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At least 757 records · Page 42

Developing stable, simplified, functional consortia from Brachypodium rhizosphere for microbial application in sustainable agriculture

The rhizosphere microbiome plays a crucial role in supporting plant productivity and ecosystem functioning by regulating nutrient cycling, soil integrity, and carbon storage. However, deciphering the intricate interplay between microbial relationships within the rhizosphere is challenging due to the overwhelming taxonomic and functional diversity. Here we present our systematic design framework built on microbial colocalization and microbial interaction, toward successful assembly of multiple rhizosphere-derived Reduced Complexity Consortia (RCC). We enriched co-localized microbes from Brachypodium roots grown in field soil with carbon substrates mimicking Brachypodium root exudates, generating 768 enrichments. By transferring the enrichments every 3 or 7 days for 10 generations, we developed both fast and slow-growing reduced complexity microbial communities. Most carbon substrates led to highly stable RCC just after a few transfers. 16S rRNA gene amplicon analysis revealed distinct community compositions based on inoculum and carbon source, with complex carbon enriching slow growing yet functionally important soil taxa like Acidobacteria and Verrucomicrobia. Network analysis showed that microbial consortia, whether differentiated by growth rate (fast vs. slow) or by succession (across generations), had significantly different network centralities. Besides, the keystone taxa identified within these networks belong to genera with plant growth-promoting traits, underscoring their critical function in shaping rhizospheric microbiome networks. Furthermore, tested consortia demonstrated high stability and reproducibility, assuring successful revival from glycerol stocks for long-term viability and use. Our study represents a significant step toward developing a framework for assembling rhizosphere consortia based on microbial colocalization and interaction, with future implications for sustainable agriculture and environmental management.

59 BASIC BIOLOGICAL SCIENCES↗

On the measurement of shape: With applications to lunar regolith

With the renewed commitment from NASA and other commercial entities for a presence on the Moon, the importance of understanding the characteristics of lunar regolith and how to utilize it have become the target of increasing scrutiny. Much of what is known about lunar regolith was collected during and immediately after the Apollo program, however, analytical techniques and instrumentation have advanced in leaps and bounds in the subsequent decades. Specifically, dynamic image analysis systems have advanced to the point that millions of particles can have morphological characteristics automatically determined in relatively short time frames. Particle morphological data was collected on several lunar samples and a pair of widely used regolith simulants to ascertain the accuracy of these simulants and to explore statistical analysis methods of these large datasets. It is found that these morphology datasets can vary widely depending on the particle size of the particles, and simple averaging of the data skews the results heavily towards the numerically abundant size ranges, the fines. Different reporting methods are suggested to ameliorate these problems. When applied to the lunar regolith, the particles are noted to be less morphologically complex than initially suspected. Compared to the lunar material, the simulants are found to contain some more morphological variability and angular grains. Such difference is likely due to the wildly different comminution processes that these different powder systems are subjected to.

2D shape↗

Machine learning insights into microstructural origins of transport and mechanical properties in porous microstructures

Multifunctional porous materials are increasingly needed across various fields, but their complex microstructures create significant challenges due to the intricate microstructure-property relationships. This complexity, combined with limitations of traditional analysis methods, hinders efforts to understand and optimize microstructure–property relationships. Here, to address this, we integrate physics-based mesoscale modeling with interpretable machine learning (ML) to uncover how microstructural features govern effective diffusivity and elastic modulus. At constant porosity, we show diffusivity varies by over 150 × and modulus by ∼50 ×, highlighting the power of microstructure engineering. Statistical analysis reveals bimodal behavior in diffusivity and unimodal in modulus. ML identifies connectivity as the dominant factor, while modulus is also sensitive to domain size and feature interactions. Controlled simulations further highlight domain shape as a critical feature for modulus. This framework enables efficient exploration of microstructure-property correlations, offering new insights to guide the design of advanced porous materials.

