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At least 685 records · Page 38

A Targeted Sequencing Assay for Serotyping Escherichia coli Using AgriSeq Technology

The gold standard method for serotyping Escherichia coli has relied on antisera-based typing of the O- and H-antigens, which is labor intensive and often unreliable. In the post-genomic era, sequence-based assays are potentially faster to provide results, could combine O-serogrouping and H-typing in a single test, and could simultaneously screen for the presence of other genetic markers of interest such as virulence factors. Whole genome sequencing is one approach; however, this method has limited multiplexing capabilities, and only a small fraction of the sequence is informative for subtyping or identifying virulence potential. A targeted, sequence-based assay and accompanying software for data analysis would be a great improvement over the currently available methods for serotyping. The purpose of this study was to develop a high-throughput, molecular method for serotyping E. coli by sequencing the genes that are required for production of O- and H-antigens, as well as to develop software for data analysis and serotype identification. To expand the utility of the assay, targets for the virulence factors, Shiga toxins ( stx 1 , and stx 2 ) and intimin ( eae ) were included. To validate the assay, genomic DNA was extracted from O-serogroup and H-type standard strains and from Shiga toxin-producing E. coli , the targeted regions were amplified, and then sequencing libraries were prepared from the amplified products followed by sequencing of the libraries on the Ion S5™ sequencer. The resulting sequence files were analyzed via the SeroType Caller™ software for identification of O-serogroup, H-type, and presence of stx 1 , stx 2 , and eae . We successfully identified 169 O-serogroups and 41 H-types. The assay also routinely detected the presence of stx 1a,c,d (3 of 3 strains), stx 2c−e,g (8 of 8 strains), stx 2f (1 strain), and eae (6 of 6 strains). Taken together, the high-throughput, sequence-based method presented here is a reliable alternative to antisera-based serotyping methods for E. coli .

Elder, Jacob R.↗

Highly Anisotropic Quasi‐Direct Organic Metal Halide Hybrids: A Platform for Polarization‐Sensitive Optoelectronics

Low-dimensional organic–inorganic metal halide hybrids (OMHHs) exhibit remarkable optical properties and enhanced environmental stability. We investigate a 1D OMHH with formula C 4 N 2 H 14 PbBr 4 , consisting of Pb–Br chains separated by organic cations, which shows a large Stokes shift (0.83 eV) and broadband emission. Through first-principles calculations and polarized Raman spectroscopy, we characterize the material's vibrational properties and identify the specific phonon modes that drive exciton self-trapping. Our novel GW/Bethe-Salpeter equation force formalism reveals that low-frequency phonons (∼ 100 cm −1 , primarily involving Pb–Br motions) couple strongly with excitons, with a remarkably high Huang-Rhys factor of 137 ± 4, and gives a pathway for ultrafast structural analysis during the absorption process. This phonon-exciton coupling mechanism explains the material's broadband emission and provides a pathway for controlling optical properties through vibrations and for tuning vibrations through optical excitations. The material also exhibits highly anisotropic optical properties and electronic transport, with bands that are dispersive along the Pb–Br chains but nearly flat in perpendicular directions, resulting in direction-dependent electrical conductivity that is calculated to be an order of magnitude higher along the chain direction and consistent with measurements. These combined properties make this system an excellent platform for polarization-sensitive optoelectronic devices.

36 MATERIALS SCIENCE↗

Improving bamboo’s fuel and storage properties with a net energy export through torrefaction paired with catalytic oxidation

