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At least 973 records · Page 54

Climate warming enhances biodiversity and stability of grassland soil phosphorus-cycling microbial communities

Abstract Climate warming poses significant challenges to global phosphorus sustainability, an essential component of Earth biogeochemistry cycling and water-food-energy nexus. Despite the crucial role of polyphosphate-accumulating organism as key functional microbial agents in phosphorus cycling, the impacts of global climate warming on polyphosphate accumulating organism communities remain largely enigmatic. This study investigates the effects of climate warming on the taxonomic, network, and functional profiles of soil bacterial polyphosphate-accumulating organisms, leveraging fluorescence-activated cell sorting and single-cell Raman spectroscopy. Climate warming enhances both taxonomic and functional biodiversity of polyphosphate-accumulating organisms via biotic interactions and environmental filtering, with observed functionality-biodiversity relationships supporting the functional redundancy theory. Furthermore, polyphosphate-accumulating organism network complexity and stability rise under warming with strengthened positive relationships, supporting stress gradient hypothesis and the belief that complexity begets stability. Finally, polyphosphate-accumulating organisms are significantly correlated to key ecosystem functioning in carbon and phosphorus cycling under warming. Our study suggests that preserving polyphosphate-accumulating organism communities is crucial for maintaining soil ecosystem functioning and sustainable phosphorus management in a warming world and opens avenues for predicting the responses of other functional microbial groups to climate change, beneficially or maliciously.

Environmental Sciences & Ecology↗

Functional characterization of diverse type I-F CRISPR-associated transposons

CRISPR-Cas systems generally provide adaptive immunity in prokaryotes through RNA-guided degradation of foreign genetic elements like bacteriophages and plasmids. Recently, however, transposon-encoded and nuclease-deficient CRISPR-Cas systems were characterized and shown to be co-opted by Tn7-like transposons for CRISPR RNA-guided DNA transposition. As a genome engineering tool, these CRISPR-Cas systems and their associated transposon proteins can be deployed for programmable, site-specific integration of sizable cargo DNA, circumventing the need for DNA cleavage and homology-directed repair involving endogenous repair machinery. Here, we selected a diverse set of type I-F3 CRISPR-associated transposon systems derived from Gammaproteobacteria, predicted all components essential for transposition activity, and deployed them for functionality testing within Escherichia coli. Our results demonstrate that these systems possess a significant range of integration efficiencies with regards to temperature, transposon size, and flexible PAM requirements. Additionally, our findings support the categorization of these systems into functional compatibility groups for efficient and orthogonal RNA-guided DNA integration. This work expands the CRISPR-based toolbox with new CRISPR RNA-guided DNA integrases that can be applied to complex and extensive genome engineering efforts.

59 BASIC BIOLOGICAL SCIENCES↗

Measurement of fifth- and sixth-order fluctuations of (net-)proton number in Au + Au collisions from phase II of the beam energy scan program at RHIC

We report high-statistics measurements of fifth- and sixth-order factorial cumulants and cumulant ratios of (net-)proton multiplicity distributions in Au+Au collisions at $\sqrt{s_{NN}}$ = 7.7–27GeV, using data from the STAR experiment collected during the Beam Energy Scan Phase II at RHIC. Protons and antiprotons are identified at midrapidity (|𝑦| < 0.5) with transverse momentum 0.4 < 𝑝 𝑇 < 2.0GeV/𝑐. The proton factorial cumulants 𝜅 4 , 𝜅 5 , and 𝜅 6 increase with order but exhibit no sign alternation within current uncertainties, offering no evidence for a two-component structure in the proton multiplicity distribution, as might be expected near a first-order phase transition. The cumulant ratios 𝐶 5 /𝐶 1 and 𝐶 6 /𝐶 2 fluctuate around zero in collisions at 0–40% centrality. The results are consistent with both the negative predictions from lattice QCD and the positive trends obtained from the ultrarelativistic quantum molecular dynamics (UrQMD) model. At $\sqrt{s_{NN}}$ ≳ 27GeV, the 𝐶 4 /𝐶 2 and 𝐶 5 /𝐶 1 results are compatible with predictions from lattice QCD, functional renormalization group (FRG), and hadron resonance gas (HRG) models, while UrQMD describes the data better at lower energies. Here, these measurements place constraints on baryon number fluctuations and offer valuable insights into the QCD phase structure.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Theory of the charge density wave in A V 3 Sb 5 kagome metals