Bicontinuous microstructure↗

Cosmological analysis of three-dimensional BOSS galaxy clustering and Planck CMB lensing cross correlations via Lagrangian perturbation theory

In this work, we present a formalism for jointly fitting pre- and post-reconstruction redshift-space clustering (RSD) and baryon acoustic oscillations (BAO) plus gravitational lensing (of the CMB) that works directly with the observed 2-point statistics. The formalism is based upon (effective) Lagrangian perturbation theory and a Lagrangian bias expansion, which models RSD, BAO and galaxy-lensing cross correlations within a consistent dynamical framework. As an example we present an analysis of clustering measured by the Baryon Oscillation Spectroscopic Survey in combination with CMB lensing measured by Planck. The post-reconstruction BAO strongly constrains the distance-redshift relation, the full-shape redshift-space clustering constrains the matter density and growth rate, and CMB lensing constrains the clustering amplitude. Using only the redshift space data we obtain Ω m = 0.303 ± 0.008, $H_0$ = 69.21 ± 0.78 and $σ_8$ = 0.743 ± 0.043. The addition of lensing information, even when restricted to the Northern Galactic Cap, improves constraints to Ω m = 0.303 ± 0.008, $H_0$ = 69.21 ± 0.77 and $σ_8$ = 0.707 ± 0.035, in tension with CMB and cosmic shear constraints. The combination of Ω m and $H_0$ are consistent with Planck, though their constraints derive mostly from redshift-space clustering. The low $σ_8$ value are driven by cross correlations with CMB lensing in the low redshift bin ($\textit{z}$ ≃ 0.38) and at large angular scales, which show a 20% deficit compared to expectations from galaxy clustering alone. We conduct several systematics tests on the data and find none that could fully explain these tensions.

79 ASTRONOMY AND ASTROPHYSICS↗

Machinable, high‐conductivity NaSICON through mitigation of humidity effects during solid‐state synthesis

The Na + super ion conductor (NaSICON, Na 1+x Zr 2 Si x P 3-x O 12 ) is a solid electrolyte well-known for fast, selective Na + transport at low temperatures, uniquely enabling sodium-based batteries. Producing high-quality NaSICON from solid-state methods, especially when cost-effective, potentially hygroscopic precursors are used, is not trivial. To understand and eliminate the influence of humidity during processing, a scheme was developed to reproducibly yield a high Na + conductivity (3.75 mS/cm at 25°C, 81.7 mS/cm at 150°C), high density (97%), and machinable NaSICON without the use of binders, sintering aids, or dopants. Controlled humidity studies over 20%–50% RH coupled with thermal, structural, and electrical analysis reveal that calcination temperatures < 1000°C leave NaSICON processing susceptible to water absorption at > 20% RH due to the presence of hygroscopic Na 3 PO 4 and Na 2 CO 3 during shaping, pressing, and sintering. Water absorption results in NaSICON with lower densities, machinability, and Na+ conductivity, due to impaired intergranular Na+ transport. At the other extreme, fully converting precursor to the NaSICON phase at 1230°C before pressing and sintering leads to poor conductivity and density. By calcining at 1000°C, excellent quality NaSICON may be produced under a range of laboratory environments, enabling low-cost production of high-conductivity, machinable NaSICON necessary the ever-growing energy storage market.

NaSICON↗

Gene expression of functionally-related genes coevolves across fungal species: detecting coevolution of gene expression using phylogenetic comparative methods

Researchers often measure changes in gene expression across conditions to better understand the shared functional roles and regulatory mechanisms of different genes. Analogous to this is comparing gene expression across species, which can improve our understanding of the evolutionary processes shaping the evolution of both individual genes and functional pathways. One area of interest is determining genes showing signals of coevolution, which can also indicate potential functional similarity, analogous to co-expression analysis often performed across conditions for a single species. However, as with any trait, comparing gene expression across species can be confounded by the non-independence of species due to shared ancestry, making standard hypothesis testing inappropriate. We compared RNA-Seq data across 18 fungal species using a multivariate Brownian Motion phylogenetic comparative method (PCM), which allowed us to quantify coevolution between protein pairs while directly accounting for the shared ancestry of the species. Our work indicates proteins which physically-interact show stronger signals of coevolution than randomly-generated pairs. Interactions with stronger empirical and computational evidence also showing stronger signals of coevolution. We examined the effects of number of protein interactions and gene expression levels on coevolution, finding both factors are overall poor predictors of the strength of coevolution between a protein pair. Simulations further demonstrate the potential issues of analyzing gene expression coevolution without accounting for shared ancestry in a standard hypothesis testing framework. Furthermore, our simulations indicate the use of a randomly-generated null distribution as a means of determining statistical significance for detecting coevolving genes with phylogenetically-uncorrected correlations, as has previously been done, is less accurate than PCMs, although is a significant improvement over standard hypothesis testing. These methods are further improved by using a phylogenetically-corrected correlation metric. Our work highlights potential benefits of using PCMs to detect gene expression coevolution from high-throughput omics scale data. This framework can be built upon to investigate other evolutionary hypotheses, such as changes in transcription regulatory mechanisms across species.

