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At least 307 records · Page 17

Contrasting decays of 3-quasiparticle isomers in 173 W: A discerning test of 𝐾 conservation and 𝐾 mixing

Two isomers with K π = 19/2 + at 1876 keV with a half-life of 21(1) ns, and K π = 23/2− at 2159 keV with a half-life of 93(6) ns have been identified in 173 W, the lightest tungsten isotope to exhibit this phenomenon. An unusually high number of 13 branches have been established in the decay of the K π = 23/2 − isomer. This decay is associated with transitions involving significantly higher degrees of K forbiddenness and is in sharp contrast with the usual preferential deexcitation through branches, which are less forbidden, as is evident for the K π = 19/2 + state in 173 W. The inclusion of K-mixing effects, arising from band crossings in the sequences to which decays with larger degrees of K forbiddenness are observed, can qualitatively account for this contrasting behavior. These results provide a striking illustration of the competition between K conservation and K mixing in the decay of such isomers.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Learning with Adaptive Conservativeness for Distributionally Robust Optimization: Incentive Design for Voltage Regulation

Information asymmetry between the Distribution System Operator (DSO) and Distributed Energy Resource Aggregators (DERAs) obstructs designing effective incentives for voltage regulation. To capture this effect, we employ a Stackelberg game-theoretic framework, where the DSO seeks to overcome the information asymmetry and refine its incentive strategies by learning from DERA behavior over multiple iterations. We introduce a model-based online learning algorithm for the DSO, aimed at inferring the relationship between incentives and DERA responses. Given the uncertain nature of these responses, we also propose a distributionally robust incentive design model to control the probability of voltage regulation failure and then reformulate it into a convex problem. This model allows the DSO to periodically revise distribution assumptions on uncertain parameters in the decision model of the DERA. Finally, we present a gradient-based method that permits the DSO to adaptively modify its conservativeness level, measured by the size of a Wasserstein metric-based ambiguity set, according to historical voltage regulation performance. The effectiveness of our proposed method is demonstrated through numerical experiments.

adaptation models↗

Reducing Conservativeness of Polytopic Linear-Parameter-Varying Robust Vehicle Sideslip Angle Observer Through Minimum-Area Convex Quadrilateral Design

The polytopic linear-parameter-varying (LPV) method has become increasingly popular for designing intelligent control and estimation systems for ground vehicles, particularly for the vehicle sideslip angle observer. In vehicle lateral dynamics, the vehicle longitudinal velocity-induced nonlinearities are conventionally outer-approximated with polytopes such as rectangles or triangles to obtain a polytopic LPV system. Yet, such polytopic approximations tend to be conservative and may lead to inadequate observer performance. To address this issue, a minimum-area convex quadrilateral construction is proposed in this paper to reduce design conservatism. The suggested design is demonstrated through the synthesis of an LPV H ∞ robust vehicle sideslip angle observer. Furthermore, a dSPACE-ASM simulation study is conducted to demonstrate the effectiveness and the advantage of the proposed polytopic construction over a baseline approach.

Zhou, Xingyu↗

Logical and Physical Reversibility of Conservative Skyrmion Logic

Magnetic skyrmions are nanoscale whirls of magnetism that can be propagated with electrical currents. The repulsion between skyrmions inspires their use for reversible computing based on the elastic billiard ball collisions proposed for conservative logic in 1982. In this letter, we evaluate the logical and physical reversibility of this skyrmion logic paradigm, as well as the limitations that must be addressed before dissipation-free computation can be realized.

42 ENGINEERING↗

Conservation Voltage Reduction with Distributed Energy Resource Management System, Grid-Edge, and Legacy Devices

Distribution utilities use conservation voltage reduction (CVR) to obtain energy savings and lower peak demand by reducing bus voltages. Traditionally, the CVR is accomplished by controlling the legacy assets such as load tap changers, voltage regulators, and capacitor banks. The deployment of the advanced distribution management system (ADMS) and distributed energy resource management system (DERMS) enables the integration of distributed energy resources into the distribution networks and provide the grid services including CVR. This paper studies the coordinated operation of an ADMS and a DERMS in achieving CVR and voltage regulation. A commercial ADMS uses legacy devices and Edge-of-Network Grid Optimization (ENGO) devices to obtain energy savings through CVR. A prototype DERMS dispatches the photovoltaic smart inverters based on real-time optimal power low to ensure voltage regulation across the feeder. The results show that the coordinated operation of ADMS and DERMS is effective in achieving CVR and voltage regulation. Specifically, energy savings of up to 4.7% are observed in the real utility distribution system used in this study.