The family of metallic kagome compounds AV 3 Sb 5 (A = K, Rb, Cs) was recently discovered to exhibit both superconductivity and charge order. The nature of the charge density wave (CDW) phase is presently unsettled, which complicates the interpretation of the superconducting ground state. In this paper, we use group theory and density functional theory (DFT) to derive and solve a phenomenological Landau model for this CDW state. The DFT results reveal three unstable phonon modes with the same in-plane momentum but different out-of-plane momenta, whose frequencies depend strongly on the electronic temperature. This is indicative of an electronically driven CDW, stabilized by features of the in-plane electronic dispersion. Motivated by the DFT analysis, we construct a Landau free-energy expansion for coupled CDW order parameters with wave vectors at the M and L points of the hexagonal Brillouin zone. We find an unusual trilinear term coupling these different order parameters, which can promote the simultaneous condensation of both CDWs even if the two modes are not nearly degenerate. We classify the different types of coupled multi-Q CDW orders, focusing on those that break the sixfold rotational symmetry and lead to a unit-cell doubling along all three crystallographic directions, as suggested by experiments. Here, we determine a region in parameter space, characterized by large nonlinear Landau coefficients, where these phases—dubbed staggered trihexagonal and staggered Star of David—are the leading instabilities of the system. Finally, we discuss the implications of our results for the kagome metals.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Infrared fixed point in the massless twelve-flavor SU(3) gauge-fermion system

We present strong numerical evidence for the existence of an infrared fixed point in the renormalization group flow of the SU(3) gauge-fermion system with twelve massless fermions in the fundamental representation. Our numerical simulations using nHYP-smeared staggered fermions with Pauli-Villars improvement do not exhibit any first-order bulk phase transition in the investigated parameter region. We utilize an infinite volume renormalization scheme based on the gradient flow transformation to determine the renormalization group β function. The gradient flow β function exhibits a zero at g GF ⋆ 2 = 6.60 ( 62 ) , implying that the system is infrared conformal. We calculate the leading irrelevant critical exponent γ g ⋆ = 0.199 ( 32 ) . Our prediction for γ g ⋆ is consistent with available literature at the 1 − 2 σ level. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Symmetric Nuclear Matter from the Strong Interaction

We study the equation of state of symmetric nuclear matter at zero temperature over a wide range of densities using two complementary theoretical approaches. At low densities, up to twice nuclear saturation density, we compute the energy per particle based on modern nucleon-nucleon and three-nucleon interactions derived within chiral effective field theory. For higher densities, we derive for the first time constraints in a Fierz-complete setting directly based on quantum chromodynamics using functional renormalization group techniques. Here, we find remarkable consistency of the results obtained from both approaches as they come together in density and the natural emergence of a maximum in the speed of sound 𝑐𝑆 at supranuclear densities. The presence of this maximum appears tightly connected to the formation of a diquark gap. Notably, this maximum is observed to exceed the asymptotic value 𝑐$^{2}_{𝑆}$ =1/3 while its exact position in terms of the density cannot yet be determined conclusively.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Experimental Validation of Subsystem Models for a Novel Variable Displacement Hydraulic Motor

A novel, variable displacement, low-speed high-torque hydraulic motor is being developed that is expected to be highly efficient across a broad operating range. To ensure the final hardware achieves the expected performance, the models used in the development of the motor must be experimentally validated and revised, as necessary. The specific focus in this work is on mechanical energy loss models that were used to guide the design of a single-cylinder motor prototype and on experimental tests used for model validation. Ideally each model, whether friction loss in a piston/cylinder interface or energy loss due to leakage in a valve , would be individually validated by an independent test. This granular approach would remove any question of where the error lies and result in highly accurate models. However, many motor components have multiple forms of energy loss, creating difficulty in validating individual losses. Additionally, it is not physically realizable to divide many components into an individual model equivalent test. Testing the motor as a full assembly is possible, but pinpointing the source of discrepancies between the model and the hardware becomes difficult with dozens of models potentially being partially responsible. A compromise was found by separating the motor into functional component groups that are characterized by the type of loss and ability to test each subcomponent independently. By checking for correlation between test observations and model predictions, revisions could be implemented into the models. This allows future solutions to be more accurately predicted in the design phase to drive the design of better machines.

