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At least 505 records · Page 28

Woodland wildfire enables fungal colonization of encroaching Douglas‐fir

Abstract Self‐reinforcing differences in fire frequency help closed‐canopy forests, which resist fire, and open woodlands, which naturally burn often, to co‐occur stably at landscape scales. Forest tree seedlings, which could otherwise encroach and overgrow woodlands, are killed by regular fire, yet fire has other effects that may also influence these feedbacks. In particular, many forest trees require symbiotic ectomycorrhizal fungi in order to establish. By restructuring soil fungal communities, fire might affect the availability of symbionts or the potential for symbiont sharing between encroaching trees and woodland vegetation. To investigate this possibility, we performed a soil bioassay experiment using inoculum from burned and unburned oak woodlands and Douglas‐fir forests. We examined how fire, ecosystem type, and neighboring heterospecific seedlings affect fungal root community assembly of Douglas‐firs and oaks. We asked whether heterospecific seedlings facilitated fungal colonization of seedling roots in non‐native soil, and if so, whether fire influenced this interaction. External fungal colonization of oak roots was more influenced by fire and ecosystem type than by the presence of a Douglas‐fir, and oaks increased the likelihood that Douglas‐fir roots would be colonized by fungi in oak woodland soil. Yet, fire increased colonization of Douglas‐fir in oak soil, diminishing the otherwise crucial role played by oak facilitation. Fire also strengthened the positive effect of Douglas‐firs on oak root‐associated fungal diversity in Douglas‐fir forest soil. Prior work shows that fire supports woodland ecosystems by stemming recruitment of encroaching seedlings. Here, we find evidence that it may contrastingly reduce fungal limitation of invasive seedling growth and establishment, otherwise relieved only by facilitation. Future work can investigate how these opposing effects might contribute to the net impact of changes in fire regime on landcover stability. Read the free Plain Language Summary for this article on the Journal blog.

54 ENVIRONMENTAL SCIENCES↗

Microbial community shifts correspond with suppression of decomposition 25 years after liming of acidic forest soils

Microbial community structure and function regularly covary with soil pH, yet effects of these interactions on soil carbon are rarely tested experimentally within natural ecosystems. We investigated the enduring (25 year) impacts of liming on microbial community structure and decomposition at an acidic northern hardwood forest, where experimental liming increased pH one unit and surprisingly doubled the organic carbon stocks of the forest floor. Here we show that this increase in carbon storage corresponded with restructuring of the bacterial and fungal communities that drive decomposition. In the Oe horizon, liming reduced the activities of five extracellular enzymes that mediate decomposition, while the Oa horizon showed an especially large (64%) reduction in the activity of a sixth, peroxidase, which is an oxidative enzyme central to lignocellulose degradation. Decreased enzyme activities corresponded with loss of microbial taxa important for lignocellulose decay, including large reductions in the dominant ectomycorrhizal genera Russula and Cenococcum, saprotrophic and wood decaying fungi, and Actinobacteria (Thermomonosporaceae). These results demonstrate the importance of pH as a dominant regulator of microbial community structure and illustrate how changes to this structure can produce large, otherwise unexpected increases in carbon storage in forest soils.

59 BASIC BIOLOGICAL SCIENCES↗

Island influences on plant functional traits and trait–trait associations across species‐ and community‐scales

The island rule predicts gigantism or dwarfism in body size of island species relative to their mainland counterparts. However, whether other functional traits shift and whether trait–trait associations on islands differ between species and community levels remains unclear. We measured 13 carbon- and water-related functional traits in 37 shared tree species across 35 eastern Chinese islands and 66 nearby mainland plots. We examined species-level trait value shifts and associations under the island rule and compared trait associations between species and communities. Most size-related, wood-anatomical, and hydraulic traits shifted on islands, with large values decreasing and small values increasing; yet, their associations remained stable, aligning with the global trait spectrum and trait–trait coevolution. This stability, despite trait value shifts, suggests evolutionary integration of functional strategies. By contrast, island community-scale trait associations diverged from shared species-level patterns and sometimes reversed, such as positive relationships between wood density and resource-acquisitive traits. Community-level trait associations were stronger on islands, likely reflecting constrained environmental filtering and migration limitation. These contrasting patterns suggest that dominant species can restructure trait associations at the community level, with implications for ecosystem functioning and carbon storage, thereby advancing understanding of plant trait strategies in island systems.