advanced distribution management system↗

Time‐series multi‐omics analysis of micronutrient stress in Sorghum bicolor reveals iron and zinc crosstalk and regulatory network conservation

Micronutrient stress impacts growth, biomass production, and grain yield in crops. Multi-omics studies are valuable resources in identifying genes for functional studies and trait improvement, such as accumulation of Fe or Zn under deficient or excess conditions for bioenergy or grain agriculture. We conducted transcriptomics and ionomics analyses on Sorghum bicolor BTx623, grown under Fe and Zn limited and excess conditions over a 21-day period. To identify early and late transcriptional response in roots and leaves, 180 RNAseq libraries were sequenced for differential expression and co-expression network analyses. Fe and Zn accumulation was measured using ICP-MS at each time point, and a fluorometer was used to estimate chlorophyll content in leaves. Among the four treatments, Fe limitation and Zn excess resulted in the largest phenotypic effects and transcriptional response in roots and leaves. Several of the reduction (Strategy I) and chelation (Strategy II) strategy genes that improve bioavailability of Fe and Zn in plant roots often used by non-grass and grass species, respectively, were differentially expressed. Gene regulatory network (GRN) analysis of roots revealed enrichment of genes from Fe limiting and Zn excess which strongly connect to homologues of SbFIT, SbPYE, and SbBTS as hub genes. The GRN for leaf responses showed homologues of SbPYE and SbBTS as hubs connecting genes for chloroplast biosynthesis, Fe-S cluster assembly, photosynthesis, and ROS scavenging. Expression analyses suggest sorghum uses Strategy II genes for Fe and Zn uptake, as expected, but can also utilize Strategy I genes, which may be advantageous in variable moisture environments. We found strong overlap between Fe and Zn responsive GRNs, indicative of micronutrient crosstalk. We also found conservation of root and leaf GRNs, and known homologous genes suggest strong constraints on homeostasis networks in plants. These data will provide a resource for functional genetics to enhance micronutrient transport in sorghum, and opportunities to conduct further comparative GRN analysis across diverse crops species.

59 BASIC BIOLOGICAL SCIENCES↗

A stoichiometrically conserved homologous series with infinite structural diversity

Here, we describe a compositionally guided structural evolution within a stoichiometrically conserved framework, BaSbQ 3 (Q = Te 1−x S x ), where each value of x gives rise to a distinct phase. The fundamental building blocks, A 1 (BaSbSTe 2 ) and B n (Ba n Sb n S n−1 Te 2n+1 ), were composed of modular double rocksalt slabs stacked with functional polytelluride zigzag chains, with each phase differing only in the size and assembly of these blocks. Ten compounds were synthesized that maintained a coherent chemical identity that arose from this isovalent, isoelectronic substitution of Te and S. We envision that the phase formation at a molecular level unfolds in stages of extension, termination, and assembly and propose a design concept of “anionic disparity,” where phase homologies and polytelluride hierarchical networks can be controlled by leveraging differences in anion electron affinity and sizes.

Zhao, Hengdi [Argonne National Laboratory (ANL), A↗

Intranasal Nanoparticle Vaccination Elicits a Persistent, Polyfunctional CD4 T Cell Response in the Murine Lung Specific for a Highly Conserved Influenza Virus Antigen That Is Sufficient To Mediate Protection from Influenza Virus Challenge

We report lung-localized CD4 T cells play a critical role in the control of influenza virus infection and can provide broadly protective immunity. However, current influenza vaccination strategies primarily target influenza hemagglutinin (HA) and are administered peripherally to induce neutralizing antibodies. We have used an intranasal vaccination strategy targeting the highly conserved influenza nucleoprotein (NP) to elicit broadly protective lung-localized CD4 T cell responses. The vaccine platform consists of a self-assembling nanolipoprotein particle (NLP) linked to NP with an adjuvant. We have evaluated the functionality, in vivo localization, and persistence of the T cells elicited. Our study revealed that intranasal vaccination elicits a polyfunctional subset of lung-localized CD4 T cells that persist long term. A subset of these lung CD4 T cells localize to the airway, where they can act as early responders following encounter with cognate antigen. Polyfunctional CD4 T cells isolated from airway and lung tissue produce significantly more effector cytokines IFN-γ and TNF-α, as well as cytotoxic functionality. When adoptively transferred to naive recipients, CD4 T cells from NLP:NP-immunized lung were sufficient to mediate 100% survival from lethal challenge with H1N1 influenza virus.

