme, as well as illustrate the impacts of stress history, mass transfer, and different pore systems on the hydromechanical response.

42 ENGINEERING↗

Nonrad: Computing nonradiative capture coefficients from first principles

Point defects in semiconductor crystals provide a means for carriers to recombine nonradiatively. This recombination process impacts the performance of devices. We present the Nonrad code that implements the first-principles approach of Alkauskas et al. (2014) [8] for the evaluation of nonradiative capture coefficients based on a quantum-mechanical description of the capture process. An approach for evaluating electron-phonon coupling within the projector augmented wave formalism is presented. We also show that the common procedure of replacing Dirac delta functions with Gaussians can introduce errors into the resulting capture rate, and implement an alternative scheme to properly account for vibrational broadening. Finally, we assess the accuracy of using an analytic approximation to the Sommerfeld parameter by comparing with direct numerical evaluation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A multi-criteria CCUS screening evaluation of the Gulf of Mexico, USA

Continued research into reservoir characterization along with offshore carbon dioxide (CO 2 ) transportation and infrastructure assets is needed to facilitate development of safe and successful carbon capture, utilization, and storage (CCUS) projects. This paper outlines a multi-criteria evaluation methodology that incorporates disparate sets of quantitative, spatially variable data into a decision-making framework for screening the Gulf of Mexico (GOM) outer continental shelf (OCS) for potentially viable CO 2 storage and enhanced oil recovery (EOR) sites. Criteria categories include favorable geologic characteristics, logistics, and potential risks. Data compiled for 14 criteria from several publicly available geographic information system (GIS) layers was aggregated over 2559 spatially balanced points across the study area using the National Energy Technology Laboratory (NETL)-developed Cumulative Spatial Impact Layers™ (CSIL) GIS tool. Criteria are weighted by qualitative expert opinion relative to their perceived importance to given scenarios— the output of combined criteria values and weights enables regional CO 2 storage suitability differentiation. The methodology considers both technical and non-technical factors impacting CCUS decision-making. The flexible methodology enables a systematic approach to regional ranking at high spatial resolution over a large study domain. Additionally, the framework enables high-grading of priority sites that warrant further characterization and follow-on analysis. Areas along the Louisiana coast and Mississippi River Delta consistently rank high for all scenarios largely a result of the favorable geology with the potential for stacked storage, as well as the density of existing pipelines and platforms, and proximity to several onshore CO 2 sources. High-graded regions for the CO 2 EOR-related scenarios are typically located further offshore towards the middle and edge of the OCS compared to higher priority regions for the geologic storage scenarios which fall closer to the Louisiana coastline.

54 ENVIRONMENTAL SCIENCES↗

Molecular basis for antiviral activity of two pediatric neutralizing antibodies targeting SARS-CoV-2 Spike RBD

Neutralizing antibodies (NAbs) hold great promise for clinical interventions against SARS-CoV-2 variants of concern (VOCs). Understanding NAb epitopedependent antiviral mechanisms is crucial for developing vaccines and therapeutics against VOCs. Here we characterized two potent NAbs, EH3 and EH8, isolated from an unvaccinated pediatric patient with exceptional plasma neutralization activity. EH3 and EH8 cross-neutralize the early VOCsandmediatestrong Fc-dependent effector activity in vitro. Structural analyses of EH3 and EH8 in complex with the receptor-binding domain (RBD) revealed the molecular determinantsoftheepitope-drivenprotectionandVOCevasion.WhileEH3represents the prevalent IGHV3-53 NAb whose epitope substantially overlaps with the ACE2 binding site, EH8 recognizes a narrow epitope exposed in both RBD-up and RBD-down conformations. When tested in vivo, a single-dose prophylactic administration of EH3 fully protected stringent K18-hACE2 micefrom lethal challenge with Delta VOC. Our study demonstrates that protective NAbs responses converge in pediatric and adult SARS-CoV-2 patients.