24 POWER TRANSMISSION AND DISTRIBUTION↗

ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data

The high-resolution and mass accuracy of Fourier transform mass spectrometry (FT-MS) has made it an increasingly popular technique for discerning the composition of soil, plant and aquatic samples containing complex mixtures of proteins, carbohydrates, lipids, lignins, hydrocarbons, phytochemicals and other compounds. Thus, there is a growing demand for informatics tools to analyze FT-MS data that will aid investigators seeking to understand the availability of carbon compounds to biotic and abiotic oxidation and to compare fundamental chemical properties of complex samples across groups. We present ftmsRanalysis, an R package which provides an extensive collection of data formatting and processing, filtering, visualization, and sample and group comparison functionalities. The package provides a suite of plotting methods and enables expedient, flexible and interactive visualization of complex datasets through functions which link to a powerful and interactive visualization user interface, Trelliscope. Example analysis using FT-MS data from a soil microbiology study demonstrates the core functionality of the package and highlights the capabilities for producing interactive visualizations.

97 MATHEMATICS AND COMPUTING↗

Pauling’s rules for oxide-based minerals: A re-examination based on quantum mechanical constraints and modern applications of bond-valence theory to Earth materials

Since their introduction in 1929, Pauling’s five rules have been used by scientists from many disciplines to rationalize and predict stable arrangements of atoms and coordination polyhedra in crystalline solids; amorphous materials such as silicate glasses and melts; nanomaterials, poorly crystalline solids; aqueous cation and anion complexes; and sorption complexes at mineral-aqueous solution interfaces. The predictive power of these simple yet powerful rules was challenged recently by George et al. (2020), who performed a statistical analysis of the performance of Pauling’s five rules for about 5000 oxide crystal structures. They concluded that only 13% of the oxides satisfy the last four rules simultaneously and that the second rule has the most exceptions. They also found that Pauling’s first rule is satisfied for only 66% of the coordination environments tested and concluded that no simple rule linking ionic radius to coordination environment will be predictive due to the variable quality of univalent radii. We address these concerns and discuss quantum mechanical calculations that complement Pauling’s rules, particularly his first (radius sum and radius ratio rule) and second (electrostatic valence rule) rules. We also present a more realistic view of the bonded radii of atoms, derived by determining the local minimum in the electron density distribution measured along trajectories between bonded atoms known as bond paths, i.e., the bond critical point (rc). Electron density at the bond critical point is a quantum mechanical observable that correlates well with Pauling bond strength. Moreover, a metal atom in a polyhedron has as many bonded radii as it has bonded interactions, resulting in metal and O atoms that may not be spherical. O atoms, for example, are not spherical in many oxide-based crystal structures. Instead, the electron density of a bonded oxygen is often highly distorted or polarized, with its bonded radius decreasing systematically from ~1.38 Å when bonded to highly electropositive atoms like sodium to 0.64 Å when bonded to highly electronegative atoms like nitrogen. Bonded radii determined for metal atoms match the Shannon (1976) radii for more electropositive atoms, but the match decreases systematically as the electronegativities of the M atoms increase. As a result, significant departures from the radius ratio rule in the analysis by George et al. (2020) is not surprising. We offer a modified, more fundamental version of Pauling’s first rule and demonstrate that the second rule has a one-to-one connection between the electron density accumulated between the bonded atoms at the bond critical point and the Pauling bond strength of the bonded interaction. Pauling’s second rule implicitly assumes that bond strength is invariant with bond length for a given pair of bonded atoms. Many studies have since shown that this is not the case, and Brown and Shannon (1973) developed an equation and a set of parameters to describe the relation between bond length and bond strength, now redefined as bond valence to avoid confusion with Pauling bond-strength. Brown (1980) used the valence-sum rule, together with the path rule and the valence-matching principle, as the three axioms of bond-valence theory (BVT), a powerful method for understanding many otherwise elusive aspects of crystals and also their participation in dynamic processes. We show how a priori bond-valence calculations can predict unstrained bond-lengths and how bond-valence mapping can locate low-Z atoms in a crystal structure (e.g., Li) or examine possible diffusion pathways for atoms through crystal structures. In addition, we briefly discuss Pauling’s third, fourth, and fifth rules, the first two of which concern the sharing of polyhedron elements (edges and faces) and the common instability associated with structures in which a polyhedron shares an edge or face with another polyhedron and contains high-valence cations. The olivine [α-(MgxFe1–x)2SiO4] crystal structure is used to illustrate the distortions from hexagonal close-packing of O atoms caused by metal-metal repulsion across shared polyhedron edges. We conclude by discussing several applications of BVT to Earth materials, including the use of BVT to: (1) locate H+ ions in crystal structures, including the location of protons in the crystal structures of nominally anhydrous minerals in Earth’s mantle; (2) determine how strongly bonded (usually anionic) structural units interact with weakly bonded (usually cationic) interstitial complexes in complex uranyl-oxide and uranyl-oxysalt minerals using the valence-matching principle; (3) calculate Lewis acid strengths of cations and Lewis base strengths of anions; (4) determine how (H2O) groups can function as bond-valence transformers by dividing one bond into two bonds of half the bond valence; (5) help characterize products of sorption reactions of aqueous cations (e.g., Co2+ and Pb2+) and oxyanions [e.g., selenate (Se6+O4)2- and selenite (Se4+O3)2-] at mineral-aqueous solution interfaces and the important role of protons in these reactions; and (6) help characterize the local coordination environments of highly charged cations (e.g., Zr4+, Ti4+, U4+, U5+, and U6+) in silicate glasses and melts.