Using torrefied char, or biocoal, as solid fuel provides an opportunity to introduce a sustainable feedstock into the energy market. The goals of this study were to investigate how torrefaction improves the energy content and the grindability of a Malaysian bamboo along with understanding the potential for integrated energy recovery from torrefaction gases. The feedstock was torrefied at 250–290 °C for 1 h and the combustion characteristics and grindability of the solid products along with the composition of torrefied gas species were measured. The results showed a beneficial increase in elemental carbon increased from 47 to 63 wt% at 290 °C torrefaction, reflecting an increase in higher heating value from 17.8 to 25.6 MJ/kg. The combustion behavior of all the products appeared to show three distinct combustion zones; however, torrefaction severity leading to higher combustion temperature and time as the fixed carbon augmented with the increase of torrefaction temperature. This increase in severity also lead to more friable and grindable material, and the 290 °C condition required a factor of 2.7 less hold-up time in the mill compared to the raw bamboo, and a factor of 8.5 less energy (938 and 111 kWh/tonne respectively). Through analysis of the gas and volatile formation, a case study showed that catalytic oxidation can convert nearly 100% of the embodied chemical energy into usable thermal energy. These experimental findings were scaled to a 100,000 tonne/y capacity torrefaction plant and in the moderate case of 270 °C operating temperature, the plant has 1.25 GJ/tonne excess energy beyond what the process needs.

09 BIOMASS FUELS↗

De-Risking High-Recovery Brackish Water Desalination via Flow Reversal and Feed Flushing Using Techno-Economic Assessment

Novel desalination technologies have demonstrated enhanced performance and improved financial metrics over existing processes adopted by industry. Establishing quantitative performance targets is essential for achieving financial benefits over the current state of the art. Herein, we demonstrate how WaterTAP, a techno-economic assessment (TEA) tool, can be used to identify minimum performance metrics necessary to achieve financial benefit over using existing processes. This study evaluates the feasibility of increasing water recovery at the Chino Desalter I above 90 % through the addition of a third variable configuration reverse osmosis (VCRO) stage. Sensitivity analyses revealed flow reversal frequency, feed flushing volume (used as a cleaning step), and membrane lifespan are key factors influencing the financial viability of the VCRO process. The TEA analysis demonstrated that the system must achieve a recovery of 84 % and a 1-year membrane lifespan to have a breakeven LCOW, while achieving 90 % recovery can ultimately reduce the LCOW by 16 %. Notably, a trade-off between decreasing frictional losses and increased osmotic pressure across the recovery range, resulted in a stable specific energy consumption across the recovery range, enabling meaningful LCOW reductions without an energy penalty, a key finding that contrasts with conventional RO. This work demonstrates how TEA can guide system design by identifying key performance targets and exploring trade-offs, enabling data-driven decisions to de-risk innovative processes. These findings underscore the importance of leveraging TEA to evaluate scaling mitigation strategies and optimize inland desalination systems for sustainable and cost-effective operation.

14 SOLAR ENERGY↗

Effects of secondary void-initiating particles on the steady-state crack growth resistance of high-strength steel

In this investigation, we focus on the dependence of stable crack growth resistance, as measured by the short-rod fracture toughness test, on secondary void-initiating particles such as AlN and Ti-based grain-refining precipitates in a variety of high-strength steels with tempered martensitic microstructures. The model developed by Ritchie and Thompson is modified to illustrate the significant amounts of toughening that can result from the refinement of secondary particles. Analysis of the data suggests that material strength is a predominant factor in increasing the short-rod fracture toughness relative to linear-elastic measures of initiation fracture toughness, but the extent of toughening is limited by the size and number density of secondary particles in the microstructure. The variation in estimates of secondary microvoid initiation and growth strains with precipitate size reinforce the notion that primary fracture at non-metallic inclusions and secondary fracture at smaller particles occur as sequential processes with a degree of concurrence that is dependent on the state of precipitation in both particle dispersions. Toughening in this connection is maximized by increases in microvoid growth strain that result from decreases in the size and areal number density of secondary void-initiating particles. Finally, the occurrence of transient instabilities during crack extension in short-rod specimens is explained with a phenomenological model that relates crack growth stability to natural variations in the dispersion of secondary void-initiating particles in the microstructure.