Archipelagos↗

Recent Hydrodynamic Modeling Enhancements in OpenFAST

To improve the hydrodynamic modeling capabilities of the offshore wind design and modeling tool OpenFAST, a restructuring of the HydroDyn hydrodynamics module was undertaken with several new features implemented. The generation of the wave field is now separated from HydroDyn into a new module called SeaState. Unlike previous versions of HydroDyn, which precomputed the wave kinematics at the undisplaced positions of the hydrodynamic nodes, the new SeaState module computes the complete time history of the wave field at the vertices of a user-defined wave grid. During the simulation, the wave kinematics at any point within the grid can be efficiently interpolated, allowing the strip-theory wave loads to be evaluated based on the wave kinematics at the displaced structure position. A phase correction was also implemented for the potential-flow wave-exciting loads to account for large structure displacements. Several wave-stretching methods were implemented for the strip-theory solution along with a wave-load redistribution method that ensures smooth variation of the nodal loads as the nodes of a discrete hydrodynamic mesh enter and exit the water. The load smoothing is included to avoid the excitation of unphysical high-frequency structural vibration during hydroelastic simulations. The MacCamy-Fuchs diffraction correction for the strip-theory solution and the capability to insert a constrained NewWave into extreme stochastic sea states with directional spreading were also added. The present article documents the formulations of the new improvements to HydroDyn with example applications and numerical results.

constrained wave↗

Design and characterization of the SPT-3G receiver (Conference Presentation)

(On behalf of the SPT-3G collaboration)The SPT-3G receiver was commissioned in early 2017 on the 10-meter South Pole Telescope (SPT) to map the Cosmic Microwave Background (CMB) with arcminute resolution. The new instrument significantly improves on previous SPT camera designs, offering unprecedented sensitivity to the CMB’s temperature and polarization anisotropies while maintaining a tight control on systematic effects.A restructured optics chain features new secondary and tertiary mirrors to increase the receiver’s field of view by a factor of four in area, coupling light through a set of four cryogenic 720 mm alumina elements, which re-image the Gregorian focus inside the receiver. The broad-band (70-270 GHz) anti-reflective coated lenses are paired with a Lyot stop and cooled to 4 K using a dedicated two-stage pulse-tube cooler (PTC) to minimize in-band attenuation, internal radiative loading, and stray light on the considerably larger focal plane, which is populated with ~2,700 diffraction-limited pixels.Each independent pixel incorporates a lenslet-coupled broadband sinuous antenna, which routes signals through superconducting transmission lines and in-line band-defining filters to six transition-edge sensors, each measuring one of three bands (90, 150, and 220 GHz) and two polarizations, yielding a total of ~16,000 bolometers distributed across ten 150 mm monolithic wafers on a 430 mm image plane. A robust mechanical and thermal architecture supports and cools all detectors across this sizable focal plane to ~250 mK using a closed-cycle Helium adsorption refrigerator backed by a PTC, allowing a duty cycle greater than 90%.This order of magnitude increase in detector count relies on an improved digital frequency-domain SQUID readout system which integrates superconducting inductor-capacitor resonators wired in series with each bolometer to achieve a 68x multiplexing factor while mitigating noise and crosstalk effects.Cumulatively, SPT-3G’s new optics, detector, and readout strategies boast a potential factor of ~20 improvement in mapping speed over its predecessor, SPT-Pol, offering the potential to improve our understanding of inflationary physics, astroparticle physics, and growth of structure. We summarize the new receiver’s core design principles, outline technology characterization results, and report on plans for future upgrades.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

