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At least 145 records · Page 8

Allometric, Growth, and Biomass Estimation Models for Acacia dealbata Link.: A Case Study in Serra da Estrela Natural Park (Portugal)

Allometric, growth, and biomass estimation models for the quantification of missing parameters in trees are widely used to estimate the productivity of a stand. However, regarding species with lower economic interest, or exotic invasive species, the creation of these tools did not occur in the same way as for other species, lacking the development of relationships to allow a deeper study of these species. Thus, data were collected in a settlement of Acacia dealbata Link. in Portugal, in an area known for the current infestation of this species. After a bibliographic review, some of the identified models were tested to select those who best fit the characteristics of this stand, which were used to develop relationships that, based on the data collected, would be able to estimate parameters, such as height, volume, or mass. It was found that the models established, at least for the initial 20 years of the life of the trees, followed close to a linear model. However, the model still presents some weaknesses. For being considered an invasive species in Portugal, A. dealbata is frequently controlled, and for this reason it is very difficult to find trees older than 20 years.

Nunes, Leonel J. R. (ORCID:0000000154048163)↗

Carrier-envelope-phase characterization of ultrafast mid-infrared laser pulses through harmonic generation and interference in argon

The propagation of an intense, femtosecond, mid-infrared laser pulse in a gaseous medium results in the efficient generation of spectrally overlapping low-order harmonics, whose optical carrier phases are linked to the carrier-envelope phase (CEP) of the mid-infrared driver pulse. Random peak-power fluctuations of the driver pulses, converted to the fluctuations of the nonlinear phases, acquired by the pulses on propagation, cause this phase correlation to smear out. We show that this seemingly irreversible loss of phase can be recovered, and that the complete information needed for the phase correction is contained in the harmonic spectra itself. The optical phases of the intense driver pulse and its harmonics, as fragile as they appear to be against even weak disturbances, evolve deterministically during highly nonlinear propagation through the extended ionization region.

nonlinear optics↗

Effective viscosity, resistivity, and Reynolds number in weakly collisional plasma turbulence

ABSTRACT We examine dissipation and energy conversion in weakly collisional plasma turbulence, employing in situ observations from the Magnetospheric Multiscale mission and kinetic particle-in-cell simulations of proton–electron plasma. A previous result indicated the presence of viscous-like and resistive-like scaling of average energy conversion rates – analogous to scalings characteristic of collisional systems. This allows for extraction of collisional-like coefficients of effective viscosity and resistivity, and thus also determination of effective Reynolds numbers based on these coefficients. The effective Reynolds number, as a measure of the available bandwidth for turbulence to populate various scales, links turbulence macroscale properties with kinetic plasma properties in a novel way.

Astronomy & Astrophysics↗

Biofilm formation and genomic features of Listeria monocytogenes strains isolated from meat and dairy industries located in Piedmont (Italy)

Listeria monocytogenes is considered a major challenge for the food industry as it can persist for long periods in food processing plants by forming biofilms. The aims of this study were: i) to assess the biofilm producing ability of 57 Listeria monocytogenes isolates previously subjected to whole-genome sequencing (WGS); ii) to compare the levels of biofilm formation with the presence or absence of biofilm associated genes. To determine the presence or absence of a known set of biofilm associated genes, a comparative genomic analysis was performed on each strain. Among Listeria monocytogenes isolates, 58 %, 38.5 % and 3.5 % exhibited weak, moderate or strong biofilm production, respectively. No difference in biofilm production was observed between food and environmental isolates. The percentage of Listeria monocytogenes strains isolated from meat products (57 %) classified as moderate or strong biofilm producers was higher than the percentage obtained for strains isolated from dairy products (28 %). Here, the presence of the Stress Survival Islet 1, the arsD stress gene and the truncated inlA protein was significantly associated with increased levels of biofilm. Combining biofilm phenotype with molecular and genotyping data may provide the opportunity to better understand the relationship between genes linked to biofilm formation in Listeria monocytogenes.