Geochemistry & Geophysics↗

Diverse PFAS produce unique transcriptomic changes linked to developmental toxicity in zebrafish

Per- and polyfluoroalkyl substances (PFAS) are a widespread and persistent class of contaminants posing significant environmental and human health concerns. Comprehensive understanding of the modes of action underlying toxicity among structurally diverse PFAS is mostly lacking. To address this need, we recently reported on our application of developing zebrafish to evaluate a large library of PFAS for developmental toxicity. In the present study, we prioritized 15 bioactive PFAS that induced significant morphological effects and performed RNA-sequencing to characterize early transcriptional responses at a single timepoint (48 h post fertilization) after early developmental exposures (8 h post fertilization). Internal concentrations of 5 of the 15 PFAS were measured from pooled whole fish samples across multiple timepoints between 24–120 h post fertilization, and additional temporal transcriptomics at several timepoints (48–96 h post fertilization) were conducted for Nafion byproduct 2. A broad range of differentially expressed gene counts were identified across the PFAS exposures. Most PFAS that elicited robust transcriptomic changes affected biological processes of the brain and nervous system development. While PFAS disrupted unique processes, we also found that similarities in some functional head groups of PFAS were associated with the disruption in expression of similar gene sets. Body burdens after early developmental exposures to select sulfonic acid PFAS, including Nafion byproduct 2, increased from the 24–96 h post fertilization sampling timepoints and were greater than those of sulfonamide PFAS of similar chain lengths. In parallel, the Nafion byproduct 2-induced transcriptional responses increased between 48 and 96 h post fertilization. PFAS characteristics based on toxicity, transcriptomic effects, and modes of action will contribute to further prioritization of PFAS structures for testing and informed hazard assessment.

59 BASIC BIOLOGICAL SCIENCES↗

What is the Quark-Gluon Plasma made of?

This article surveys our present understanding of the internal structure of the fully developed quark-gluon plasma at temperatures outside the crossover region. The theoretical part of the review covers perturbative and nonperturbative approaches to quark-gluon plasma structure, in particular, hard-thermal loop effective theory, lattice QCD and the functional renormalization group. The phenomenological part of the review scrutinizes the information that has been derived from bulk observables and hard probes in relativistic heavy ion collisions in terms of how it informs our knowledge about the structure of the quark-gluon plasma. The final section lists possible avenues for future progress.

FOS: Physical sciences↗

Whole-soil warming decreases abundance and modifies the community structure of microorganisms in the subsoil but not in surface soil