SU-D-18A-02: Towards Real-Time On-Board Volumetric Image Reconstruction for Intrafraction Target Verification in Radiation Therapy

Purpose: To expedite on-board volumetric image reconstruction from limited-angle kV—MV projections for intrafraction verification. Methods: A limited-angle intrafraction verification (LIVE) system has recently been developed for real-time volumetric verification of moving targets, using limited-angle kV—MV projections. Currently, it is challenged by the intensive computational load of the prior-knowledge-based reconstruction method. To accelerate LIVE, we restructure the software pipeline to make it adaptable to model and algorithm parameter changes, while enabling efficient utilization of rapidly advancing, modern computer architectures. In particular, an innovative two-level parallelization scheme has been designed: At the macroscopic level, data and operations are adaptively partitioned, taking into account algorithmic parameters and the processing capacity or constraints of underlying hardware. The control and data flows of the pipeline are scheduled in such a way as to maximize operation concurrency and minimize total processing time. At the microscopic level, the partitioned functions act as independent modules, operating on data partitions in parallel. Each module is pre-parallelized and optimized for multi-core processors (CPUs) and graphics processing units (GPUs). Results: We present results from a parallel prototype, where most of the controls and module parallelization are carried out via Matlab and its Parallel Computing Toolbox. The reconstruction is 5 times faster on a data-set of twice the size, compared to recently reported results, without compromising on algorithmic optimization control. Conclusion: The prototype implementation and its results have served to assess the efficacy of our system concept. While a production implementation will yield much higher processing rates by approaching full-capacity utilization of CPUs and GPUs, some mutual constraints between algorithmic flow and architecture specifics remain. Based on a careful analysis of the prototype performance, it will be feasible to resolve such issues through appropriate algorithmic modifications or special-purpose hardware, thus enabling target verification in seconds with the LIVE system. This work was partially supported by a research grant from Varian Medical Systems.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

TU-C-9A-01: IROC Organization and Clinical Trial Credentialing

As a response to recommendations from a report from the Institute of Medicine, NCI is reorganizing it clinical trial groups into a National Clinical Trial Network (NCTN) that consists of four adult groups (Alliance, ECOGACRIN, NRG, and SWOG) and one children’s group (COG). NRG will house CIRO, a center to promote innovative radiation therapy research and intergroup collaboration in radiation. The quality assurance groups that support clinical trials have also been restructured. ITC, OSU Imaging corelab, Philadelphia Imaging core-lab, QARC, RPC, and RTOGQA have joined together to create the Imaging and Radiation Oncology Core (IROC) Group. IROC’s mission is to provide integrated radiation oncology and diagnostic imaging quality control programs in support of the NCI’s NCTN thereby assuring high quality data for clinical trials designed to improve the clinical outcomes for cancer patients worldwide. This will be accomplished through five core services: site qualification, trial design support, credentialing, data management, case review.These changes are important for physicist participating in NCI clinical trials to understand. We will describe in detail the IROC’s activities and five core services so that as a user, the medical physicist can learn how to efficiently utilize this group. We will describe common pitfalls encountered in credentialing for current protocols and present methods to avoid them. These may include the which benchmarks are required for NSABP B-51/RTOG 1304 and how to plan them as well as tips for phantom planning. We will explain how to submit patient and phantom cases in the TRIAD system used by IROC. Learning Objectives: To understand the basic organization of IROC, its mission and five core services To learn how to use TRIAD for patient and phantom data submission To learn how to avoid common pitfalls in credentialing for current trials.