42 ENGINEERING↗

Configurational stability of a crack propagating in a material with mode-dependent fracture energy – Part II: Drift of fracture facets in mixed-mode I+II+III

In earlier papers (Leblond et al., 2011; 2019), we presented linear stability analyses of the coplanar propagation of a crack loaded in mixed-mode I+III, based on a “double” propagation criterion combining (Griffith, 1920)’s energetic condition and (Goldstein and Salganik, 1974)’s principle of local symmetry. The difference between the two papers was that in the more recent one, the local value of the critical energy-release-rate was no longer considered as a constant, but heuristically allowed to depend upon the ratio of the local mode III to mode I stress intensity factors. This led to a much improved, qualitatively acceptable agreement of theory and experiments, for the “threshold” value of the ratio of the unperturbed mode III to mode I stress intensity factors, above which coplanar propagation becomes unstable. In this paper, the analysis is extended to the case where a small additional mode II loading component is present in the initially planar configuration of the crack, generating a small, general kink of this crack from the moment it is applied. The main new effect resulting from presence of such a loading component is that the instability modes present above the threshold must drift along the crack front during its propagation. This prediction may be useful for future theoretical interpretations of a number of experiments where such a drifting motion was indeed observed.

36 MATERIALS SCIENCE↗

Effect of Si impurities on microstructure and tensile properties of a cast Al-Mg-Fe alloy

Al-Mg alloys are attractive for structural castings owing to their superior strength and ductility in the as-cast state. However, given the tight tolerance for impurities, Al-Mg alloys produced from secondary sources still face multiple challenges. Here, we report the effect of increased Si impurity (0.05–1.6 wt%), which is commonly found in secondary Al sources, on microstructure and tensile properties of a cast Al-4.3Mg-1.6Fe (wt%) alloy, commercially referred to as Castaduct-42 alloy. Microstructural characterization revealed that Si addition increased the volume fraction, size, and aspect ratio of primary Al13Fe4 intermetallic particles as well as the volume fraction of other binary and ternary eutectic phases. Tensile testing results demonstrated that increasing Si impurities from 0.05 to 1.6 wt% reduced ductility from 14.3 ± 1.4 % to 2.2 ± 1.0 %. A particle cracking damage accumulation model coupled with failure analysis indicated primary Al13Fe4 intermetallic particles to be the major contributing factor to the deterioration in ductility with increasing Si content. Additionally, the stabilizing effect of Si on primary Al 13 Fe 4 was inconsistent with the CALPHAD calculation results based on existing CALPHAD databases which predict a slightly decreasing primary Al13Fe4 phase fraction with increasing Si concentration. This work provides new insights into the phase stability and mechanical behavior of the lesser studied Al-Mg-Fe-Si alloy system that will contribute to the development of sustainable cast Al-Mg based alloys.

36 MATERIALS SCIENCE↗

Beam impedance and heating analysis of the diagnostic stripline

In this work the heat transfer analysis has been performed for the stripline kicker, design of which is used at many accelerator facilities as a part of the transverse bunch-by-bunch feed-back system, including NSLS-II. The experimental data of the electrode temperature have been collected from a special diagnostic stripline designed with six infrared view ports. The temperature analysis is based on the power loss calculations and the loss factor computed by the 3-D electromagnetic simulation code GdfidL. To estimate the power loss, we analyze the real part of the longitudinal impedance and the loss factor for two different regimes. We use the ANSYS finite element code to correlate the temperature with the power loss. Lambertson and Shafer formalisms of the longitudinal and transverse beam impedances are discussed for the simplified stripline geometries. The required characteristic impedances and the geometric factors are determined analytically for the simplified geometries and compared with the results for the designed stripline geometry using the 2-D POISSON code by solving the Laplace’s equation in two dimensions. Lambertson’s equations are compared with numerical results. We introduce the frequency range, within which we can apply the analytical approach.

