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At least 991 records · Page 55

Scaling neural simulations in STACS

Abstract As modern neuroscience tools acquire more details about the brain, the need to move towards biological-scale neural simulations continues to grow. However, effective simulations at scale remain a challenge. Beyond just the tooling required to enable parallel execution, there is also the unique structure of the synaptic interconnectivity, which is globally sparse but has relatively high connection density and non-local interactions per neuron. There are also various practicalities to consider in high performance computing applications, such as the need for serializing neural networks to support potentially long-running simulations that require checkpoint-restart. Although acceleration on neuromorphic hardware is also a possibility, development in this space can be difficult as hardware support tends to vary between platforms and software support for larger scale models also tends to be limited. In this paper, we focus our attention on Simulation Tool for Asynchronous Cortical Streams (STACS), a spiking neural network simulator that leverages the Charm++ parallel programming framework, with the goal of supporting biological-scale simulations as well as interoperability between platforms. Central to these goals is the implementation of scalable data structures suitable for efficiently distributing a network across parallel partitions. Here, we discuss a straightforward extension of a parallel data format with a history of use in graph partitioners, which also serves as a portable intermediate representation for different neuromorphic backends. We perform scaling studies on the Summit supercomputer, examining the capabilities of STACS in terms of network build and storage, partitioning, and execution. We highlight how a suitably partitioned, spatially dependent synaptic structure introduces a communication workload well-suited to the multicast communication supported by Charm++. We evaluate the strong and weak scaling behavior for networks on the order of millions of neurons and billions of synapses, and show that STACS achieves competitive levels of parallel efficiency.

59 BASIC BIOLOGICAL SCIENCES↗

City Climate Action Plans Through the Lens of The Food-Energy-Water Nexus

Interdependent resource management concepts originated in the mid-20th century, and the recent use of the term “nexus” highlights interconnected relationships among resources like food, energy, and water. United States and European science foundations have shown a growing interest in the food-energy-water (FEW) nexus, leading to increased research on their joint management. However, one major criticism of the FEW nexus is the limited translation of the research into practical policies and implementation, such as climate action plans. To assess the incorporation of FEW nexus principles into climate planning, we systematically evaluate 100 climate action plans from large U.S. cities. Our findings show that the most discussed FEW links involve energy, particularly the water-for-energy and food-for-energy connections, found in over half of the documents (56%). Our analysis promotes the integration of the FEW nexus into climate action plans while addressing the barriers to its effective implementation.

Mounir, Adil [Air Force Institute of Technology]↗

Spatio-temporal differences in leaf physiology are associated with fire, not drought, in a clonally integrated shrub

Abstract In highly disturbed environments, clonality facilitates plant survival via resprouting after disturbance, resource sharing among interconnected stems and vegetative reproduction. These traits likely contribute to the encroachment of deep-rooted clonal shrubs in tallgrass prairie. Clonal shrubs have access to deep soil water and are typically thought of as relatively insensitive to environmental variability. However, how leaf physiological traits differ among stems within individual clonal shrubs (hereafter ‘intra-clonal’) in response to extreme environmental variation (i.e. drought or fire) is unclear. Accounting for intra-clonal differences among stems in response to disturbance is needed to more accurately parameterize models that predict the effects of shrub encroachment on ecosystem processes. We assessed intra-clonal leaf-level physiology of the most dominant encroaching shrub in Kansas tallgrass prairie, Cornus drummondii, in response to precipitation and fire. We compared leaf gas exchange rates from the periphery to centre within shrub clones during a wet (2015) and extremely dry (2018) year. We also compared leaf physiology between recently burned shrubs (resprouts) with unburned shrubs in 2018. Resprouts had higher gas exchange rates and leaf nitrogen content than unburned shrubs, suggesting increased rates of carbon gain can contribute to recovery after fire. In areas recently burned, resprouts had higher gas exchange rates in the centre of the shrub than the periphery. In unburned areas, leaf physiology remained constant across the growing season within clonal shrubs (2015 and 2018). Results suggest single measurements within a shrub are likely sufficient to parameterize models to understand the effects of shrub encroachment on ecosystem carbon and water cycles, but model parameterization may require additional complexity in the context of fire.