59 BASIC BIOLOGICAL SCIENCES↗

Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron

Ordered transposon-insertion collections, in which specific transposon-insertion mutants are stored as monocultures in a genome-scale collection, represent a promising tool for genetic dissection of human gut microbiota members. However, publicly available collections are scarce and the construction methodology remains in early stages of development. Here, we describe the assembly of a genome-scale ordered collection of transposon-insertion mutants in the model gut anaerobe Bacteroides thetaiotaomicron VPI-5482 that we created as a resource for the research community. We used flow cytometry to sort single cells from a pooled library, located mutants within this initial progenitor collection by applying a pooling strategy with barcode sequencing, and re-arrayed specific mutants to create a condensed collection with single-insertion strains covering >2500 genes. To demonstrate the potential of the condensed collection for phenotypic screening, we analyzed growth dynamics and cell morphology. We identified both growth defects and altered cell shape in mutants disrupting sphingolipid synthesis and thiamine scavenging. Finally, we analyzed the process of assembling the B. theta condensed collection to identify inefficiencies that limited coverage. We demonstrate as part of this analysis that the process of assembling an ordered collection can be accurately modeled using barcode sequencing data. We expect that utilization of this ordered collection will accelerate research into B. theta physiology and that lessons learned while assembling the collection will inform future efforts to assemble ordered mutant collections for an increasing number of gut microbiota members.

59 BASIC BIOLOGICAL SCIENCES↗

Data for Photosynthetic responses to temperature across the tropics: a meta-analytic approach

This data package contains raw data, data output, and code of photosynthetic temperature response curves from tropical forests. Data are used in "Photosynthetic responses to temperature across the tropics: a meta-analytic approach". The research investigates how photosynthetic optimum temperatures and shapes of photosynthetic temperature response curves varies across tropical forest climates and growth conditions. Growth climate variables include mean annual temperature, max and max temperature, diurnal temperature range, and aridity index. Meta-analysis combines 18 datasets with representation from Africa, Oceana, North American, and South America. Growth conditions analyzed considers deciduousness, successional status, light conditions, and whether plants are grown in situ or ex situ. All files, except for the raw datafile (Tropical_MetaAnalysis_Master_3.8.22_Edit.csv), have been processed using R code, which is provided.

54 ENVIRONMENTAL SCIENCES↗

Higgs Self Couplings Measurements at Future proton-proton Colliders

The Higgs boson trilinear and quartic self-couplings are directly related to the shape of the Higgs potential; measuring them with precision is extremely important, as they provide invaluable information on the electroweak symmetry breaking and the electroweak phase transition.In this paper, we perform a detailed analysis of double Higgs boson production, through the gluon-gluon fusion process, in the most promising decay channels $b\bar{b} \gamma\gamma$, $b\bar{b} \tau\tau$, and $b\bar{b}b\bar{b}$ for several future colliders: the HL-LHC at 14 TeV and the FCC-hh at 100 TeV, assuming respectively 3 $ab^{-1}$ and 30 $ab^{-1}$ of integrated luminosity.In the HL-LHC scenario, we expect an upper limit on the di-Higgs cross-section production of 0.76 at 95\% confidence level, corresponding to a significance of 2.8 $\sigma$.In the FCC-hh scenario, depending on the assumed detector performance and systematic uncertainties, we expect that the Higgs self-coupling will be measured with a precision in the range 4.8-8.5\% at 95\% confidence level.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Invertible Temper Modeling using Normalizing Flows and the Effects of Structure Preserving Loss

