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At least 469 records · Page 26

Using supervised machine-learning approaches to understand abiotic stress tolerance and design resilient crops

Abiotic stresses such as drought, heat, cold, salinity and flooding significantly impact plant growth, development and productivity. As the planet has warmed, these abiotic stresses have increased in frequency and intensity, affecting the global food supply and making it imperative to develop stress-resilient crops. In the past 20 years, the development of omics technologies has contributed to the growth of datasets for plants grown under a wide range of abiotic environments. Integration of these rapidly growing data using machine-learning (ML) approaches can complement existing breeding efforts by providing insights into the mechanisms underlying plant responses to stressful conditions, which can be used to guide the design of resilient crops. In this review, we introduce ML approaches and provide examples of how researchers use these approaches to predict molecular activities, gene functions and genotype responses under stressful conditions. Finally, we consider the potential and challenges of using such approaches to enable the design of crops that are better suited to a changing environment. This article is part of the theme issue ‘Crops under stress: can we mitigate the impacts of climate change on agriculture and launch the ‘Resilience Revolution’?’.

abiotic stress↗

MicroFisher: Fungal taxonomic classification for metatranscriptomic and metagenomic data using multiple short hypervariable markers

AbstractProfiling the taxonomic and functional composition of microbes using metagenomic (MG) and metatranscriptomic (MT) sequencing is advancing our understanding of microbial functions. However, the sensitivity and accuracy of microbial classification using genome– or core protein-based approaches, especially the classification of eukaryotic organisms, is limited by the availability of genomes and the resolution of sequence databases. To address this, we propose the MicroFisher, a novel approach that applies multiple hypervariable marker genes to profile fungal communities from MGs and MTs. This approach utilizes the hypervariable regions of ITS and large subunit (LSU) rRNA genes for fungal identification with high sensitivity and resolution. Simultaneously, we propose a computational pipeline (MicroFisher) to optimize and integrate the results from classifications using multiple hypervariable markers. To test the performance of our method, we applied MicroFisher to the synthetic community profiling and found high performance in fungal prediction and abundance estimation. In addition, we also used MGs from forest soil and MTs of root eukaryotic microbes to test our method and the results showed that MicroFisher provided more accurate profiling of environmental microbiomes compared to other classification tools. Overall, MicroFisher serves as a novel pipeline for classification of fungal communities from MGs and MTs.

Wang, Haihua↗

BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA

Gene prediction has remained an active area of bioinformatics research for a long time. Still, gene prediction in large eukaryotic genomes presents a challenge that must be addressed by new algorithms. The amount and significance of the evidence available from transcriptomes and proteomes vary across genomes, between genes, and even along a single gene. User-friendly and accurate annotation pipelines that can cope with such data heterogeneity are needed. The previously developed annotation pipelines BRAKER1 and BRAKER2 use RNA-seq or protein data, respectively, but not both. A further significant performance improvement integrating all three data types was made by the recently released GeneMark-ETP. We here present the BRAKER3 pipeline that builds on GeneMark-ETP and AUGUSTUS, and further improves accuracy using the TSEBRA combiner. BRAKER3 annotates protein-coding genes in eukaryotic genomes using both short-read RNA-seq and a large protein database, along with statistical models learned iteratively and specifically for the target genome. We benchmarked the new pipeline on genomes of 11 species under an assumed level of relatedness of the target species proteome to available proteomes. BRAKER3 outperforms BRAKER1 and BRAKER2. The average transcript-level F1-score is increased by about 20 percentage points on average, whereas the difference is most pronounced for species with large and complex genomes. BRAKER3 also outperforms other existing tools, MAKER2, Funannotate, and FINDER. The code of BRAKER3 is available on GitHub and as a ready-to-run Docker container for execution with Docker or Singularity. Overall, BRAKER3 is an accurate, easy-to-use tool for eukaryotic genome annotation.