59 BASIC BIOLOGICAL SCIENCES↗

Transcriptomic and functional analyses uncover a conserved effector driving genotype-dependent virulence in the Sphaerulina musiva-Populus trichocarpa interaction

The introduction of invasive microbes compromises the structure, biodiversity, and function of naïve ecosystems. Sphaerulina musiva, a hemibiotrophic pathogen that causes leaf spot and stem cankers in Populus species, exemplifies an invasive fungal pathogen spread by human activities. However, the genetic mechanisms of pathogenicity and virulence are poorly understood, impeding mitigation strategies. We utilized RNA sequencing to identify fungal effectors linked to stem canker formation, informing the development of future strategies for effective disease management. Our analysis revealed 70 genes differentially expressed at 2 weeks and 110 genes at 3 weeks between inoculated trees and controls. Notably, the gene with the highest expression at 2 weeks and the second highest at 3 weeks was homologous to Extracellular protein 2 (Ecp2). Complementary genome-wide association studies linked sequence polymorphisms in this locus to phenotypic variation in disease severity. Infiltration of S. musiva Ecp2 into Populus trichocarpa leaves induced necrosis in susceptible genotypes. Gene disruption using a CRISPR-Cas9 RNP system resulted in a genotype-dependent reduction of stem canker and disease severity. Tracing the evolutionary history of this effector across the fungal kingdom, we uncovered clade-specific gene-family expansions and orthologs in new species. These findings raise questions about the function and adaptive significance of these gene families in fungal lifestyles. Our study provides the first tractable target for breeding resistant poplar genotypes, addressing the challenges of managing S. musiva and uncovering mechanisms that drive its virulence, and provides deeper insights into the evolutionary dynamics of a conserved small-secreted protein with a diversity of functions.

Sondreli, Kelsey L [Oregon State University]↗

Predicting variable gene content in Escherichia coli using conserved genes

Having the ability to predict the protein-encoding gene content of an incomplete genome or metagenome-assembled genome is important for a variety of bioinformatic tasks. In this study, as a proof of concept, we built machine learning classifiers for predicting variable gene content in Escherichia coli genomes using only the nucleotide k-mers from a set of 100 conserved genes as features. Protein families were used to define orthologs, and a single classifier was built for predicting the presence or absence of each protein family occurring in 10%–90% of all E. coli genomes. The resulting set of 3,259 extreme gradient boosting classifiers had a per-genome average macro F1 score of 0.944 [0.943–0.945, 95% CI]. We show that the F1 scores are stable across multi-locus sequence types and that the trend can be recapitulated by sampling a smaller number of core genes or diverse input genomes. Surprisingly, the presence or absence of poorly annotated proteins, including “hypothetical proteins” was accurately predicted (F1 = 0.902 [0.898–0.906, 95% CI]). Models for proteins with horizontal gene transfer-related functions had slightly lower F1 scores but were still accurate (F1s = 0.895, 0.872, 0.824, and 0.841 for transposon, phage, plasmid, and antimicrobial resistance-related functions, respectively). Finally, using a holdout set of 419 diverse E. coli genomes that were isolated from freshwater environmental sources, we observed an average per-genome F1 score of 0.880 [0.876–0.883, 95% CI], demonstrating the extensibility of the models. Overall, this study provides a framework for predicting variable gene content using a limited amount of input sequence data.

59 BASIC BIOLOGICAL SCIENCES↗

Adaptive Uncertainty Quantification for Stochastic Hyperbolic Conservation Laws

Here, we propose a predictor-corrector adaptive method for the study of hyperbolic partial differential equations (PDEs) under uncertainty. Constructed around the framework of stochastic finite volume (SFV) methods, our approach circumvents sampling schemes or simulation ensembles while also preserving fundamental properties, in particular hyperbolicity of the resulting systems and conservation of the discrete solutions. Furthermore, we augment the existing SFV theory with a priori convergence results for statistical quantities, in particular push-forward densities, which we demonstrate through numerical experiments. By linking refinement indicators to regions of the physical and stochastic spaces, we drive anisotropic refinements of the discretizations, introducing new degrees of freedom where deemed profitable. To illustrate our proposed method, we consider a series of numerical examples for nonlinear hyperbolic PDEs based on Burgers’ and Euler’s equations.