Advanced manufacturing research and development is typically small-scale, owing to costly experiments associated with these novel processes. Deep learning techniques could help accelerate this development cycle but frequently struggle in small-data regimes like the advanced manufacturing space. While prior work has applied deep learning to modeling visually plausible advanced manufacturing microstructures, little work has been done on data-driven modeling of how microstructures are affected by heat treatment, or assessing the degree to which synthetic microstructures are able to support existing workflows. We propose to address this gap by using invertible neural networks (normalizing flows) to model the effects of heat treatment, e.g., tempering. The model is developed using scanning electron microscope imagery from samples produced using shear-assisted processing and extrusion (ShAPE) manufacturing. This approach not only produces visually and topologically plausible samples, but also captures information related to a sample’s material properties or experimental process parameters. We also demonstrate that topological data analysis, used in prior work to characterize microstructures, can also be used to stabilize model training, preserve structure, and improve downstream results. We assess directions for future work and identify our approach as an important step towards end-to-end deep learning system for accelerating advanced manufacturing research and development.

Howland, Sylvia↗

Driving mode analysis—How uncertain functional inputs propagate to an output

Abstract Driving mode analysis elucidates how correlated features of uncertain functional inputs jointly propagate to produce uncertainty in the output of a computation. Uncertain input functions are decomposed into three terms: the mean functions, a zero‐mean driving mode, and zero‐mean residual. The random driving mode varies along a single direction, having fixed functional shape and random scale. It is uncorrelated with the residual, and under linear error propagation, it produces an output variance equal to that of the full input uncertainty. Finally, the driving mode best represents how input uncertainties propagate to the output because it minimizes expected squared Mahalanobis distance amongst competitors. These characteristics recommend interpretation of the driving mode as the single‐degree‐of‐freedom component of input uncertainty that drives output uncertainty. We derive the functional driving mode, show its superiority to other seemingly sensible definitions, and demonstrate the utility of driving mode analysis in an application. The application is the simulation of neutron transport in criticality experiments. The uncertain input functions are nuclear data that describe how Pu reacts to bombardment by neutrons. Visualization of the driving mode helps scientists understand what aspects of correlated functional uncertainty have effects that either reinforce or cancel one another in propagating to the output of the simulation.

97 MATHEMATICS AND COMPUTING↗

VRC34-Antibody Lineage Development Reveals How a Required Rare Mutation Shapes the Maturation of a Broad HIV-Neutralizing Lineage

Rare mutations have been proposed to restrict the development of broadly neutralizing antibodies against HIV-1, but this has not been explicitly demonstrated. We hypothesized that such rare mutations might be identified by comparing broadly neutralizing and non-broadly neutralizing branches of an antibody-developmental tree. Because sequences of antibodies isolated from the fusion peptide (FP)-targeting VRC34-antibody lineage suggested it might be suitable for such rare mutation analysis, we carried out next-generation sequencing (NGS) on B cell transcripts from donor N123, the source of the VRC34 lineage, and functionally and structurally characterized inferred intermediates along broadly neutralizing and poorly neutralizing developmental branches. The broadly neutralizing VRC34.01 branch required the rare heavy-chain mutation Y33P to bind FP, whereas the early bifurcated VRC34.05 branch did not require this rare mutation and evolved less breadth. Our results demonstrate how a required rare mutation can restrict development and shape the maturation of a broad HIV-1-neutralizing antibody lineage.

59 BASIC BIOLOGICAL SCIENCES↗

Demonstration of gold nanorod systems for enhanced total efficiency: Experimental and numerical analysis