60 APPLIED LIFE SCIENCES↗

MO-DE-BRA-01: Flipped Physics Courses Within a Radiologic Technologist Program: Video Production and Long Term Outcomes

Purpose: To determine if the flipped class format has an effect on examination results for a radiologic technologist (RT) program and discuss benefits from creating video resources. Methods: From 2001–2015, students had taken both a radiological physics and quality control (QC) class as a part of their didactic training. In 2005/2006, the creation of videos of didactic lectures and QC test demonstrations allowed for a flip where content was studied at home while exercises and reviews were done in-class. Final examinations were retrospectively reviewed from this timeframe. 12 multiple choice physics questions (MCP) and 5 short answer QC questions (SAQC) were common to pre and post flip exams. The RT program’s ARRT exam scores were also obtained and compared to national averages. Results: In total, 36 lecture videos and 65 quality control videos were created for the flipped content. Data was ∼2.4GB and distributed to students via USB or CD media. For MCP questions, scores improved by 7.9% with the flipped format and significance (Student’s t-test, p<0.05) was found for 3 of the 12 questions. SAQC questions showed improvement by 14.6% and significance was found for 2 of the 5 questions. Student enrollment increased from ∼14 (2001–2004) to ∼23 students (2005–15). Content was continuously added post-flip due to the efficiency of delivery. The QC class in 2003 covered 45 test setups in-class while 65 were covered with video segments in 2014. Flipped materials are currently being repurposed. In 2015, this video content was restructured into an ARRT exam review guide and in 2016, the content was reorganized for fluoroscopy training for physicians. Conclusion: We believe that flipped classes can improve efficiency of content delivery and improve student performance even with an increase in class size. This format allows for flexibility in learning as well as re-use in multiple applications.

07 ISOTOPE AND RADIATION SOURCES↗

First demonstration of tuning between the Kitaev and Ising limits in a honeycomb lattice

Recent observations of novel spin-orbit coupled states have generated interest in 4d/5d transition metal systems. A prime example is the J eff = $\frac{1}{2}$ state in iridate materials and α-RuCl 3 that drives Kitaev interactions. Here, by tuning the competition between spin-orbit interaction (λ SOC ) and trigonal crystal field (Δ T ), we restructure the spin-orbital wave functions into a previously unobserved μ = $\frac{1}{2}$ state that drives Ising interactions. This is done via a topochemical reaction that converts Li 2 RhO 3 to Ag 3 LiRh 2 O 6 . Using perturbation theory, we present an explicit expression for the μ = $\frac{1}{2}$ state in the limit Δ T ≫ λ SOC realized in Ag 3 LiRh 2 O 6 , different from the conventional J eff = $\frac{1}{2}$ state in the limit λ SOC ≫ Δ T realized in Li 2 RhO 3 . The change of ground state is followed by a marked change of magnetism from a 6 K spin-glass in Li 2 RhO 3 to a 94 K antiferromagnet in Ag 3 LiRh 2 O 6 .

36 MATERIALS SCIENCE↗

Tunable phononic quantum interference induced by two-dimensional metals

Harnessing quantum interference among bosons provides opportunities due to their longer coherence time than fermions. Fano resonance, an example of quantum interference between discrete and continuous states, is marked by an asymmetric lineshape. While photon-based Fano resonance has enabled high-sensitivity molecule sensing, phonon-based Fano resonance remains underexplored because of ineffective interference between discrete phonons and electronic continuum. In this work, we report phonon-based Fano resonance in a graphene/2D Ag/SiC heterostructure, arising from frequency and lifetime matching between discrete and continuous phonons of SiC. The observed Fano asymmetry is tunable over two orders of magnitude, surpassing previously reported phonon-based systems. The 2D Ag layer restructures the interfacial SiC and facilitates resonant scattering to enhance Fano asymmetry, which is unattainable in conventional Ag. We further demonstrated that this Fano resonance allows ultrasensitive molecule detection at the single-molecule level. Our work highlights phonon-based Fano resonance, opening avenues for engineering quantum interference with phonons.