59 BASIC BIOLOGICAL SCIENCES↗

Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies

The cancer genome is commonly altered with thousands of structural rearrangements including insertions, deletions, translocation, inversions, duplications, and copy number variations. Thus, structural variant (SV) characterization plays a paramount role in cancer target identification, oncology diagnostics, and personalized medicine. As part of the SEQC2 Consortium effort, the present study established and evaluated a consensus SV call set using a breast cancer reference cell line and matched normal control derived from the same donor, which were used in our companion benchmarking studies as reference samples. We systematically investigated somatic SVs in the reference cancer cell line by comparing to a matched normal cell line using multiple NGS platforms including Illumina short-read, 10X Genomics linked reads, PacBio long reads, Oxford Nanopore long reads, and high-throughput chromosome conformation capture (Hi-C). We established a consensus SV call set of a total of 1788 SVs including 717 deletions, 230 duplications, 551 insertions, 133 inversions, 146 translocations, and 11 breakends for the reference cancer cell line. To independently evaluate and cross-validate the accuracy of our consensus SV call set, we used orthogonal methods including PCR-based validation, Affymetrix arrays, Bionano optical mapping, and identification of fusion genes detected from RNA-seq. We evaluated the strengths and weaknesses of each NGS technology for SV determination, and our findings provide an actionable guide to improve cancer genome SV detection sensitivity and accuracy. A high-confidence consensus SV call set was established for the reference cancer cell line. A large subset of the variants identified was validated by multiple orthogonal methods.

59 BASIC BIOLOGICAL SCIENCES↗

The 2024 July 16 solar event: a challenge to the coronal mass ejection origin of long-duration gamma-ray flares

We present a multi-spacecraft analysis of the 2024 July 16 long-duration gamma-ray flare (LDGRF) detected by the Large Area Telescope on the Fermi satellite. The measured > 100 MeV γ-ray emission persisted for over seven hours after the flare impulsive phase, and was characterized by photon energies exceeding 1 GeV and a remarkably hard parent-proton spectrum. In contrast, the phenomena related to the coronal mass ejection (CME)-driven shock linked to this eruption were modest, suggesting an inefficient proton acceleration unlikely to achieve energies well above the 300 MeV pion-production threshold to account for the observed γ-ray emission. Specifically, the CME was relatively slow (∼600 km/s) and the accompanying interplanetary type-II/III radio bursts were faint and short-lived, unlike those typically detected during large events. In particular, the type-II emission did not extend to kilohertz frequencies and disappeared ∼5.5 hours prior to the LDGRF end time. Furthermore, the associated solar energetic particle (SEP) event was very weak, short-duration, and limited to a few tens of MeV, even at magnetically well-connected spacecraft. These findings demonstrate that a very fast CME resulting in a high-energy SEP event is not a necessary condition for the occurrence of LDGRFs, challenging the idea that the high-energy γ-ray emission is produced by the back-precipitation of shock-accelerated ions into the solar surface. The alternative origin scenario based on local particle trapping and acceleration in large-scale coronal loops is instead favored by the observation of giant arch-like structures of hot plasma over the source region that persisted for the entire duration of this LDGRF.

Sun: UV radiation↗

Accessing new physics with an undoped, cryogenic CsI CEvNS detector for COHERENT at the SNS

We consider the potential for a 10 kg undoped cryogenic CsI detector operating at the Spallation Neutron Source to measure coherent elastic neutrino-nucleus scattering and its sensitivity to discover new physics beyond the standard model (BSM). Through a combination of increased event rate, lower threshold, and good timing resolution, such a detector would significantly improve on past measurements. We considered tests of several BSM scenarios such as neutrino nonstandard interactions and accelerator-produced dark matter. This detector’s performance was also studied for relevant questions in nuclear physics and neutrino astronomy, namely the weak charge distribution of Cs and I nuclei and detection of neutrinos from a core-collapse supernova. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