54 ENVIRONMENTAL SCIENCES↗

Warming and disturbance alter soil microbiome diversity and function in a northern forest ecotone

ABSTRACT The response to global change by soil microbes is set to affect important ecosystem processes. These impacts could be most immediate in transitional zones, such as the temperate-boreal forest ecotone, yet previous work in these forests has primarily focused on specific subsets of microbial taxa. Here, we examined how bacterial and fungal communities respond to simulated above- and below-ground warming under realistic field conditions in closed and open canopy treatments in Minnesota, USA. Our results show that warming and canopy disturbance shifted bacterial and fungal community structure as dominant bacterial and fungal groups differed in the direction and intensity of their responses. Ectomycorrhizal and saprotrophic fungal communities with greater connectivity (higher prevalence of strongly interconnected taxa based on pairwise co-occurrence relationships) were more resistant to compositional change. Warming effects on soil enzymes involved in the hydrolytic and oxidative liberation of carbon from plant cell walls and nutrients from organic matter were most strongly linked to fungal community responses, although community structure–function relationships differed between fungal guilds. Collectively, these findings indicate that warming and disturbance will influence the composition and function of microbial communities in the temperate-boreal ecotone, and fungal responses are particularly important to understand for predicting future ecosystem functioning.

Microbiology↗

Mob4 is essential for spermatogenesis in Drosophila melanogaster

Abstract Gamete formation is essential for sexual reproduction in metazoans. Meiosis in males gives rise to spermatids that must differentiate and individualize into mature sperm. In Drosophila melanogaster, individualization of interconnected spermatids requires the formation of individualization complexes that synchronously move along the sperm bundles. Here, we show that Mob4, a member of the Mps-one binder family, is essential for male fertility but has no detectable role in female fertility. We show that Mob4 is required for proper axonemal structure and its loss leads to male sterility associated with defective spermatid individualization and absence of mature sperm in the seminal vesicles. Transmission electron micrographs of developing spermatids following mob4RNAi revealed expansion of the outer axonemal microtubules such that the 9 doublets no longer remained linked to each other and defective mitochondrial organization. Mob4 is a STRIPAK component, and male fertility is similarly impaired upon depletion of the STRIPAK components, Strip and Cka. Expression of the human Mob4 gene rescues all phenotypes of Drosophila mob4 downregulation, indicating that the gene is evolutionarily and functionally conserved. Together, this suggests that Mob4 contributes to the regulation of the microtubule- and actin-cytoskeleton during spermatogenesis through the conserved STRIPAK complex. Our study advances the understanding of male infertility by uncovering the requirement for Mob4 in sperm individualization.

Santos, Inês B.↗

Pseudomonas aeruginosa : One Health approach to deciphering hidden relationships in Northern Portugal

Abstract Aims Antimicrobial resistance in Pseudomonas aeruginosa represents a major global challenge in public and veterinary health, particularly from a One Health perspective. This study aimed to investigate antimicrobial resistance, the presence of virulence genes, and the genetic diversity of P. aeruginosa isolates from diverse sources. Methods and results The study utilized antimicrobial susceptibility testing, genomic analysis for resistance and virulence genes, and multilocus sequence typing to characterize a total of 737 P. aeruginosa isolates that were collected from humans, domestic animals, and aquatic environments in Northern Portugal. Antimicrobial resistance profiles were analyzed, and genomic approaches were employed to detect resistance and virulence genes. The study found a high prevalence of multidrug-resistant isolates, including high-risk clones such as ST244 and ST446, particularly in hospital sources and wastewater treatment plants. Key genes associated with resistance and virulence, including efflux pumps (e.g. MexA and MexB) and secretion systems (T3SS and T6SS), were identified. Conclusions This work highlights the intricate dynamics of multidrug-resistant P. aeruginosa across interconnected ecosystems in Northern Portugal. It underscores the importance of genomic studies in revealing the mechanisms of resistance and virulence, contributing to the broader understanding of resistance dynamics and informing future mitigation strategies.

de Sousa, Telma↗

The overlooked interaction of emerging contaminants and microbial communities: a threat to ecosystems and public health