59 BASIC BIOLOGICAL SCIENCES↗

Measurement of 𝐵 meson production fraction ratios in proton-proton collisions at √𝑠 = 13 TeV using open-charm and charmonium decays

Production fraction ratios of 𝐵 + , 𝐵 0 , and 𝐵$^{0}_{𝑠}$ mesons are measured in proton-proton collisions at √𝑠 = 13 TeV using a special dataset recorded in 2018 with high-rate triggers designed to collect an unbiased sample of 1⁢010 𝑏 hadrons with the CMS experiment at the LHC. These data allow the study of the open-charm decays of 𝐵 mesons (𝐵 (𝑠) → 𝜋⁢𝐷 (𝑠) ) where the 𝐷 meson decays into fully hadronic final states. By utilizing known branching fractions and precise theoretical calculations, production fraction ratios as functions of 𝐵 meson transverse momentum (𝑝 T ) and rapidity (𝑦) are measured using open-charm decays in the kinematic range of 8 < 𝑝 T < 60 GeV and |𝑦| <2.25. In addition, the same dataset is used to measure the relative production fraction ratios with the charmonium decay channels [𝐵 (𝑠) →𝑋⁢𝐽/𝜓 with 𝑋 indicating a 𝐾 + , 𝐾*(892) 0 , or 𝜙⁡(1020) meson] where the 𝐽/𝜓 meson decays into a pair of muons. The open-charm results are used to normalize the relative production fraction ratios obtained from the charmonium samples. Measurements of the ratios of branching fractions of 𝐵 meson decays to charmonium and open-charm final states are also reported, which will improve the world-average values of these ratios. Finally, we test isospin invariance in 𝐵 meson production in proton-proton collisions and observe that it holds within the experimental precision.

Bottom mesons↗

Measuring the growth of Alfvén wave parametric decay instability using counter-propagating waves: Theory and simulations

The parametric decay instability (PDI) of Alfvén waves—where a pump Alfvén wave decays into a backward-propagating child Alfvén wave and a forward ion acoustic wave—is a fundamental nonlinear wave-wave interaction and holds significant implications for space and laboratory plasmas. However, to date there has been no direct experimental measurement of PDI. Here, we propose a novel and experimentally viable scheme to quantify the growth of Alfvén wave PDI on a linear device using a large pump Alfvén wave and a small counter-propagating seed Alfvén wave, with the seed-wave frequency tuned to match the backward Alfvén wave generated by standard PDI. Using hybrid simulations, we show that energy transfer from the pump to the seed reduces the latter's spatial damping. By comparing seed-wave amplitudes with and without the pump wave, this damping reduction can be used as a direct and reliable proxy for PDI growth. The method is validated in our simulations across a range of plasma and wave parameters and agrees well with theoretical predictions. Notably, the scheme exhibits no threshold for PDI excitation and is, in principle, readily implementable under current laboratory conditions. Finally, this scheme is a critical step toward solving the challenge of experimentally accessing Alfvén wave PDI and provides an elegant method that may be used to validate fundamental theories of parametric instabilities in controlled laboratory settings.

heliosphere↗

New constraint on the Np 237 ( n , γ ) Np 238 integral cross section using the Godiva-IV critical assembly

Accurate knowledge of the 237 Np(n, γ) 238 Np cross section at fast neutron energies is important for applied nuclear science. The presently available experimental data has large disagreements in the fast neutron region. Perform a model-independent measurement of the 237 Np(n, γ) 238 Np integral cross section using a well characterized fast neutron source and compare the result with previous measurements and current nuclear data evaluations. Provide an integral measurement that can be used as a benchmark for current evaluations. Multiple samples of 237 Np were irradiated in the Godiva-IV critical assembly. Following the irradiation, the samples placed in a γ-ray counting setup and the γ-rays emitted from the decay of 238 Np were measured over a time period of approximately 7 days. Multiple γ-ray decay branches of 238 Np were observed. The observed activity of 238 Np was used to calculate the amount of 238 Np produced during the irradiation via the 237 Np(n, γ) 238 Np reaction and an integral cross section of 342(11) mb was measured for the Godiva-IV neutron spectrum. Further, the 238 Np half-life has been measured with a result of 50.31(5) hours. The 237 Np(n, γ) 238 Np integral cross section measured in this work is in agreement with overlapping 1σ error bands to ENDF/B-VIII.0. However, the measured value is 3σ away from the calculated integral cross section using JENDL-5. This measurement offers a reliable benchmark for future 237 Np(n, γ) 238 Np cross section evaluations.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Investigation of post-breakup Coulomb acceleration using a trajectory model