Science & Technology - Other Topics↗

Strain release through hydrogen bond–mediated layer twisting

Strain engineering, enabling the precise control over structure and functional properties, is a key strategy for the design of advanced materials. However, the mechanisms governing strain evolution and release at the nanoscale remain largely unexplored. In this study, we leverage in situ heating transmission electron microscopy and synchrotron x-ray spectroscopy to investigate the strain relaxation pathways of boehmite (γ-AlOOH) at 575 kelvin by revealing real-time structural dynamics. Through tracking the moiré pattern evolution, we identify distinct strain release mechanisms, including layer twisting, defect formation, and domain restructuring. Our neural network potential calculations reveal that energy fluctuations at small twist angles are dominated by an interference-like interaction modulation of hydrogen bonds between boehmite interlayers, with metastable twisted structures corresponding to local minima of the potential energy landscape. This work establishes a previously unidentified paradigm of two-dimensional layer twisting mediated by hydrogen bonding, offering insights into strain-driven transformation mechanisms, and thus may have broad implications for strain in material and earth sciences.

36 MATERIALS SCIENCE↗

Assessing China’s efforts to pursue the 1.5 degrees C warming limit

Given the increasing interest in keeping global warming below 1.5 ?, a key question is what this would mean for China’s emission pathway, energy restructuring and decarbonization. By conducting a multi-model study, we find that the 1.5 ?-consistent goal would require China to reduce its carbon emissions and energy consumption by over 90% and 39%, respectively, compared to the No Policy case. Negative emission technologies play an important role in achieving near-zero emissions, with captured carbon averagely accounting for 23% of the total reductions in 2050. Our multi-model comparisons reveal large differences in necessary emission reductions across sectors, while what’s consistent is that the power sector is required to achieve full decarbonization by 2050. The cross-model averages indicate that China’s accumulated policy costs may amount to 2.75-5.73% of its GDP by 2050, given the 1.5 ? warming limit.

1.5 degrees, China, Paris agreement, ENGAGE↗

Structure of a ribonucleotide reductase R2 protein radical

Aerobic ribonucleotide reductases (RNRs) initiate synthesis of DNA building blocks by generating a free radical within the R2 subunit; the radical is subsequently shuttled to the catalytic R1 subunit through proton-coupled electron transfer (PCET). Here we present a high-resolution room temperature structure of the class Ie R2 protein radical captured by x-ray free electron laser serial femtosecond crystallography. The structure reveals conformational reorganization to shield the radical and connect it to the translocation path, with structural changes propagating to the surface where the protein interacts with the catalytic R1 subunit. Restructuring of the hydrogen bond network, including a notably short O–O interaction of 2.41 angstroms, likely tunes and gates the radical during PCET. These structural results help explain radical handling and mobilization in RNR and have general implications for radical transfer in proteins.

59 BASIC BIOLOGICAL SCIENCES↗

Structure of a Light-Activated LOV Protein Dimer That Regulates Transcription

Light, oxygen, or voltage (LOV) protein domains are present in many signaling proteins in bacteria, archaea, protists, plants, and fungi. The LOV protein VIVID (VVD) of the filamentous fungus Neurospora crassa enables the organism to adapt to constant or increasing amounts of light and facilitates proper entrainment of circadian rhythms. Here, we determined the crystal structure of the fully light-adapted VVD dimer and reveal the mechanism by which light-driven conformational change alters the oligomeric state of the protein. Light-induced formation of a cysteinyl-flavin adduct generated a new hydrogen bond network that released the amino (N) terminus from the protein core and restructured an acceptor pocket for binding of the N terminus on the opposite subunit of the dimer. Substitution of residues critical for the switch between the monomeric and the dimeric states of the protein had profound effects on light adaptation in Neurospora. The mechanism of dimerization of VVD provides molecular details that explain how members of a large family of photoreceptors convert light responses to alterations in protein-protein interactions.