60 APPLIED LIFE SCIENCES↗

Changes in serum-neutralizing antibody potency and breadth post-SARS-CoV-2 mRNA vaccine boost

A better understanding of the durability and breadth of serum-neutralizing antibody responses against multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants elicited by COVID-19 vaccines is crucial in addressing the current pandemic. In this study, we quantified the decay of serum neutralization antibodies (nAbs) after second and third doses of the original COVID-19 mRNA vaccine. Using an authentic virus-neutralization assay, we found that decay half-lives of WA1- and Delta-nAbs were both ~60 days after second and third vaccine dose. Unexpectedly, the durability of serum antibodies that neutralize three different Omicron subvariants (BA.1.1, BA.5, BA.2.12.1) was substantially better, with half-lives of ≥6 months. A booster dose of the original COVID-19 vaccine was also found to broaden antibody responses against SARS-CoV and four other sarbecoviruses, in addition to multiple SARS-CoV-2 strains. These findings suggest that repeated vaccinations with the COVID-19 vaccine may confer a degree of protection against future spillover of sarbecoviruses from animal reservoirs.

59 BASIC BIOLOGICAL SCIENCES↗

High temperature transition aluminas in gamma-Al2O3: Review

High temperature treated transition aluminas display adsorptive and catalytic properties that are in many ways comparable to those of their low temperature counterpart gamma-Al2O3. While being important industrial catalysts as well as catalytic supports, their very basic crystallographic and structural characteristics remain poorly understood and thus actively studied. In this review, we critically examine the crystallography and structural complexity of these materials. Specifically, we address the crystallography of delta- and theta-Al2O3 polymorphs and show how structural intergrowth and disorder are accommodated in these phases. The structural complexity at the scale of overall microstructure is also examined, and the challenges and recent progress in quantification of the structure at ensemble level are discussed. Most pertinently to catalysis, we review the surfaces properties of high temperature treated Al2O3 and discuss the implications for understanding attributes relevant to heterogeneous catalysis.

Kovarik, Libor↗

Restoring wetlands on intensive agricultural lands modifies nitrogen cycling microbial communities and reduces N 2 O production potential

The concentration of nitrous oxide (N 2 O), an ozone-depleting greenhouse gas, is rapidly increasing in the atmosphere. Most atmospheric N 2 O originates in terrestrial ecosystems, of which the majority can be attributed to microbial cycling of nitrogen in agricultural soils. Here, in this study, we demonstrate how the abundance of nitrogen cycling genes vary across intensively managed agricultural fields and adjacent restored wetlands in the Sacramento-San Joaquin Delta in California, USA. We found that the abundances of nirS and nirK genes were highest at the intensively managed organic-rich cornfield and significantly outnumber any other gene abundances, suggesting very high N 2 O production potential. The quantity of nitrogen transforming genes, particularly those responsible for denitrification, nitrification and DNRA, were highest in the agricultural sites, whereas nitrogen fixation and ANAMMOX was strongly associated with the wetland sites. Although the abundance of nosZ genes was also high at the agricultural sites, the ratio of nosZ genes to nir genes was significantly higher in wetland sites indicating that these sites could act as a sink of N 2 O. These findings suggest that wetland restoration could be a promising natural climate solution not only for carbon sequestration but also for reduced N 2 O emissions.

59 BASIC BIOLOGICAL SCIENCES↗

Integrated lipidomic and proteomic profiling reveals metabolic network disruption by SARS-CoV-2 variants

The rapid evolution of SARS-CoV-2 has produced myriad viral strains with increasing transmissibility and capacity for immune evasion. While effective vaccination campaigns have reduced the fatalities associated with SARS-CoV-2, infections continue, and a detailed understanding of how this virus manipulates host biochemical pathways remains elusive. We asked both whether the patterns of host lipid rewiring remained consistent across variants and whether the changes in the abundance of lipid classes are related to changes in the expression of the enzymes involved in their biosynthesis. We compared global nontargeted lipidomics on A549-ACE2 cells infected with the delta variant (B.1.617.2), or the omicron (B.1.1.529) variant to our previous results of global nontargeted lipidomics on A549-ACE2 cells infected with the original WA1 strain and further performed quantitative proteomics to assess changes in the host proteome. We found that metabolic rewiring, both on the lipid and the enzymatic level, is remarkably consistent across all three variants. We further mapped changes in the expression of host metabolic enzymes, linking enzyme expression to alterations in the abundance of specific lipids during infection. This analysis identified key proteins related to virus-mediated changes in lipid abundance, including fatty acid synthase (FASN), lysosomal acid lipase (LIPA), and ORMDL, a regulator of sphingolipid biosynthesis. These integrated lipidomic and proteomic experiments shed light on the importance of the complex network of host metabolism networks that support SARS-CoV-2 infection and suggest that lipid metabolism may be a promising avenue for uncovering conserved therapeutic targets.