Abstract Context and aims Emerging contaminants (ECs) and microbial communities should not be viewed in isolation, but through the One Health perspective. Both ECs and microorganisms lie at the core of this interconnected framework, as they directly influence the health of humans, animals, and the environment. The interactions between ECs and microbial communities can have profound implications for public health, affecting all three domains. However, these ECs-microorganism interactions remain underexplored, potentially leaving significant public health and ecological risks unrecognized. Therefore, this article seeks to alert the scientific community to the overlooked interactions between ECs and microbial communities, emphasizing the pivotal role these interactions may play in the management of ‘One Health.’ Results The most extensively studied interaction between ECs and microbial communities is biodegradation. However, other more complex and concerning interactions demand attention, such as the impact of ECs on microbial ecology (disruptions in ecosystem balance affecting nutrient and energy cycles) and the rise and spread of antimicrobial resistance (a growing global health crisis). Although these ECs-microbial interactions had not been extensively studied, there are scientific evidence that ECs impact on microbial communities may be concerning for public health and ecosystem balance. Conclusions So, this perspective summarizes the impact of ECs through a One Health lens and underscores the urgent need to understand their influence on microbial communities, while highlighting the key challenges researchers must overcome. Tackling these challenges is vital to mitigate potential long-term consequences for both ecosystems and public health.

Gomes, Inês B. (ORCID:0000000207313662)↗

Unveiling shared genetic regulators of plant architectural and biomass yield traits in the Sorghum Association Panel

Abstract Sorghum is emerging as an ideal genetic model for designing high-biomass bioenergy crops. Biomass yield, a complex trait influenced by various plant architectural characteristics, is typically regulated by numerous genes. This study aimed to dissect the genetic regulators underlying 14 plant architectural traits and 10 biomass yield traits in the Sorghum Association Panel across two growing seasons. We identified 321 associated loci through genome-wide association studies (GWAS), involving 234 264 single nucleotide polymorphisms (SNPs). These loci include genes with known associations to biomass traits, such as maturity, dwarfing (Dw), and leafbladeless1, as well as several uncharacterized loci not previously linked to these traits. We also identified 22 pleiotropic loci associated with variation in multiple phenotypes. Three of these loci, located on chromosomes 3 (S03_15463061), 6 (S06_42790178; Dw2), and 9 (S09_57005346; Dw1), exerted significant and consistent effects on multiple traits across both growing seasons. Additionally, we identified three genomic hotspots on chromosomes 6, 7, and 9, each containing multiple SNPs associated with variation in plant architecture and biomass yield traits. Chromosome-wise correlation analyses revealed multiple blocks of positively associated SNPs located near or within the same genomic regions. Finally, genome-wide correlation-based network analysis showed that loci associated with flowering, plant height, leaf traits, plant density, and tiller number per plant were highly interconnected with other genetic loci influencing plant architectural and biomass yield traits. The pyramiding of favorable alleles related to these traits holds promise for enhancing the future development of bioenergy sorghum crops.

Singh, Anuradha (ORCID:0000000197149095)↗

A nitrate transporter 1/peptide transporter family gene impacts nitrogen homeostasis and phenylpropanoid production in hybrid poplar

In plants, nitrogen and carbon metabolism are tightly interconnected, and nitrogen availability often negatively correlates with phenylpropanoids that are associated with xylem formation and stress responses. A nitrate transporter 1/peptide transporter (NRT1/PTR) family (NPF) gene (PtNPF6.1), which is expressed in the vasculature, was previously found to have a genetic association with the variation in syringyl lignin content in poplar trees (Populus trichocarpa). PtNPF6.1 belongs to an evolutionarily distinct NPF superfamily with limited taxonomic distribution. RNAi-mediated suppression of PtNPF6.1 led to increases in total foliar nitrogen and amino acids related to nitrogen transport and storage in source leaves. There was also a concomitant decrease in soluble phenolics, including attenuated stress-induced production of anthocyanins and condensed tannins. The proportions of syringyl and p-hydroxyphenyl units in lignin were slightly but significantly decreased in down-regulated lines grown under high nitrogen conditions, while there was an increase in the level of ester-linked p-hydroxybenzoate groups. Together, these results suggest that PtNPF6.1 is involved in maintaining internal nitrogen homeostasis in trees, indirectly impacting the production of nitrogen-free phenolics including lignin and soluble secondary metabolites.