Abstract. The microbial community composition in subsoils remains understudied, and it is largely unknown whether subsoil microorganisms show a similar response to global warming as microorganisms at the soil surface do. Since microorganisms are the key drivers of soil organic carbon decomposition, this knowledge gap causes uncertainty in the predictions of future carbon cycling in the subsoil carbon pool (> 50 % of the soil organic carbon stocks are below 30 cm soil depth). In the Blodgett Forest field warming experiment (California, USA) we investigated how +4 ∘C warming in the whole-soil profile to 100 cm soil depth for 4.5 years has affected the abundance and community structure of microorganisms. We used proxies for bulk microbial biomass carbon (MBC) and functional microbial groups based on lipid biomarkers, such as phospholipid fatty acids (PLFAs) and branched glycerol dialkyl glycerol tetraethers (brGDGTs). With depth, the microbial biomass decreased and the community composition changed. Our results show that the concentration of PLFAs decreased with warming in the subsoil (below 30 cm) by 28 % but was not affected in the topsoil. Phospholipid fatty acid concentrations changed in concert with soil organic carbon. The microbial community response to warming was depth dependent. The relative abundance of Actinobacteria increased in warmed subsoil, and Gram+ bacteria in subsoils adapted their cell membrane structure to warming-induced stress, as indicated by the ratio of anteiso to iso branched PLFAs. Our results show for the first time that subsoil microorganisms can be more affected by warming compared to topsoil microorganisms. These microbial responses could be explained by the observed decrease in subsoil organic carbon concentrations in the warmed plots. A decrease in microbial abundance in warmed subsoils might reduce the magnitude of the respiration response over time. The shift in the subsoil microbial community towards more Actinobacteria might disproportionately enhance the degradation of previously stable subsoil carbon, as this group is able to metabolize complex carbon sources.

54 ENVIRONMENTAL SCIENCES↗

Interconnections for fluidic circuits

Circuit elements are grouped on functional basis in rectangular two-dimensional planar arrays or modules. Another interconnection method brings all connections out to module edge. For smaller fluidic circuits, manifold and interconnections are fabricated as single blocks. Advantages of methods are given.

Mangion, C.↗

Experiment module concepts study. Volume 2: Experiments and mission operations

The baseline experiment program is concerned with future space experiments and cover the scientific disciplines of astronomy, space physics, space biology, biomedicine and biotechnology, earth applications, materials science, and advanced technology. The experiments within each discipline are grouped into functional program elements according to experiments that support a particular area of research or investigation and experiments that impose similar or related demand on space station support systems. The experiment requirements on module subsystems, experiment operating modes and time profiles, and the role of the astronaut are discussed. Launch and rendezvous with the space station, disposal, and on-orbit operations are delineated. The operational interfaces between module and other system elements are presented and include space station and logistic system interfaces. Preliminary launch and on-orbit environmental criteria and requirements are discussed, and experiment equipment weights by functional program elements are tabulated.

Macdonald, J. M.↗

Utilization of oxygen difluoride for syntheses of fluoropolymers

The reaction oxygen difluoride, OF2, with ethylenically unsaturated fluorocarbon compounds is examined. Depending upon the fluorocarbon material and reaction conditions, OF2 can chain extend fluoropolyenes, convert functional perfluorovinyl groups to acyl fluoride and/or epoxide groups, and act as a monomer for an addition type copolymerization with diolefins.

Toy, M. S.↗

Controlled flexibility in technical editing - The levels-of-edit concept at JPL

The levels-of-edit concept, which can be used to specify the amount of editorial effort involved in the preparation of a manuscript for publication, is discussed. Nine types of editing are identified and described. These include coordination edit (preparing estimates, gathering cost data, monitoring production processes), policy edit, integrity edit (making sure that parts of a publication match in a physical or numerical sense), screening edit (ensuring that the quality of camera-ready copy is sufficient for external publication), copy clarification edit, format edit, mechanical style edit, language edit, and substantive edit (reviewing the manuscript for content coherence, emphasis, subordination and parallelism). These functions are grouped into five levels of edit. An edit-level number is assigned to each manuscript, providing a quantitative and qualitative indicator of the editing to be done which is clearly understood by authors, managers, and editors alike. In addition, clear boundaries are drawn between normal and extraordinary editing tasks. Individual organizations will group various edits in different ways to reflect their needs and priorities; the essential element of the system is unambiguous definition and coding of the types and amount of work to be done.

Buehler, M. F.↗

The correlation function for density perturbations in an expanding universe. II - Nonlinear theory

A formalism is developed to find the two-point and higher-order correlation functions for a given distribution of sizes and shapes of perturbations which are randomly placed in three-dimensional space. The perturbations are described by two parameters such as central density and size, and the two-point correlation function is explicitly related to the luminosity function of groups and clusters of galaxies

Mcclelland, J.↗