97 MATHEMATICS AND COMPUTING↗

Efficient Reformulation of Linear and Nonlinear Solid-Phase Diffusion in Lithium-ion Battery Models using Symmetric Polynomials: Mass Conservation and Computational Efficiency

Lithium-ion batteries are typically modeled using porous electrode theory coupled with various transport and reaction mechanisms, along with suitable discretization or approximations for the solid-phase diffusion equation. The solid-phase diffusion equation represents the main computational burden for typical pseudo-2-dimensional (p2D) models since these equations in the pseudo r -dimension must be solved at each point in the computational grid. This substantially increases the complexity of the model as well as the computational time. Traditional approaches towards simplifying solid-phase diffusion possess certain significant limitations, especially in modeling emerging electrode materials which involve phase changes and variable diffusivities. A computationally efficient representation for solid-phase diffusion is discussed in this paper based on symmetric polynomials using Orthogonal Collocation and Galerkin formulation (weak form). A systematic approach is provided to increase the accuracy of the approximation (p form in finite element methods) to enable efficient simulation with a minimal number of semi-discretized equations, ensuring mass conservation even for non-linear diffusion problems involving variable diffusivities. These methods are then demonstrated by incorporation into the full p2D model, illustrating their advantages in simulating high C-rates and short-time dynamic operation of Lithium-ion batteries.

25 ENERGY STORAGE↗

Simulating pitch angle scattering using an explicitly solvable energy-conserving algorithm

Particle distribution functions evolving under the Lorentz operator can be simulated with the Langevin equation for pitch angle scattering. This approach is frequently used in particle based Monte-Carlo simulations of plasma collisions, among others. However, most numerical treatments do not guarantee energy conservation, which may lead to unphysical artifacts such as numerical heating and spectra distortions. We present a novel structure-preserving numerical algorithm for the Langevin equation for pitch angle scattering. Similar to the well-known Boris algorithm, the proposed numerical scheme takes advantage of the structure-preserving properties of the Cayley transform when calculating the velocity-space rotations. The resulting algorithm is explicitly solvable, while preserving the norm of velocities down to machine precision. We demonstrate that the method has the same order of numerical convergence as the traditional stochastic Euler-Maruyama method.

Zhang, Xin↗

Conserving Land–Atmosphere Synthesis Suite (CLASS)

Accurate estimates of terrestrial water and energy cycle components are needed to better understand climate processes and improve models’ ability to simulate future change. Various observational estimates are available for the individual budget terms; however, these typically show inconsistencies when combined in a budget. In this work, a Conserving Land–Atmosphere Synthesis Suite (CLASS) of estimates of simultaneously balanced surface water and energy budget components is developed. Individual CLASS variable datasets, where possible, 1) combine a range of existing variable product estimates, and hence overcome the limitations of estimates from a single source; 2) are observationally constrained with in situ measurements; 3) have uncertainty estimates that are consistent with their agreement with in situ observations; and 4) are consistent with each other by being able to solve the water and energy budgets simultaneously. First, available datasets of a budget variable are merged by implementing a weighting method that accounts both for the ability of datasets to match in situ measurements and the error covariance between datasets. Then, the budget terms are adjusted by applying an objective variational data assimilation technique (DAT) that enforces the simultaneous closure of the surface water and energy budgets linked through the equivalence of evapotranspiration and latent heat. Comparing component estimates before and after applying the DAT against in situ measurements of energy fluxes and streamflow showed that modified estimates agree better with in situ observations across various metrics, but also revealed some inconsistencies between water budget terms in June over the higher latitudes.