amino acids↗

Effect of Acid Etching Time in Ti 3 C 2 MXene’s Interlayer Spacing and Conductivity

Materials with sheet-like morphologies often form interconnected networks of layers or flakes, offering continuous channels for electron and ion transport in electrochemical energy storage applications. One such material is the recently discovered class of 2-D transition metal carbides/nitrides, called MXene, whose general formula is M n+1 X n T x (where M = transition metal; n = 1, 2, or 3; X = carbon or nitrogen; and T x = termination group such as –F, –OH, and/or =O). Ti 3 C 2 , one of the most studied MXene, can be synthesized by selectively etching the aluminum layer in Ti 3 AlC 2 (also called MAX phase). The most straightforward technique to exfoliate this layer is by wet-chemical etching with high-concentration hydrofluoric acid (HF). In this study, the effect of etching time on the morphology, interlayer spacing, and electrical conductivity of the resultant MXene was studied.

25 ENERGY STORAGE↗

TroR is the primary regulator of the iron homeostasis transcription network in the halophilic archaeon Haloferax volcanii

Abstract Maintaining the intracellular iron concentration within the homeostatic range is vital to meet cellular metabolic needs and reduce oxidative stress. Previous research revealed that the haloarchaeon Halobacterium salinarum encodes four diphtheria toxin repressor (DtxR) family transcription factors (TFs) that together regulate the iron response through an interconnected transcriptional regulatory network (TRN). However, the conservation of the TRN and the metal specificity of DtxR TFs remained poorly understood. Here we identified and characterized the TRN of Haloferax volcanii for comparison. Genetic analysis demonstrated that Hfx. volcanii relies on three DtxR transcriptional regulators (Idr, SirR, and TroR), with TroR as the primary regulator of iron homeostasis. Bioinformatics and molecular approaches revealed that TroR binds a conserved cis-regulatory motif located ∼100 nt upstream of the start codon of iron-related target genes. Transcriptomics analysis demonstrated that, under conditions of iron sufficiency, TroR repressed iron uptake and induced iron storage mechanisms. TroR repressed the expression of one other DtxR TF, Idr. This reduced DtxR TRN complexity relative to that of Hbt. salinarum appeared correlated with natural variations in iron availability. Based on these data, we hypothesize that variable environmental conditions such as iron availability appear to select for increasing TRN complexity.

59 BASIC BIOLOGICAL SCIENCES↗

Controlled environment agriculture: An opportunity to strengthen interagency research collaboration in the US government

Challenges facing food production and agricultural systems are increasingly interconnected with economic, security, health, and equity issues, among others. Threats such as extreme weather, economic volatility, and shrinking water resources and arable land, influence our ability to maintain a safe and resilient food supply. One promising solution to these threats is controlled environment agriculture (CEA). In many cases, CEA can drastically reduce the amount of water and land used in crop production while increasing productivity. Operations may be established in nearly any environment and harvests can take place year-round, supporting food system resiliency and sustainability. CEA sits at the nexus of a number of disciplines and industries, making it well suited for transdisciplinary and multi-institutional research coordination. Herein, authors from multiple US government agencies present CEA as a case study in improving cross-agency research collaboration. The federal government houses a range of scientific expertise and research capabilities, positioning scientists to lead national and global efforts in transdisciplinary, interagency approaches to complex challenges. Navigating cross-agency collaboration can be a challenge, especially coordinating across different scientific disciplines, geographic locations, and funding mechanisms. To enhance multiagency efforts, collaborators could prioritize (i) organizing personnel and resources, (ii) enhancing existing multiagency collaborations, and (iii) focusing on further opportunities for coordination. Adopting these approaches could enable federal researchers to reinforce and advance academic and industry efforts to address current CEA challenges while solidifying the United States as a leader in this arena.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Bio‐Imaging quorum sensing signal molecules in a soil‐mimic gel