High mass and halo resolution from fast low resolution simulations

Generating mocks for future sky surveys requires large volumes and high resolutions, which is computationally expensive even for fast simulations. Here we try to develop numerical schemes to calibrate various halo and matter statistics in fast low resolution simulations compared to high resolution N-body and hydrodynamic simulations. For the halos, we improve the initial condition resolution and develop a halo finder "relaxed-FoF", where we allow different linking lengths for different halo mass and velocity dispersions. We show that our relaxed-FoF halo finder improves the common statistics, such as halo bias, halo mass function, halo auto power spectrum, cross correlation coefficient with the reference halo catalog, and halo-matter cross power spectrum. We also calibrate small-scale velocities of small halos to improve the power spectrum in redshift space. For the matter statistics, we incorporate the potential gradient descent (PGD) method into fast simulations to improve the matter distribution at nonlinear scales. By building a lightcone output, we show that the PGD method significantly improves the weak lensing convergence tomographic power spectrum. With these improvements FastPM is comparable to the high resolution full N-body simulation of the same mass resolution, with two orders of magnitude fewer time steps. These techniques can be used to improve the halo and matter statistics of FastPM simulations for mock catalogs of future surveys such as DESI and LSST.

79 ASTRONOMY AND ASTROPHYSICS↗

Thermally Insulating, Thermal Shock Resistant Calcium Aluminate Phosphate Cement Composites for Reservoir Thermal Energy Storage

This paper presents the use of hydrophobic silica aerogel (HSA) and hydrophilic fly ash cenosphere (FCS) aggregates for improvements in the thermal insulating and mechanical properties of 100- and 250 °C-autoclaved calcium aluminate phosphate (CaP) cement composites reinforced with micro-glass (MGF) and micro-carbon (MCF) fibers for deployment in medium- (100 °C) and high-temperature (250 °C) reservoir thermal energy storage systems. The following six factors were assessed: (1) Hydrothermal stability of HSA; (2) Pozzolanic activity of the two aggregates and MGF in an alkali cement environment; (3) CaP cement slurry heat release during hydration and chemical reactions; (4) Composite phase compositions and phase transitions; (5) Mechanical behavior; (6) Thermal shock (TS) resistance at temperature gradients of 150 and 225 °C. The results showed that hydrophobic trimethylsilyl groups in trimethylsiloxy-linked silica aerogel structure were susceptible to hydrothermal degradation at 250 °C. This degradation was followed by pozzolanic reactions (PR) of HSA, its dissolution, and the formation of a porous microstructure that caused a major loss in the compressive strength of the composites at 250 °C. The pozzolanic activities of FCS and MGF were moderate, and they offered improved interfacial bonding at cement-FCS and cement-MGF joints through a bridging effect by PR products. Despite the PR of MGF, both MGF and MCF played an essential role in minimizing the considerable losses in compressive strength, particularly in toughness, engendered by incorporating weak HSA. As a result, a FCS/HSA ratio of 90/10 in the CaP composite system was identified as the most effective hybrid insulating aggregate composition, with a persistent compressive strength of more than 7 MPa after three TS tests at a 150 °C temperature gradient. This composite displayed thermal conductivity of 0.28 and 0.35 W/mK after TS with 225 and 150 °C thermal gradients, respectively. These values, below the TC of water (TC water = 0.6 W/mK), were measured under water-saturated conditions for applications in underground reservoirs. However, considering the hydrothermal disintegration of HSA at 250 °C, these CaP composites have potential applications for use in thermally insulating, thermal shock-resistant well cement in a mid-temperature range (100 to 175 °C) reservoir thermal energy storage system.

58 GEOSCIENCES↗

Linking leaf dark respiration to leaf traits and reflectance spectroscopy across diverse forest types

Leaf dark respiration (R dark ), an important yet rarely quantified component of carbon cycling in forest ecosystems, is often simulated from leaf traits such as the maximum carboxylation capacity (V cmax ), leaf mass per area (LMA), nitrogen (N) and phosphorus (P) concentrations, in terrestrial biosphere models. However, the validity of these relationships across forest types remains to be thoroughly assessed. Here, in this study, we analyzed R dark variability and its associations with V cmax and other leaf traits across three temperate, subtropical and tropical forests in China, evaluating the effectiveness of leaf spectroscopy as a superior monitoring alternative. We found that leaf magnesium and calcium concentrations were more significant in explaining cross-site R dark than commonly used traits like LMA, N and P concentrations, but univariate trait–R dark relationships were always weak (r 2 ≤ 0.15) and forest-specific. Although multivariate relationships of leaf traits improved the model performance, leaf spectroscopy outperformed trait–R dark relationships, accurately predicted cross-site R dark (r 2 = 0.65) and pinpointed the factors contributing to R dark variability. Our findings reveal a few novel traits with greater cross-site scalability regarding R dark , challenging the use of empirical trait–R dark relationships in process models and emphasize the potential of leaf spectroscopy as a promising alternative for estimating R dark , which could ultimately improve process modeling of terrestrial plant respiration.