43 PARTICLE ACCELERATORS↗

Genetic and epigenetic signatures of Populus trichocarpa in response to abiotic stresses

Plants respond to abiotic stresses such as drought, heat, and salinity through both shared and stress-specific regulatory pathways. However, the role of epigenetic mechanisms, particularly DNA methylation, in modulating these responses is still underexplored. Here, we integrated transcriptome profiling with whole-genome bisulfite sequencing (WGBS) to investigate the dynamic relationship between gene expression and DNA methylation in Populus trichocarpa during brief early-stage exposure to abiotic stress. Each stress elicited distinct transcriptional and methylation signatures; however, a subset of conserved stress-responsive genes was commonly regulated across treatments. We found that ∼5-6% of differentially expressed genes also displayed differential methylation patterns, suggesting a coordinated role for DNA methylation in regulating gene expression. Motif enrichment analysis of differentially methylated regions revealed binding sites of key transcription factor families, including ERF, bHLH, and ABF, highlighting potential role for methylation in modulating transcription factor targeting. Furthermore, we identified stress-inducible molecular markers with potential applications in early stress detection and functional dissection of gene regulatory pathways. Together, these findings provide new insights into the coordinated genetic and epigenetic responses to abiotic stress and provide a foundation for developing biosensors and breeding strategies to enhance stress resilience woody plants.

DNA methylation↗

Effects of Nonequilibrium Atomic Structure on Ionic Diffusivity in LLZO: A Classical and Machine Learning Molecular Dynamics Study

To improve the performance of electrochemical devices, it is essential to understand the effects of nonequilibrium motifs in solids, such as grain boundaries, amorphous phases, and highly strained regions, on atomic-scale transport and stability. Molecular dynamics simulations are used to explore the combined effect of far-from-equilibrium atomic structures and the choice of interatomic potential on ionic diffusivity predictions for Li 7 La 3 Zr 2 O 12 (LLZO), a promising solid electrolyte for all-solid-state batteries. Amorphization and high strain are considered using both classical Buckingham interatomic potentials and machine learning force fields. Here we find that both crystalline expansion and amorphization tend to slow diffusion, although the different physical encodings in the two potentials impact the properties in different ways. We trace these variations to a combination of structural and transport factors, the contributions of which are deconvoluted computationally. Graph-based analysis reveals that the variations for amorphous LLZO arise from the connectivity of diffusion pathways within the predicted structures, which generally correlates with diffusivity and is notably higher for structures generated by the machine learning force fields. Our study provides additional insight into the relationship between atomic structure and diffusivity in LLZO, while also highlighting the need for care in choosing and validating potentials to simulate far from equilibrium structures.

25 ENERGY STORAGE↗

Northern Hemisphere Snow Drought in Earth System Model Simulations and ERA5‐Land Data in 1980–2014

Abstract Low snow levels over the past few decades and predictions of a low‐to‐no snow future have spurred research into snow droughts, which pose a threat to water security and management. Systematic data‐model comparisons of snow drought have been lacking, hindering our understanding of the drivers of snow drought in the past. To address this gap, we analyzed snow drought events using standardized snow water equivalent index derived from monthly results of four numerical experiments using the E3SM Land Model (ELM) and ERA5‐Land data during the period of 1980–2014. Additionally, we compared snow drought duration calculated from models with those from the ERA5‐Land data during selected El Niño‐Southern Oscillation (ENSO) years. The numerical experiments were conducted with ELM driven by two prescribed atmospheric forcings, and with the coupled land‐atmosphere configuration of E3SM with and without plant hydraulics scheme feedback. Analysis reveals that 20%–30% of snow droughts occur due to factors other than above‐normal temperature and low snowfall, such as low soil moisture, warm soil temperature, and low relative humidity, etc., especially in high latitudes (50° North). Furthermore, our study highlights the exacerbating effect of ENSO events on snow drought conditions in various regions, despite some discrepancies between model and ERA5‐Land results. We also identified limitations of the coupled land‐atmosphere models in our current configuration in capturing the spatial patterns of snow droughts. This study underscores the challenge of predicting and mitigating snow drought and the need for a comprehensive understanding of the factors contributing to snow drought.