SARS-CoV-2↗

Effects of ion sputtering on plutonium surfaces

Scanning tunneling microscopy has been performed on an electro-polished gallium-stabilized delta-phase plutonium sample under ultra-high vacuum conditions. The images obtained were used to measure surface roughness as ion sputtering and annealing was applied to the plutonium sample. It was demonstrated that sputter/anneal cycles progressively increased the surface roughness of the plutonium. Furthermore, Auger and scanning tunneling spectroscopy measurements revealed an initially unstable and dynamically changing surface that became increasingly stable as sputter/anneal cycles were applied. The stabilized surface region contained within the sputter crater was observed to be unchanged for up to 17 months after the final sputter anneal cycle.

36 MATERIALS SCIENCE↗

A study on texture stability and the biaxial creep behavior of as-hydrided CWSR Zircaloy-4 cladding at the effective stresses from 55 MPa to 65 MPa and temperatures from 300°C to 400°C

The creep rupture of high burnup used nuclear fuel (> 45 GWD/MTU) cladding is regarded as one of the failure mechanisms during long-term dry storage. A high amount of zirconium hydride in the cladding matrix would degrade the mechanical properties of the cladding especially leading to delayed hydride cracking. To better understand the influence of zirconium hydride on the biaxial thermal creep performance and the crystalline texture stability of Zircaloy-4 cladding, the pressurized tube technique is applied to test the durability of the as-hydrided material. Tests were performed on as-received Zircaloy-4 tubular specimens as well as-hydrided ones with targeted 300 wt parts per million (wppm) or 750 wppm hydrogen. The biaxial creep experiments were conducted at temperatures from 300 degrees C to 400 degrees C and at equivalent stresses at mid-wall from 55 MPa to 65 MPa. The hydridation process prior to creep tests induces the formation of FCC delta-hydride platelets along the circumferential direction of the tube. This alignment and phase structure of hydride show no significant change after biaxial creep tests. The creep strain-rate negatively depends on the hydrogen content. The synchrotron wide-angle X-ray diffraction (WAXD) technique and electron backscatter diffraction (EBSD) analysis were applied for the study of the crystallographic orientation relationship. zirconium-to-hydride grain orientation follows Shoji-Nishiyama crystallographic relationship. This relationship is stable before and after creep deformation. These results of creep performance and texture stability of Zircaloy-4 claddings can help support the design basis of interim and long-term dry storage facilities.

creep↗

The effect of secondary phases on microstructure and irradiation damage in an as-built additively manufactured 316 L stainless steel with a hafnium compositional gradient

Additive manufacturing (AM) or rapid prototyping has become a crucial tool for reducing both cost and time while increasing efficiency in qualifying structural materials for reactor use. In this study, directed energy deposition (DED) was used to develop an as-built 316 L stainless steel sample with three regions of increasing Hf-dopant to study the effects of Hf on the irradiation response of the material. Morphological and microstructural changes were analyzed before and after 2 MeV proton irradiation at 360 °C to a damage of 2.5 dpa at ~ 10 µm below the surface. The addition of Hf effectively suppressed radiation-induced damage (dislocation loops, radiation-induced segregation) due to enhanced point defect recombination. The radiation damage seen in the as-built sample was further compared to a thermo-mechanically treated counterpart of the same fabrication and irradiation parameters which was found to behave superiorly. In conclusion, the increased radiation resistance of this material may be attributed to the as-built microstructure, which includes undissolved Hf particles, delta ferrite grains and cellular sub-grain boundaries that can hinder defect motion.

316L Stainless Steel↗

Hydraulic performance and wave transmission through nature-inspired perforated hollow-base piles breakwater