59 BASIC BIOLOGICAL SCIENCES↗

Measurements and models of enhanced recombination following inner-shell vacancies in liquid xenon

Electron-capture decays of 125 Xe and 127 Xe , and double-electron-capture decays of 124 Xe , are backgrounds in searches for weakly interacting massive particles (WIMPs) conducted by dual-phase xenon time projection chambers such as LUX-ZEPLIN (LZ). These decays produce signals with more light and less charge than equivalent-energy 𝛽 decays and correspondingly overlap more with WIMP signals. We measure three electron-capture charge yields in LZ: the 1.1 keV M-shell, 5.2 keV L-shell, and 33.2 keV K-shell at drift fields of 193 and 96.5 V/cm. The LL double-electron-capture decay of 124 Xe exhibits even more pronounced shifts in charge and light. We provide a first model of double-electron-capture charge yields using the link between ionization density and electron-ion recombination, and identify a need for more accurate calculations. Finally, we discuss the implications of the reduced charge yield of these decays and other interactions creating inner-shell vacancies for future dark matter searches.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

$\testit{d}$-wave superconductivity and Bogoliubov-Fermi surfaces in Rarita-Schwinger-Weyl semimetals

In this work, we uncover the properties of complex tensor ($\textit{d}$-wave) superconducting order in three-dimensional Rarita-Schwinger-Weyl semimetals that host pseudospin-$\frac{3}{2}$ fermions at a fourfold linear band-crossing point. Although the general theory of $\textit{d}$-wave order was originally developed for materials displaying quadratic band touching, it directly applies to the case of semimetals with linear dispersion, several candidate compounds of which have been discovered experimentally very recently. The spin-$\frac{3}{2}$ nature of the fermions allows for the formation of spin-2 Cooper pairs which may be described by a complex second-rank tensor order parameter. In the case of linear dispersion, for the chemical potential at the Fermi point and at strong coupling, the energetically preferred superconducting state is the uniaxial nematic state, which preserves time-reversal symmetry and provides a full (anisotropic) gap for quasiparticle excitations. In contrast, at a finite chemical potential, we find that the usual weak-coupling instability is toward the “cyclic state,” well known from the studies of multicomponent Bose-Einstein condensates, which breaks time-reversal symmetry maximally, has vanishing average value of angular momentum, and features 16 small Bogoliubov-Fermi surfaces. The Rarita-Schwinger-Weyl semimetals provide therefore the first example of weakly coupled, three-dimensional, isotropic $\textit{d}$-wave superconductors where the $\textit{d}$-wave superconducting phase is uniquely selected by the quartic expansion of the mean-field free energy, and is not afflicted by the accidental degeneracy first noticed by Mermin over 40 years ago. We discuss the appearance and stability of the Bogoliubov-Fermi surfaces in absence of inversion symmetry in the electronic Hamiltonian, as in the case at hand.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Diabatization with Electrostatic Embedding for Studying Photophysics in Organic Molecular Crystals

Highly emissive organic molecular crystals find applications in several areas, such as organic electronics, solar cells, and sensors. Understanding the excited-state mechanisms underlying these applications is essential for optimizing and controlling them effectively. Exciton models coupled with nonadiabatic dynamics, particularly quantum dynamics, provide crucial insights into photochemical and photophysical processes in molecular crystals. Nevertheless, there remains a lack of general tools and automated workflows to facilitate such simulations. In this paper, we present a computational strategy to investigate the photoactivated dynamics of organic molecular crystals, bridging methodologies traditionally used for molecular systems and materials science, with a particular focus on the interplay between local excitations and charge transfer (CT) processes. We have implemented an interface between the fromage and Overdia programs, enabling the construction of vibronic Hamiltonians for molecular crystals within an excited-state ONIOM(QM:QM′) framework, incorporating long-range electrostatics through a RESP-based Ewald summation. Fragment-based diabatization provides a route to quantum dynamics simulations in weak-to-intermediate coupling regimes. The method was applied to the photophysics of dibenzo[g,p]chrysene (DBC) crystals using time-dependent DFT. The fromage/ Overdia interface was employed to compute the couplings of local excitations and CT states for 18 unique DBC dimers in the crystal and to quantify the influence of electrostatic embedding, which was found to be modest (10−20%). Simulations on π-stacked dimers reproduced the small red shift observed experimentally from solution to crystal, attributed to electronic interactions among fixed monomers rather than crystal electrostatics. Quantum dynamics simulations revealed ultrafast population transfer from bright local excitations to CT states. This approach establishes a robust framework linking molecular and solid-state excited-state dynamics, with potential applications for studying excitations, defects, and impurities in molecular crystals.