54 ENVIRONMENTAL SCIENCES↗

NO 2 -mediated voloxidation for iodine separation from cesium iodide surrogates

Heterogeneous NO 2 -mediated oxidation of uranium, also known as advanced voloxidation, is a proposed head-end reprocessing method for used nuclear fuel. An advantage of advanced voloxidation is the removal of volatile fission products, which complicate downstream separation and containment challenges leading to increased processing economics. Iodine, one of the volatile species of interest, has exhibited varied results in this process. Using CsI as a surrogate material, this work mimics the effect of NO 2 -based voloxidation on iodine and sheds light on the factors that influence the solid–gas phase reaction. Solid-state analysis using Fourier transform infrared attenuated total reflectance spectroscopy and scanning electron microscopy with energy-dispersive X-ray spectroscopy confirmed the conversion of CsI to CsNO 3 . Iodine separation ranged from 46% to 100% across multiple tests. Iodine separation was most effective when multiple recharges of NO 2 were administered. In conclusion, at the bench scale, liberating iodine from CsI appears to occur within 1 h, but the presence of surface H 2 O and the composition of the NO x reagent mixtures greatly influence its success.

advanced voloxidation↗

Modeling methane dynamics in three wetlands in Northeastern China by using the CLM-Microbe model

Wetlands account for up to 70% of the natural source of methane (CH 4 ) in terrestrial ecosystems on a global scale. Soil microbes are the ultimate producers and biological consumers of CH 4 in wetlands. Therefore, simulating microbial mechanisms of CH 4 production and consumptionwould improve the predictability of CH 4 flux in wetland ecosystems. In this study, we applied a microbial-explicit model, the CLM-Microbe, to simulate CH 4 flux in three major natural wetlands in northeastern China. The CLM-Microbe model was able to capture the seasonal variation of gross primary productivity (GPP), dissolved organic carbon (DOC), and CH 4 flux. The CLM-Microbe model explained more than 40% of the variation in GPP and CH 4 flux across sites. Marsh wetlands had higher CH 4 flux than mountain peatlands. Ebullition dominated the CH 4 transport pathway in all three wetlands. The methanogenesis dominates while methanotroph makes a minor contribution to the CH 4 flux, making all wetlands a CH 4 source. Sensitivity analysis indicated that microbial growth and death rates are the key factors governing CH 4 emission and vegetation physiological properties (flnr) and maintenance respiration predominate GPP variation. Explicitly simulating microbial processes allows genomic information to be incorporated, laying a foundation for better predicting CH 4 dynamics under the changing environment.

54 ENVIRONMENTAL SCIENCES↗

DESI DR1 Lyα 1D power spectrum: the optimal estimator measurement

The one-dimensional power spectrum P 1D of Lyα forest offers rich insights into cosmological and astrophysical parameters, including constraints on the sum of neutrino masses, warm dark matter models, and the thermal state of the intergalactic medium. We present the measurement of P 1D using the optimal quadratic maximum likelihood estimator applied to over 300,000 Lyα quasars from Data Release 1 (DR1) of the Dark Energy Spectroscopic Instrument (DESI) survey. This sample represents the largest to date for P 1D measurements and is larger than the Extended Baryon Oscillation Spectroscopic Survey (eBOSS) by a factor of 1.7. We conduct a meticulous investigation of instrumental and analysis systematics and quantify their impact on P 1D . This includes the development of a cross-exposure estimator that eliminates the need to model the pipeline noise and has strong potential for future P 1D measurements. We also present new insights into metal contamination through the 1D correlation function. Using a fitting function we measure the evolution of the Lyα forest bias with high precision: b F (z) = (-0.218 ± 0.002) × ((1 + z)/4) 2.96±0.06 . In a companion validation paper, we substantially extend our previous suite of CCD image simulations to quantify the pipeline's exquisite performance accurately. In another companion paper, we present DR1 P 1D measurements using the Fast Fourier Transform (FFT) approach to power spectrum estimation. These two measurements produce a forest bias parameter that differs by 2.2 sigma. However, our model is simplistic, so this disagreement will be investigated in future work.