Intermediate mass fragments ejected during the deexcitation of excited projectilelike fragments may promptly decay following ejection; the daughter particles that are subsequently produced are subject to interactions with the residual nucleus that affect final-state observables, a process herein referred to as post-breakup Coulomb acceleration. A simple classical Coulomb interaction model was used to study modification of 8 Be (2 + ), 5 Li (3/2 – ), 7 Li (7/2 – ), 7 Be (7/2 – ), and states in 12 B emitted following heavy-ion collisions of 28 Si + 12 C at 35 MeV/nucleon. Here, in contrast to previous work studying 8 Be (2 + ), excellent agreement between simulation and experiment was obtained using only Coulomb forces when either a Lorentzian or R-matrix line shape was used to describe the initial relative energy rather than a Gaussian. In consideration of the obtained results, improvements to the model and evaluation of experimental data are discussed as future directions, but it was concluded that the effects observed in the present data can be accurately described using only elements of classical mechanics and that the process is largely understood for a wide range of state lifetimes and mass and charge (a)symmetries.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Constraining gravity with a new precision 𝐸 𝐺 estimator using Planck + SDSS BOSS data

The 𝐸 𝐺 statistic is a discriminating probe of gravity developed to test the prediction of general relativity (GR) for the relation between gravitational potential and clustering on the largest scales in the observable Universe. We present a novel high-precision estimator for the 𝐸 𝐺 statistic using CMB lensing and galaxy clustering correlations that carefully matches the effective redshifts across the different measurement components to minimize corrections. A suite of detailed tests is performed to characterize the estimator’s accuracy, its sensitivity to assumptions and analysis choices, and the non-Gaussianity of the estimator’s uncertainty is characterized. After finalization of the estimator, it is applied to Planck CMB lensing and SDSS CMASS and LOWZ galaxy data. We report the first harmonic space measurement of 𝐸 𝐺 using the LOWZ sample and CMB lensing and also updated constraints using the final CMASS sample and the latest Planck CMB lensing map. We find $\hat{𝐸}$$^{Planck+CMASS}_{𝐺}$ = 0.3⁢6$^{+0.06}_{−0.05}$⁢(68.27%) and $\hat{𝐸}$$^{Planck+LOWZ}_{𝐺}$ = 0.4⁢0$^{+0.11}_{−0.09}$⁢(68.27%), with additional subdominant systematic error budget estimates of 2% and 3%, respectively. Using Ω m,0 constraints from Planck and SDSS BAO observations, Λ⁢CDM-GR predicts 𝐸$^{GR}_ {𝐺}$⁡(𝑧 =0.555) = 0.401 ± 0.005 and 𝐸$^{GR}_{𝐺}$⁡(𝑧 =0.316) = 0.452 ± 0.005 at the effective redshifts of the CMASS and LOWZ based measurements. We report the measurement to be in good statistical agreement with the Λ⁢CDM-GR prediction and report that the measurement is also consistent with the more general GR prediction of scale independence for 𝐸 𝐺 . Furthermore, this work provides a carefully constructed and calibrated statistic with which 𝐸 𝐺 measurements can be confidently and accurately obtained with upcoming survey data.

79 ASTRONOMY AND ASTROPHYSICS↗

Expanding neutrino oscillation parameter measurements in NOvA using a Bayesian approach

NOvA is a long-baseline neutrino oscillation experiment that measures oscillations in charged-current ν μ → ν μ (disappearance) and ν μ → ν e (appearance) channels, and their antineutrino counterparts, using neutrinos of energies around 2 GeV over a distance of 810 km. In this work we reanalyze the dataset first examined in our previous paper [] using an alternative statistical approach based on Bayesian Markov chain Monte Carlo. We measure oscillation parameters consistent with the previous results. We also extend our inferences to include the first NOvA measurements of the reactor mixing angle θ 13 , where we find 0.071 ≤ sin 2 2 θ 13 ≤ 0.107 , and the Jarlskog invariant, where we observe no significant preference for the C P -conserving value J = 0 over values favoring C P violation. We use these results to examine the effects of constraints from short-baseline measurements of θ 13 using antineutrinos from nuclear reactors when making NOvA measurements of θ 23 . Our long-baseline measurement of θ 13 is shown to be consistent with the reactor measurements, supporting the general applicability and robustness of the Pontecorvo-Maki-Nakagawa-Sakata framework for neutrino oscillations. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Characterization of the astrophysical diffuse neutrino flux using starting track events in IceCube