This study investigates the photothermal performance of gold nanorods engineered to exhibit longitudinal plasmon resonances at 695 nm, 780 nm, and 970 nm. The work combines synthesis, structural characterization, extinction measurements, numerical modeling, and controlled temperature experiments to quantify how nanorod geometry, resonance tuning, concentration, and chamber shape jointly influence heat generation. Transmission electron microscopy confirms that increasing nanorod aspect ratio systematically shifts the longitudinal plasmon peak toward the near-infrared region. Extinction measurements show strong agreement with theoretical predictions, validating the numerical model across two independent datasets. Three chamber geometries were tested under laser excitation at 640 nm, 808 nm, and 980 nm: an ascending stepped base, a flat base, and a descending stepped base. Without nanorods, the ascending geometry produced the highest efficiency due to enhanced natural convection. After introducing gold nanorods, all geometries exhibited substantial thermal enhancement, with total efficiencies exceeding 20%. The strongest improvement was obtained for nanorods resonant at 780 nm with a mass concentration of 4.6 mg/mL implemented on the descending stepped-base geometry. This performance resulted from the combined effect of spectral overlapping with the 808 nm laser, the highest nanorod concentration, and localized heat accumulation that intensified buoyancy-driven flow. The findings demonstrate that total efficiency is governed by a synergistic interplay between optical resonance, nanoparticle concentration, and macroscopic chamber design, revealing the system-level coupling between nanoscale plasmonic absorption and macroscale heat-transfer phenomena. The results provide a validated framework for tuning nanoscale plasmonic absorbers and optimizing thermal systems for applications requiring efficient light-to-heat conversion.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Particle production as a function of charged-particle flattenicity in 𝑝⁢𝑝 collisions at $\sqrt{s}$ = 13 TeV

This paper reports the first measurement of the transverse momentum (𝑝 T ) spectra of primary charged pions, kaons, (anti)protons, and unidentified particles as a function of the charged-particle flattenicity in pp collisions at $\sqrt{s}$ =13 TeV. Flattenicity is a novel event shape observable that is measured in the pseudorapidity intervals covered by the V0 detector, 2.8 < 𝜂 < 5.1 and −3.7 < 𝜂 < −1.7. According to QCD-inspired phenomenological models, it shows sensitivity to multiparton interactions and is less affected by biases toward larger 𝑝 T due to local multiplicity fluctuations in the V0 acceptance than multiplicity. The analysis is performed in minimum-bias (MB) as well as in high-multiplicity events up to 𝑝 T = 20 GeV/⁢𝑐. The event selection requires at least one charged particle produced in the pseudorapidity interval |𝜂| < 1. The measured 𝑝 T distributions, average 𝑝 T , kaon-to-pion and proton-to-pion particle ratios, presented in this paper, are compared to model calculations using pythia 8 based on color strings and EPOS LHC. The modification of the 𝑝 T -spectral shapes in low-flattenicity events that have large event activity with respect to those measured in MB events develops a pronounced peak at intermediate 𝑝 T (2 < 𝑝 T < 8 GeV/𝑐), and approaches the vicinity of unity at higher 𝑝 T . The results are qualitatively described by pythia, and they show different behavior than those measured as a function of charged-particle multiplicity based on the V0M estimator.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Availability Estimates of Low-Cost, Dispatch-Constrained Electricity (LDE)

This dataset accompanies the report "Potential Availability of and Supply Curves for Low-Cost, Dispatch-Constrained Electricity", which provides initial estimates of the quantity and availability of the potential low-cost, dispatch-constrained electricity (LDE) resource in the United States under scenarios with high variable renewable energy (VRE) penetrations. The analysis also estimates supply curves that can be used in subsequent analysis of the opportunity to use the LDE. The estimated LDE resource could be used for various applications that value low-cost electricity and can operate at reduced capacity factors, including electrolytic hydrogen production and carbon capture. The analysis accompanying this dataset was performed in 2018-2019 to support an analysis of "The Technical and Economic Potential of the H2@Scale Concept within the United States" ( https://www.nlr.gov/docs/fy21osti/77610.pdf ). This dataset includes the quantity of estimated LDE resource for each hour of the year in 2050, aggregated to both the national level and the ReEDS balancing area level. As described in the accompanying report, the ReEDS model was used to project the evolution of the power sector over time. Links to the mapping of ReEDS balancing areas to states and ReEDS balancing area shape files are provided. This dataset also includes the report figure data.