Crystals↗

VWC-BERT: Scaling Vulnerability–Weakness–Exploit Mapping on Modern AI Accelerators

Defending cybersystems needs accurate mapping of software and hardware vulnerabilities to generalized descriptions of weaknesses, and weaknesses to exploits. These mappings enable cyber defenders to build plans for effective defense and assessment of potential risks to a cybersystem. With close to 170k vulnerabilities, manual mapping is not a feasible option. However, automated mapping is challenging due to limited training data, computational intractability, and limitations in computational natural language processing. Tools based on breakthroughs in Transformer-based language models have been demonstrated to classify vulnerabilities with high accuracy. We make three key contributions in this paper: (1) We present a new framework, \VWCBERT, that augments the Transformer-based hierarchical multi-class classification framework of Das et al. (\textsc{V2W-BERT}) with the ability to map weaknesses to exploits. (2) We implement \VWCBERT~ on modern AI accelerator platforms using two data parallel techniques for the pre-training phase and demonstrate nearly linear speedups across NVIDIA and Graphcore accelerator platforms. We observe nearly linear speedups for up to 16 V100 and 8 A100 GPUs, and about 3.4$\times$ speedup for A100 relative to V100 GPUs. We also observe excellent speedups on Graphcore, with $5.7\times$ speedup on 128 IPUs relative to 16 IPUs. Enabled by scaling, we also demonstrate higher accuracy using a larger language model, RoBERTa-Large. We show up to 87\% accuracy for strict and up to 98\% accuracy for relaxed classification. (3) We develop a novel parallel link manager for the link prediction phase and demonstrate up to 21$\times$ speedup with 16 V100 GPUs relative to one V100 GPU, and thus reducing the runtime from 2.5 hours to 10 minutes. We believe that generalizability and scalability of \VWCBERT~ will benefit both the theoretical development and practical deployment of novel cyberdefense solutions and vulnerability classification.

Das, Siddhartha Shankar↗

Multi-Port Autonomous Reconfigurable Solar Power Plant

As the penetration level of power electronics increases and remote photovoltaic (PV) generation is integrated into the alternating current (ac) grid, the short-circuit ratio (SCR) at the point of interconnection of a hybrid PV–energy storage system (ESS) plant may be low. Additionally, the inertia of the alternating current (ac) grid may be low. The low SCRs and inertias can lead to reliability challenges in the power grid. These operating conditions require additional reinforcements, such as synchronous condensers, static var compensators, static synchronous compensators, and high-voltage direct current (HVdc) links/grids. HVdc links or grids may also provide the additional capability of connecting the plant to asynchronous grids and/or connecting asynchronous grids, among others. This scenario leads to discrete development of solar inverters, energy storage inverters, HVdc converters, and several transformers. Some of the problems associated with this discrete development and inverter-based generation include increased cost, lower reliability, and reduced efficiency associated with duplication of power electronics (PEs); competing controls of several individual discrete inverter-based generators due to the presence of multiple PEs, which leads to derating of the system; and transient stability problems arising from inverter-based generation, such as voltage/frequency events leading inverter shutdowns, voltage instability and control interactions in the formed weak grid, and harmonics caused by resonances of multiple inverters.