54 ENVIRONMENTAL SCIENCES↗

Advancing stem cell technologies for conservation of wildlife biodiversity

ABSTRACT Wildlife biodiversity is essential for healthy, resilient and sustainable ecosystems. For biologists, this diversity also represents a treasure trove of genetic, molecular and developmental mechanisms that deepen our understanding of the origins and rules of life. However, the rapid decline in biodiversity reported recently foreshadows a potentially catastrophic collapse of many important ecosystems and the associated irreversible loss of many forms of life on our planet. Immediate action by conservationists of all stripes is required to avert this disaster. In this Spotlight, we draw together insights and proposals discussed at a recent workshop hosted by Revive & Restore, which gathered experts to discuss how stem cell technologies can support traditional conservation techniques and help protect animal biodiversity. We discuss reprogramming, in vitro gametogenesis, disease modelling and embryo modelling, and we highlight the prospects for leveraging stem cell technologies beyond mammalian species.

Developmental Biology↗

BEPAM Model Code and CABBI Simulation Results for "Assessing the Returns to Land and Greenhouse Gas Savings from Producing Energy Crops on Conservation Reserve Program Land"

This dataset contains BEPAM model code and input data to the replicate the results for "Assessing the Returns to Land and Greenhouse Gas Savings from Producing Energy Crops on Conservation Reserve Program Land." The dataset consists of: (1) The replication codes and data for the BEPAM model. The code file is named as output_0213-2020_Complete_daycent-agversion-[rental payment level]%_[biomass price].gms. (BEPAM-CRP model-Sep2020.zip) (2) Simulation results from the BEPAM model (BEPAM_Simulation_Results.csv) * Item (1) is in GAMS format. Item (2) is in text format.

biomass price↗

EfgA is a conserved formaldehyde sensor that leads to bacterial growth arrest in response to elevated formaldehyde

Normal cellular processes give rise to toxic metabolites that cells must mitigate. Formaldehyde is a universal stressor and potent metabolic toxin that is generated in organisms from bacteria to humans. Methylotrophic bacteria such as Methylorubrum extorquens face an acute challenge due to their production of formaldehyde as an obligate central intermediate of single-carbon metabolism. Mechanisms to sense and respond to formaldehyde were speculated to exist in methylotrophs for decades but had never been discovered. Here, we identify a member of the DUF336 domain family, named efgA for enhanced formaldehyde growth, that plays an important role in endogenous formaldehyde stress response in M . extorquens PA1 and is found almost exclusively in methylotrophic taxa. Our experimental analyses reveal that EfgA is a formaldehyde sensor that rapidly arrests growth in response to elevated levels of formaldehyde. Heterologous expression of EfgA in Escherichia coli increases formaldehyde resistance, indicating that its interaction partners are widespread and conserved. EfgA represents the first example of a formaldehyde stress response system that does not involve enzymatic detoxification. Thus, EfgA comprises a unique stress response mechanism in bacteria, whereby a single protein directly senses elevated levels of a toxic intracellular metabolite and safeguards cells from potential damage.

59 BASIC BIOLOGICAL SCIENCES↗

Biophysical and biochemical studies support TP0094 as a phosphotransacetylase in an acetogenic energy-conservation pathway in Treponema pallidum

The mechanisms of energy generation and carbon-source utilization in the syphilis spirochete Treponema pallidum have remained enigmatic despite complete genomic sequence information. Whereas the bacterium harbors enzymes for glycolysis, the apparatus for more efficient use of glucose catabolites, namely the citric-acid cycle, is apparently not present. Yet, the organism’s energy needs likely exceed the modest output from glycolysis alone. Recently, building on our structure-function studies of T . pallidum lipoproteins, we proposed a “flavin-centric” metabolic lifestyle for the organism that partially resolves this conundrum. As a part of the hypothesis, we have proposed that T . pallidum contains an acetogenic energy-conservation pathway that catabolizes D-lactate, yielding acetate, reducing equivalents for the generation and maintenance of chemiosmotic potential, and ATP. We already have confirmed the D-lactate dehydrogenase activity in T . pallidum necessary for this pathway to operate. In the current study, we focused on another enzyme ostensibly involved in treponemal acetogenesis, phosphotransacetylase (Pta). This enzyme is putatively identified as TP0094 and, in this study, we determined a high-resolution (1.95 Å) X-ray crystal structure of the protein, finding that its fold comports with other known Pta enzymes. Further studies on its solution behavior and enzyme activity confirmed that it has the properties of a Pta. These results are consistent with the proposed acetogenesis pathway in T . pallidum , and we propose that the protein be referred to henceforth as TpPta.

59 BASIC BIOLOGICAL SCIENCES↗