Rhizosphere, the narrow region surrounding plant roots directly influenced by root exudates and the root associated microbiome, plays an important role in plant productivity and the rhizosphere is well known for stimulating microbial metabolic activities. How microbial communities interact to form stable, metabolically interconnected functional communities is an area of intense interest. The question remains on how microbially produced secreted molecules that function as intercellular communication signals shape the structure and function of microbial communities. Our goal is to detect and quantify signal molecules produced by microbes or plants in the root‐soil environment, spatially and temporarily. As a proof‐of‐concept, we are imaging diffusible extracellular microbial metabolites involved in a bacteria‐bacteria communication process called quorum‐sensing. Quorum‐sensing relies on the accumulation of high concentrations of signal molecules in the environment to control bacterial gene expression, influencing rhizosphere colonization and plant health. Local concentration of quorum sensing molecules are determined using aptamer based sensors. Aptamers that can specifically bind the desired signal molecules are selected through SELEX and immobilized on the surface of nano‐porous membranes. Binding of the signal molecules and aptamer covered surface results in changes in surface charge distribution and steric hinderance and thus modifying the transmembrane ionic transport. Changes in transmembrane impedance can be measured through electrochemical impedance spectroscopy methods to monitor local concentrations of signal molecules. Sensor responses were determined for different concentrations of signal molecules and results showed detection of C4‐HSL in a soil‐mimic solution with K D of 10 nM. We demonstrate that the quorum‐sensing signal molecule C4‐homoserine lactone and (C4‐HSL) can rapidly diffuse in a soil‐mimic gel, providing evidence for our use of a soil‐mimic for further aptasensor development and validation. The sensors were then inserted into soil mimic gel for monitoring C4‐HSL diffusion and the resulted impedance changes were used to determine the C4‐HSL concentration at different positions in the gel. Measurements of local C4‐HSL concentrations variation and numerical solution of diffusion equation were used to create 4D images of C4‐HSL molecule diffusion in the soil‐mimic gel.

Jiang, Nianyu↗

Electrostatic gate-controlled quantum interference in a high-mobility two-dimensional electron gas at the (La 0.3 ⁢Sr 0.7 )(Al 0.65 ⁢Ta 0.35 )O 3 /SrTiO 3 interface

Here, we report quantum oscillations in magnetoresistance that are periodic in magnetic field (𝐵), observed at the interface between (La 0.3 ⁢Sr 0.7 )(Al 0.65 ⁢Ta 0.35 )O 3 and SrTiO 3 . Unlike Shubnikov–de Haas oscillations, which appear at magnetic fields > 7 T and diminish quickly as the temperature rises, these 𝐵-periodic oscillations emerge at low fields and persist up to 10 K. Their amplitude decays exponentially with both temperature and field, specifying dephasing of quantum interference. Increasing the carrier density through electrostatic gating results in a systematic reduction in both the amplitude and frequency of the oscillations, with complete suppression beyond a certain gate voltage. We attribute these oscillations to the Altshuler-Aronov-Spivak effect, likely arising from naturally formed closed-loop paths due to the interconnected quasi-one-dimensional conduction channels along SrTiO 3 domain walls. The relatively long phase coherence length (≃ 1.8 µ⁢m at 0.1 K), estimated from the oscillation amplitude, highlights the potential of complex oxide interfaces as a promising platform for exploring quantum interference effects and advancing device concepts in quantum technologies, such as mesoscopic interferometers and quantum sensors.

36 MATERIALS SCIENCE↗

Suppression of neutral-pion production in deep-inelastic scattering off nuclei with the CLAS detector

We present the first threefold differential measurement for neutral-pion multiplicity ratios produced in semi-inclusive deep-inelastic electron scattering on carbon, iron, and lead nuclei normalized to deuterium from CLAS at Jefferson Lab. We found that the neutral-pion multiplicity ratio is maximally suppressed for the leading hadrons (energy fraction 𝑧 → 1), suppression varying from 25% in carbon up to 75% in lead. An enhancement of the multiplicity ratio at low 𝑧 and high 𝑝$^2_𝑇$ is observed, suggesting an interconnection between these two variables. This behavior is qualitatively similar to the previous twofold differential measurement of charged pions by the HERMES Collaboration and, recently, by CLAS Collaboration. The largest enhancement was observed at high 𝑝$^2_𝑇$ for heavier nuclei, namely, iron and lead, while the smallest enhancement was observed for the lightest nucleus, carbon. This behavior suggests a competition between partonic multiple scattering, which causes enhancement, and hadronic inelastic scattering, which causes suppression.