In this article, a measurement of the diffuse astrophysical neutrino spectrum is presented using IceCube data collected from 2011-2022 (10.3 years). We developed novel detection techniques to search for events with a contained vertex and exiting track induced by muon neutrinos undergoing a charged-current interaction. Searching for these starting track events allows us to not only more effectively reject atmospheric muons but also atmospheric neutrino backgrounds in the southern sky, opening a new window to the sub-100 TeV astrophysical neutrino sky. The event selection is constructed using a dynamic starting track veto and machine learning algorithms. We use this data to measure the astrophysical diffuse flux as a single power law flux (SPL) with a best-fit spectral index of γ=2.58$_{-0.09}^{+0.10}$ and per-flavor normalization of $\phi$$_{per-flavor}^{Astro}$=1.68$_{-0.22}^{+0.19}$×10 -18 ×GeV -1 cm -2 s -1 sr -1 (at 100 TeV). The sensitive energy range for this dataset is 3-550 TeV under the SPL assumption. This data was also used to measure the flux under a broken power law, however we did not find any evidence of a low energy cutoff.

79 ASTRONOMY AND ASTROPHYSICS↗

Classification of compact objects and model comparison using EOS knowledge

Nuclear theory and experiments, alongside astrophysical observations, constrain the equation of state (EOS) of supranuclear-dense matter. Conversely, knowledge of the EOS allows an improved interpretation of nuclear or astrophysical data. In this article, we use several established constraints on the EOS and the new NICER measurement of PSR J0437-4715 to comment on the nature of the primary companion in GW230529 and the companion of PSR J0514-4002E. We find that, with a probability of ≳84% and ≳68%, respectively, both objects are black holes. These likelihoods increase to above 95% when one uses GW170817’s remnant as an upper limit on the TOV mass. We also demonstrate that the current knowledge of the EOS substantially disfavors high masses and radii for PSR J⁢0030+0451, inferred recently when combining NICER with XMM-Newton background data and using particular hot-spot models. Lastly, we also use our obtained EOS knowledge to comment on measurements of the nuclear symmetry energy, finding that the large value predicted by the PREX-II measurement displays some mild tension with other constraints on the EOS.

79 ASTRONOMY AND ASTROPHYSICS↗

Demonstration of new MeV-scale capabilities in large neutrino LArTPCs using ambient radiogenic and cosmogenic activity in MicroBooNE

Large neutrino liquid argon time projection chamber (LArTPC) experiments can broaden their physics reach by reconstructing and interpreting MeV-scale energy depositions, or blips, present in their data. We demonstrate new calorimetric and particle discrimination capabilities at the MeV energy scale using reconstructed blips in data from the MicroBooNE LArTPC at Fermilab. We observe a concentration of low-energy (<3 MeV) blips around fiberglass mechanical support struts along the time projection chamber edges with energy spectrum features consistent with the Compton edge of 2.614 MeV 208 Tl decay 𝛾 rays. These features are used to verify proper calibration of electron energy scales in MicroBooNE’s data to few percent precision and to measure the specific activity of 208 Tl in the fiberglass composing these struts, (11.7 ± 0.2⁢(stat) ± 3.1⁢(syst)) Bq/kg. Cosmogenically produced blips above 3 MeV in reconstructed energy are used to showcase the ability of large LArTPCs to distinguish between low-energy proton and electron energy depositions. An enriched sample of low-energy protons selected using this new particle discrimination technique is found to be smaller in data than in dedicated corsika cosmic-ray simulations, suggesting either incorrect corsika modeling of incident cosmic fluxes or particle transport modeling issues in geant4.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Optimizing temperature distributions for training neural quantum states using parallel tempering