Lyman alpha forest↗

Divergent Evolution of Early Terrestrial Fungi Reveals the Evolution of Mucormycosis Pathogenicity Factors

Abstract Fungi have evolved over millions of years and their species diversity is predicted to be the second largest on the earth. Fungi have cross-kingdom interactions with many organisms that have mutually shaped their evolutionary trajectories. Zygomycete fungi hold a pivotal position in the fungal tree of life and provide important perspectives on the early evolution of fungi from aquatic to terrestrial environments. Phylogenomic analyses have found that zygomycete fungi diversified into two separate clades, the Mucoromycota which are frequently associated with plants and Zoopagomycota that are commonly animal-associated fungi. Genetic elements that contributed to the fitness and divergence of these lineages may have been shaped by the varied interactions these fungi have had with plants, animals, bacteria, and other microbes. To investigate this, we performed comparative genomic analyses of the two clades of zygomycetes in the context of Kingdom Fungi, benefiting from our generation of a new collection of zygomycete genomes, including nine produced for this study. We identified lineage-specific genomic content that may contribute to the disparate biology observed in these zygomycetes. Our findings include the discovery of undescribed diversity in CotH, a Mucormycosis pathogenicity factor, which was found in a broad set of zygomycetes. Reconciliation analysis identified multiple duplication events and an expansion of CotH copies throughout the Mucoromycotina, Mortierellomycotina, Neocallimastigomycota, and Basidiobolus lineages. A kingdom-level phylogenomic analysis also identified new evolutionary relationships within the subphyla of Mucoromycota and Zoopagomycota, including supporting the sister-clade relationship between Glomeromycotina and Mortierellomycotina and the placement of Basidiobolus as sister to other Zoopagomycota lineages.

59 BASIC BIOLOGICAL SCIENCES↗

Signatures of the attractive interaction in spin spectra of one-dimensional cuprate chains

Identifying the minimal model for cuprates is crucial for explaining the high- T c pairing mechanism. Recent photoemission experiments have suggested a significant near-neighbor attractive interaction V in cuprate chains, favoring pairing instability. To determine its strength, we systematically investigate the dynamical spin structure factors S ( q , ω ) using the density matrix renormalization group. Our analysis quantitatively reveals a notable softening in the two-spinon continuum, particularly evident in the intense spectrum at large momentum. This softening is primarily driven by the renormalization of the superexchange interaction, as determined by a comparison with the slave-boson theory. We also demonstrate the feasibility of detecting this spectral shift in thin-film samples using resonant inelastic x-ray scattering. Therefore, this provides a distinctive fingerprint for the attractive interaction, motivating future experiments to unveil essential ingredients in cuprates. Published by the American Physical Society 2024

Shen, Zecheng↗

Optimal Balance of Privacy and Utility with Differential Privacy Deep Learning Frameworks

As the number of online services has increased, the amount of sensitive data being recorded is rising. Simultaneously, the decision-making process has improved by using the vast amounts of data, where machine learning has transformed entire industries. This paper addresses the development of optimal private deep neural networks and discusses the challenges associated with this task. We focus on differential privacy implementations and finding the optimal balance between accuracy and privacy, benefits and limitations of existing libraries, and challenges of applying private machine learning models in practical applications. Our analysis shows that learning rate, and privacy budget are the key factors that impact the results, and we discuss options for these settings.

Kotevska, Olivera↗

Market Implications of Alternative Operating Reserve Modeling in Wholesale Electricity Markets

Pricing and settlement mechanisms are crucial for efficient resource allocation, investment incentives, market competition, and regulatory oversight. In the United States, Regional Transmission Operators (RTOs) adopts a uniform pricing scheme that hinges on the marginal costs of supplying additional electricity. This study investigates the pricing and settlement impacts of alternative reserve constraint modeling, highlighting how even slight variations in the modeling of constraints can drastically alter market clearing prices, reserve quantities, and revenue outcomes. Focusing on the diverse market designs and assumptions in ancillary services by U.S. RTOs, particularly in relation to capacity sharing and reserve substitutions, the research examines four distinct models that combine these elements based on a large-scale synthetic power system test data. Our study provides a critical insight into the economic implications and the underlying factors of these alternative reserve constraints through market simulations and data analysis.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