color confinement↗

Anisotropic Thermal Transport in Quasi-2D Ruddlesden-Popper Hybrid Perovskite Superlattices

Two-dimensional hybrid metal-halide perovskites (2D-MHPs) have emerged as important solution-processed semiconductors with favorable optical and electronic properties for diverse applications in photovoltaics, optoelectronics, and spintronics. The quasi-2D layered structures, featuring large acoustic impedance mismatches between the organic and inorganic sublattices, are expected to result in distinct and anisotropic thermal transport properties along the cross-plane and in-plane directions. Here, we introduce transducer-free vibrational-pump-visible-probe (VPVP) approaches that enable accurate quantification of anisotropic thermal transport properties in various archetypical single-crystalline 2D-MHPs. Specifically, using VPVP spectroscopy and VPVP microscopy, we measure the anisotropic thermal diffusivities of 2D-MHPs with systematically varied Pb-I octahedral layer thicknesses, as well as organic spacer types and lengths, revealing how these structural parameters alter the cross-plane and in-plane thermal transport properties in distinct ways. While diffuse interface scattering plays an important role in dictating cross-plane thermal transport, in-plane thermal transport is primarily determined by phonon transport within interconnected inorganic layers. Density functional theory incorporating four-phonon scatterings provides further insight into the low thermal conductivity and modest thermal conduction anisotropy in 2D-MHPs. Our work demonstrates a new all-optical and noncontact method, which requires minimal sample preparation and allows direct visualization of cross-plane and in-plane thermal transport, potentially compatible with sample environments. The demonstrated VPVP approaches can advance understanding of thermal transport in 2D-MHPs as well as wide-ranging hybrid and polymeric semiconductors beyond 2D-MHPs.

36 MATERIALS SCIENCE↗

Quantum states of cylindrical surface charge density for modeling plasmonic circuit elements: Nanowires, nanorods, cavities, and waveguides

Nanostructures in the form of ellipsoids, prolate spheroids, rings, and cylinders are known to exhibit resonant surface and cavity modes with applications in nanophotonics and plasmonics and, more recently, in novel quantum experiments, in which control of plasmons and their interactions with plasmons, photons, phonons, excitons, and quantum emitters are desired. Nanorods and nanowires are examples of plasmonic structures with spectral properties of potential use as interconnects and circuit components. Additionally, estimates of the surface properties of these components are needed in circuit design and integrated systems. Here, we present a quantum Hamiltonian for the cylindrical surface charge density. We then study the photon excitation of plasmons on the cylindrical surface and calculate their scattering and radiative decay rate. Nonradiative decay of plasmons induces an efficient heating of the nanoparticle and can photoacoustically excite mechanical oscillations. Computational calculations are also presented for the plasmonic modes and the ensuing excitations of nanomechanical eigenmodes of nanoparticles with near-cylindrical symmetries.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Spin-liquid behavior of the three-dimensional magnetic system Ba 3 NiIr 2 O 9 with S = 1

The quantum spin liquid (QSL) is an exotic phase of magnetic materials where the spins continue to fluctuate without any symmetry breaking down to zero temperature. Among the handful reports of QSL with spin S ≥ 1, examples with magnetic ions on a three-dimensional (3D) magnetic lattice are extremely rare since both larger spin and higher dimension tend to suppress quantum fluctuations. In this work, we offer a new strategy to achieve 3D QSL with high spin by utilizing two types of transition metal ions; both are magnetically active but located at crystallographically inequivalent positions. Furthermore, we design a 3D magnetic system Ba 3 NiIr 2 O 9 consisting of interconnected corner-shared NiO 6 octahedra and face-shared Ir 2 O 9 dimer, both having triangular arrangements in a-b plane. X-ray absorption spectroscopy measurements confirm the presence of Ni 2+ (S = 1). Furthermore, our detailed thermodynamic and magnetic measurements reveal that this compound is a realization of gapless QSL state down to at least 100 mK. Ab initio calculations find a strong magnetic exchange between Ir and Ni sublattices and in-plane antiferromagnetic coupling between the dimers, resulting in dynamically fluctuating magnetic moments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