Parametrized artificial neural networks (ANNs) can be very expressive ansatzes for variational algorithms, reaching state-of-the-art energies on many quantum many-body Hamiltonians. Nevertheless, the training of the ANN can be slow and stymied by the presence of local minima in the parameter landscape. One approach to mitigate this issue is to use parallel tempering methods, and in this work, we focus on the role played by the temperature distribution of the parallel tempering replicas. Using an adaptive method that adjusts the temperatures in order to equate the exchange probability between neighboring replicas, we show that this temperature optimization can significantly increase the success rate of the variational algorithm with negligible computational cost by eliminating bottlenecks in the replicas' random walk. Furthermore, we demonstrate this using two different neural networks, a restricted Boltzmann machine and a feedforward network, which we use to study a toy problem based on a permutation invariant Hamiltonian with a pernicious local minimum and the 𝐽 1 −𝐽 2 model on a rectangular lattice.

Neural network simulations↗

First Constraints on the Epoch of Reionization Using the Non-Gaussianity of the Kinematic Sunyaev-Zel’dovich Effect from the South Pole Telescope and Herschel-SPIRE Observations

We report results from an analysis aimed at detecting the trispectrum of the kinematic Sunyaev-Zel’dovich (kSZ) effect by combining data from the South Pole Telescope (SPT) and Herschel-SPIRE experiments over a 100 deg 2 field. The SPT observations combine data from the previous and current surveys, namely SPTpol and SPT-3G, to achieve depths of 4.5, 3, and 16 μ K - arcmin in bands centered at 95, 150, and 220 GHz. For SPIRE, we include data from the 600 and 857 GHz bands. We reconstruct the velocity-induced large-scale correlation of the small-scale kSZ signal with a quadratic estimator that uses two cosmic microwave background (CMB) temperature maps, constructed by optimally combining data from all the frequency bands. We reject the null hypothesis of a zero trispectrum at 10.3 σ level. However, the measured trispectrum contains contributions from both the kSZ and other undesired components, such as CMB lensing and astrophysical foregrounds, with kSZ being sub-dominant. We use the agora simulations to estimate the expected signal from CMB lensing and astrophysical foregrounds. After accounting for the contributions from CMB lensing and foreground signals, we do not detect an excess kSZ-only trispectrum and use this nondetection to set constraints on reionization. By applying a prior based on observations of the Gunn-Peterson trough, we obtain an upper limit on the duration of reionization of Δ z re , 50 < 4.5 (95% confidence level). We find these constraints are fairly robust to foregrounds assumptions. This trispectrum measurement is independent of, but consistent with, Planck’s optical depth measurement. This result is the first constraint on the epoch of reionization using the non-Gaussian nature of the kSZ signal.

79 ASTRONOMY AND ASTROPHYSICS↗

Achieving a near-ideal silicon crystal neutron interferometer using submicrometer fabrication techniques

Perfect-crystal neutron interferometry, which is analogous to Mach-Zehnder interferometry, uses Bragg diffraction to form interfering neutron paths. The measured phase shifts can be used to probe many types of interactions whether it be nuclear, electromagnetic, gravitational, or topological in nature. For a perfect-crystal interferometer to preserve coherence, the crystal must possess a high degree of dimensional tolerance as well as being relatively defect-free with minimal internal stresses. In the past, perfect-crystal neutron interferometers have been produced by a two-step process. First, a resin diamond wheel would be used to remove excess material and shape the interferometer. Afterword, the crystal would be etched to remove surface defects and elevate strains. This process has had limitations in terms of repeatability and in maximizing the final contrast, or fringe visibility, of the interferometer. We have tested various fabrication and post-fabrication techniques on a single perfect-crystal neutron interferometer and measured the interferometer's performance at each step. Here we report a robust, nonetching fabrication process with high final contrast. For the interferometer used in this work, we achieved contrasts of greater than 90% several times and ultimately finished with an interferometer that has 92% contrast and a uniform phase distribution. Published by the American Physical Society 2024

Huber, M. G. (ORCID:0000000237958445)↗

Modeling betatron radiation using particle-in-cell codes for plasma wakefield accelerator diagnostics