08 HYDROGEN↗

Mapping the soil microbiome functions shaping wetland methane emissions

Accounting for only 8% of Earth’s land cover, freshwater wetlands remain the foremost contributors to global methane emissions. Yet the microorganisms and processes underlying methane emissions from wetland soils remain poorly understood. Over a five-year period, we surveyed the microbial membership and in situ methane measurements from over 700 samples in one of the most prolific methane-emitting wetlands in the United States. We constructed a catalog of 2,502 metagenome-assembled genomes (MAGs), with more than half of the 70 bacterial and archaeal phyla sampled containing novel lineages. Integration of these data with 133 soil metatranscriptomes provided a genome-resolved view of the biogeochemical specialization and versatility expressed over wetland soil spatial and temporal gradients. Centimeter-scale depth differences best explained patterns of microbial community structure and transcribed functionalities, even more than land cover or temporal information. Moreover, while extended flooding restructured soil redox, this perturbation failed to reconfigure the transcriptional profiles of methane-cycling microorganisms, contrasting with theoretically expected responses to hydrological perturbations. Co-expression analyses, coupled with depth-resolved methane measurements, revealed the metabolisms and trophic structures most predictive of methane hotspots. Mapping the spatiotemporal transcriptional patterns on this compendium of biogeochemically classified soil-derived genomes begins to untangle the microbial carbon, energy, and nutrient processing contributing to wetland methane production.

MAG↗

Specificities of Local Dynamics and Orientational State of Rigid-Chain Liquid-Crystal Polymers

Proton magnetic resonance (PMR) spectra and terahertz IR spectra of Vectra A950 fibers and granules and Armos fibers before and after heat treatment were obtained and analyzed in order to understand the molecular mobility mechanisms that ensure the self-organization and restructurization of these rigid-chain liquid-crystal polymers, as well as their similarity and difference. It is shown that large-scale thermal (quasi-segmental) mobility in such LC polymers is due to the reptation of macromolecules with respect to each other and the conformational transitions necessary for the motion of chains in them are the result of random accumulation of displacements that occur during local bending and torsional-vibrational movements in the links of polymer chains according to the Bresler–Frenkel mechanism.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Physical insights into biological memory using phospholipid membranes

Electrical signals may propagate along neuronal membranes in the brain, thus enabling communication between nerve cells. In doing so, lipid bilayers, fundamental scaffolds of all cell membranes, deform and restructure in response to such electrical activity. These changes impact the electromechanical properties of the membrane, which then physically store biological memory. This memory can exist either over a short or long period of time. Traditionally, biological memory is defined by the strengthening or weakening of transmissions between individual neurons. In this report we show that electrical stimulation may also alter the properties of the lipid membrane, thus pointing toward a novel mechanism for memory storage. Furthermore, based on the analysis of existing electrophysiological data, we study molecular mechanisms underlying the long-term potentiation in phospholipid membranes. Finally, we examine possible relationships between the memory capacitive properties of lipid membranes, neuronal learning, and memory.

59 BASIC BIOLOGICAL SCIENCES↗

PolyCheck: Dynamic Verification of Iteration Space Transformations on Affine Programs

High-level compiler transformations, especially loop transformations, are widely recognized as critical optimizations to restructure programs to improve data locality and expose parallelism. Guaranteeing the correctness of program transformations is essential, and to date three main approaches have been developed: proof of equivalence of affine programs, matching the execution traces of programs, and checking bit-by-bit equivalence of the outputs of the programs. Each technique suffers from limitations in either the kind of transformations supported, space complexity, or the sensitivity to the testing dataset. In this paper, we take a novel approach addressing all three limitations to provide an automatic bug checker to verify any iteration reordering transformations on affine programs, including non-affine transformations, with space consumption proportional to the original program data, and robust to arbitrary datasets of a given size. We achieve this by exploiting the structure of affine program control- and data-flow to generate at compile-time lightweight checker code to be executed within the transformed program. Experimental results assess the correctness and effectiveness of our method, and its increased coverage over previous approaches.

affine programs↗