08 HYDROGEN↗

Determining protein polarization proteome-wide using physical dissection of individual Stentor coeruleus cells

Cellular components are non-randomly arranged with respect to the shape and polarity of the whole cell. Patterning within cells can extend down to the level of individual proteins and mRNA. But how much of the proteome is actually localized with respect to cell polarity axes? Proteomics combined with cellular fractionation has shown that most proteins localize to one or more organelles but does not tell us how many proteins have a polarized localization with respect to the large-scale polarity axes of the intact cell. Genome-wide localization studies in yeast found that only a few percent of proteins have a localized position relative to the cell polarity axis defined by sites of polarized cell growth. Here, we describe an approach for analyzing protein distribution within a cell with a visibly obvious global patterning - the giant ciliate Stentor coeruleus. Ciliates, including Stentor, have highly polarized cell shapes with visible surface patterning. A Stentor cell is roughly 2mmlong, allowing a ‘‘proteomic dissection’’ in which microsurgery is used to separate cellular fragments along the anterior-posterior axis, followed by comparative proteomic analysis. In our analysis, 25% of the proteome, including signaling proteins, centrin/SFI proteins, and GAS2 orthologs, shows a polarized location along the cell’s anterior-posterior axis. We conclude that a large proportion of all proteins are polarized with respect to global cell polarity axes and that proteomic dissection provides a simple and effective approach for spatial proteomics.

59 BASIC BIOLOGICAL SCIENCES↗

Understanding the structural and morphological effects of synthesis route on NpO 2

The availability of actinide standard materials for use in nuclear safeguard applications is critical, as is thorough characterization thereof. Although accurate trace element compositions and isotopic considerations are paramount for deployment of reference standards, structural characterization is also essential towards accurately describing the chemical form and potential matrix effects in candidate materials. Here, to this end, samples of NpO 2 were synthesized via a direct denitration (DD) method and probed with powder X-ray diffraction (PXRD), Raman spectroscopy, and scanning electron microscopy (SEM) for structural and morphological characterization and comparison with NpO 2 materials produced via modified direct denitration (MDD). PXRD confirmed the bulk identity of NpO 2 , and no additional phases were identified using this method. Analysis of Raman data collected using a 532 nm excitation wavelength indicates that samples are mostly phase pure; however, some variability in spectral features is observed. Analysis of additional spectroscopic data collected with a 785 nm excitation wavelength revealed variability in the relative intensity of spectral features. Raman spectroscopy indicates that the sample is primarily NpO 2 ; however, additional signals indicate possible structural disorder, oxidized species, or potential contributions from other Np phases. To further investigate the possibility of additional phase contributions within the sample of NpO 2 , Raman spectroscopic mapping was employed to examine the homogeneity of the sample produced via DD. From this analysis, we determined that despite variability in the intensity of Raman-active vibrational modes, consistent spectra are obtained throughout the area of the sample investigated. SEM images show aggregates with variable sizes and shapes, with rounded, primary particles possessing an average diameter of approximately 100 nm. Comparison of the results of these multimodal analyses to the literature indicates that the crystal chemical, spectroscopic, and microstructural properties of NpO 2 vary based on synthesis method, even if X-ray diffraction data indicate that the bulk phase is NpO 2 .

Direct denitration↗

A small-volume, high-throughput approach for surface tension and viscosity measurements of liquid fuels

An ongoing effort looking at bioblendstocks to function as drop-in replacements or blending components for gasoline has identified a large number of candidate fuels. This work documents an approach for rapid screening of candidate fuels using relatively small sample sizes ($\mathcal{O}(\mu\,{\rm l})$) that targets two key physical properties of liquid fuels—surface tension and viscosity. The approach utilizes shape oscillation dynamics of single droplets generated by a piezo-electric device and their decay over time. Strobed imaging of the oscillation process is used along with image processing, edge detection, and data analysis to capture the decay of the oscillation over time. The time constant of the decay process along with oscillation frequency are then used to estimate viscosity and surface tension using a theory for small amplitude droplet oscillations. Measurements are obtained for primary reference fuels (isooctane and n-heptane) as well as candidate fuels from four bio-derived functional groups of interest. Measurement results for surface tension and viscosity are correlated with literature data as well as measurements from standard reference instruments. The measurement results show that the droplet oscillation based approach is capable of reproducing surface tension and viscosity values for the tested fuels within deviations of 7% and 13% respectively from literature data. Results are obtained using an average of 5 µl per fuel within about 20 s, thus demonstrating a small-volume, high-throughput approach that can be used for screening of candidate bioblendstock fuels.

09 BIOMASS FUELS↗