The analysis of plasma wakefield acceleration experimental measurements, particularly in the characterization of photons emitted through the betatron radiation mechanism, requires the development of accurate numerical models. These computational models are crucial for supporting modern instrumentation designed to measure the single-shot, double-differential angular-energy radiation spectra resulting from interactions between beams and plasmas. Motivated by the needs of such applications, this paper presents detailed numerical models of betatron radiation generated in beam-plasma acceleration experiments. These models are based on the integration of the Liénard-Wiechert (LW) potentials, applied to computed particle trajectories. The particle trajectories are generated using three distinct methods: first, by tracking particles through idealized fields in the blowout regime of PWFA; second, by obtaining trajectories using the fast quasistatic particle-in-cell (PIC) code quickpic; and third, obtaining trajectories from the fully self-consistent PIC code osiris. To ensure the accuracy and reliability of these models, the paper includes various benchmark tests using analytical expressions, as well as employing the PIC code epoch, which takes an alternative approach by using a Monte Carlo quantum electrodynamics (QED)-based radiation model. Additionally, the paper presents simulations of the expected experimental betatron radiation spectra, taking into account parameters relevant to PWFA and plasma photocathode experiments at the SLAC FACET-II facility.

Yadav, M. [University of California, Los Angeles, ↗

Efficient analysis of small-angle scattering curves for large biomolecular assemblies using Monte Carlo methods

Structure elucidation from small-angle scattering curves of large biomolecular assemblies is notoriously challenging. This is because the simulation of high-resolution features in the structure of large macromolecular assemblies, such as de novo protein assemblies, is computationally demanding when it needs to cover a broad range of length scales. Conventional methods, such as the numerical approximation to the Debye equation or the use of spherical harmonics, do not scale well as the size of the assembly increases, which limits their application to small structures (e.g. individual proteins). This work explores the effectiveness of a Monte Carlo method to simulate and fit scattering curves for large biomolecular assemblies spanning over ranges covering atomic and molecular detail (e.g. spacing and orientation of proteins in an assembly) as well as large-scale (hundreds of nanometres) features. Owing to its speed and scalability, it can be combined with a fitting algorithm to extract structural features from experimental small-angle scattering curves in biomolecular assemblies that are otherwise intractable for interpretation. This work first demonstrates the effectiveness of the tool using experimental small-angle X-ray scattering (SAXS) data from tile-like proteins that assemble into 1D tube-like macromolecular structures. Here, the diameter distribution of tubes is extracted from SAXS fits, and this is quantitatively compared with distributions from electron microscopy. SAXS data are also obtained from 2D sheet-like protein assemblies, and the proposed method is used to quantify structural features such as the separation distance between protein building blocks and the flexing of the sheet. An open-source implementation of the methodology is provided for use in a broad range of biological systems involving multi-scale scattering analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deconvoluting thermomechanical effects in X-ray diffraction data using machine learning

X-ray diffraction is ideal for probing the sub-surface state during complex or rapid thermomechanical loading of crystalline materials. However, challenges arise as the size of diffraction volumes increases due to spatial broadening and because of the inability to deconvolute the effects of different lattice deformation mechanisms. Here, we present a novel approach that uses combinations of physics-based modeling and machine learning to deconvolve thermal and mechanical elastic strains for diffraction data analysis. The method builds on a previous effort to extract thermal strain distribution information from diffraction data. The new approach is applied to extract the evolution of the thermomechanical state during laser melting of an Inconel 625 wall specimen which produces significant residual stress upon cooling. A combination of heat transfer and fluid flow, elasto-plasticity and X-ray diffraction simulations is used to generate training data for machine-learning (Gaussian process regression, GPR) models that map diffracted intensity distributions to underlying thermomechanical strain fields. First-principles density functional theory is used to determine accurate temperature-dependent thermal expansion and elastic stiffness used for elasto-plasticity modeling. The trained GPR models are found to be capable of deconvoluting the effects of thermal and mechanical strains, in addition to providing information about underlying strain distributions, even from complex diffraction patterns with irregularly shaped peaks.

36 MATERIALS SCIENCE↗