Nature-based Solutions (NbS) are critical to achieving long-term sustainable coastlines in deltaic coastlines, particularly susceptible to severe impacts under climate change. In recent years, coastal erosion has accelerated in the Vietnam Mekong Delta (VMD), particularly in the West Sea (from Ca Mau to Kien Giang). Due to the characteristics of muddy coastlines and eroded mangrove forests in this region, only a few engineering solutions have effectively reduced waves and promoted sediment accumulation to facilitate beach accretion. However, these solutions require significant investment and cannot be relocated or reused. Therefore, this study introduces a coastal mangrove-inspired perforated hollow-base piles breakwater (PHBPB), which uses the principle of biomimicry by studying the ability of mangrove groups to protect the coastline, stimulate sediment deposition, and over time, restore mangrove forests in the VMD. The hydraulic parameters of PHBPB were tested in 260 scenarios using a physical model, which included varying parameters such as crest width (B), pile row numbers (n c ), crest freeboard (R c ), and wave parameters (H s , T p ) in determining the capabilities of wave transmission, reflection, and wave dissipation. The results showed that the process of wave energy dissipation through perforated hollow-base breakwaters without piles (PHBBWP) is governed by three main parameters, including the relative water depth of the crest (R c /H m0,i ), the relative width of the crest (B/H m0,i ), and the wave slope at the structure location (s m = H m0,i /L m ). In contrast, for PHBPB, the primary influencing factors are the relative submergence depth or the length of the submerged pile portion (R c /H m0,i ) and the relative width of the pile system (X b /L m ). Finally, the hollow structure is suitable for the soft, weak mud geology in this region with poor load-bearing capacity, allows for rapid installation, is reasonably cost-effective, and can be relocated and reused once regeneration has been completed in each stretch of coastline.

54 ENVIRONMENTAL SCIENCES↗

Beam-spin asymmetry Σ for Σ – hyperon photoproduction off the neutron

We report a new measurement of the beam-spin asymmetry $\boldsymbol{\Sigma}$ for the $\vec{\gamma} n \rightarrow K^+\Sigma^-$ reaction using quasi-free neutrons in a liquid-deuterium target. The new dataset includes data at previously unmeasured photon energy and angular ranges, thereby providing new constraints on partial wave analyses used to extract properties of the excited nucleon states. The experimental data were obtained using the CEBAF Large Acceptance Spectrometer (CLAS), housed in Hall B of the Thomas Jefferson National Accelerator Facility (JLab). The CLAS detector measured reaction products from a liquid-deuterium target produced by an energy-tagged, linearly polarised photon beam with energies in the range 1.1 to 2.3 GeV. Predictions from an isobar model indicate strong sensitivity to $N(1720)3/2^+$, $\Delta(1900)1/2^-$, and $N(1895)1/2^-$, with the latter being a state not considered in previous photoproduction analyses. When our data are incorporated in the fits of partial-wave analyses, one observes significant changes in $\gamma$-$n$ couplings of the resonances which have small branching ratios to the $\pi N$ channel.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Substrate stiffness modulates endothelial cell function via the YAP-Dll4-Notch1 pathway

Highlights: • Soft stiffness increases Dll4 expression in endothelial cells via YAP suppression. • Soft substrate-induced Dll4-Notch1 signaling is facilitated by VEGF stimulation. • Elevated Dll4-Notch1 signaling contributes to the regulation of VEGFRs expression. • Substrate stiffness modulates gene expression linked to endothelial cell function. Endothelial cells adapt their functions as a consequence of sensing extracellular substrate stiffness; these alterations allow them to maintain their vascular structure and function. Substrate stiffness-mediated yes-associated protein 1 (YAP) activation plays an important role in mechano-transduction and pro-angiogenic phenotype of endothelial cells, and Delta-like ligand 4 (Dll4)-Notch1 signaling is closely related to angiogenesis; however, the impact of substrate stiffness-mediated interrelation of these pathways on endothelial cell functions remains elusive. We confirmed that endothelial cells on softer substrates not only elongate cellular aspects but also attenuate YAP activation compared to cells on stiffer substrates. Endothelial cells on softer substrates also upregulate the vascular endothelial growth factor receptor 1 (VEGFR1) and VEGFR2 mRNA expression that is enhanced by VEGF stimulation. We determined that endothelial cells on softer substrates increased Dll4 expression, but not Notch1 expression, via YAP signaling. Moreover, endothelial cells on soft substrates induced not only VEGFRs upregulation but also suppression of pro-inflammatory interleukin-6 and plasminogen activator inhibitor-1 mRNA expression and the facilitation of anti-coagulant thrombomodulin and pro-coagulant tissue factor mRNA expression. Our results suggest that endothelial cells activate the YAP-Dll4-Notch signaling pathway in response to substrate stiffness and dictate cellular function.

60 APPLIED LIFE SCIENCES↗