14 SOLAR ENERGY↗

Experimental Quantification of Spin–Phonon Coupling in Molecular Qubits Using Inelastic Neutron Scattering

Electronic spin superposition states enable nanoscale sensing through their sensitivity to the local environment, yet their sensitivity to vibrational motion also limits their coherence times. In molecular spin systems, chemical tunability and atomicscale resolution are accompanied by a dense, thermally accessible phonon spectrum that introduces efficient spin relaxation pathways. Despite extensive theoretical work, there is little experimental consensus on which vibrational energies dominate spin relaxation or how molecular structure controls spin−phonon coupling (SPC). We present a fully experimental method to quantify SPC coefficients by combining temperature-dependent vibrational spectra from inelastic neutron scattering with spin relaxation rates measured by electron paramagnetic resonance. We apply this framework to two model S = 1/2 systems, copper(II) phthalocyanine (CuPc) and copper(II) octaethylporphyrin (CuOEP). Two distinct relaxation regimes emerge: below 40 K, weakly coupled lattice modes below 50 cm −1 dominate, whereas above 40 K, optical phonons above ∼185 cm −1 become thermally populated and drive relaxation with SPC coefficients nearly 3 orders of magnitude larger. Structural distortions in CuOEP that break planar symmetry soften the crystal lattice and enhance anharmonic scattering but also raise the energy of stretching modes at the molecular core where the spins reside. This redistributes vibrational energy toward the molecular periphery and out of plane, ultimately reducing SPC relative to CuPc and enabling room-temperature spin coherence in CuOEP. Although our method does not provide mode-specific SPC coefficients, it quantifies contributions from distinct spectral regions and establishes a broadly applicable, fully experimental link between crystal structure, lattice dynamics, and spin relaxation.

Lohaus, Stefan H. [California Institute of Technol↗

MicroRNAs as diagnostic and prognostic biomarkers of age-related macular degeneration: advances and limitations

A main cause of vision loss in the elderly is age-related macular degeneration (AMD). Among the cellular, biochemical, and molecular changes linked to this disease, inflammation and angiogenesis appear as being crucial in AMD pathogenesis and progression. There are two forms of the disease: dry AMD, accounting for 80–90% of cases, and wet AMD. The disease usually begins as dry AMD associated with retinal pigment epithelium and photoreceptor degeneration, whereas wet AMD is associated with choroidal neovascularization resulting in severe vision impairment. The new vessels are largely malformed, leading to blood and fluid leakage within the disrupted tissue, which provokes inflammation and scar formation and results in retinal damage and detachment. MicroRNAs are dysregulated in AMD and may facilitate the early detection of the disease and monitoring disease progression. Two recent reviews of microRNAs in AMD had indicated weaknesses or limitations in four earlier investigations. Studies in the last three years have shown considerable progress in overcoming some of these concerns and identifying specific microRNAs as biomarkers for AMD. Further large-scale studies are warranted using appropriate statistical methods to take into account gender and age disparity in the study populations and confounding factors such as smoking status.

60 APPLIED LIFE SCIENCES↗

The Two Arctic Wintertime Boundary Layer States: Disentangling the Role of Cloud and Wind Regimes in Reanalysis and Observations During MOSAiC

The wintertime central Arctic atmosphere comprises a radiatively clear and a radiatively opaque state, which are linked to synoptic forcing and mixed-phase clouds. Weather and climate models often lack process representations surrounding these states, but prior work mostly treated the problem as an aggregate of synoptic conditions, resulting in partially overlapping biases. Here, we disaggregate the Arctic states and confront ERA5 reanalysis with observations from the MOSAiC campaign over the central Arctic sea ice during winter 2019/2020. Low-level winds and liquid water path (LWP) are combined to derive different synoptic classes. Results show that the clear state is primarily formed by weak/moderate winds and the absence of liquid-bearing clouds, while strong winds and enhanced LWP primarily form the radiatively opaque state. ERA5 struggles to reproduce these basic statistics, shows too weak sensitivity of thermal radiation to synoptic forcing, and overestimates thermal radiation for similar LWP amounts. The latter is caused by a warm bias, which has a pronounced inversion structure and is largest in clear and calm conditions. Under strong synoptic forcing, the warm bias is constant with height and discrepancies in mixed-phase cloud altitude appear. Separating synoptic conditions is regarded as useful for process-oriented evaluation of the Arctic troposphere in models.

54 ENVIRONMENTAL SCIENCES↗